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Cobalt in PDB 2yye: Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp

Enzymatic activity of Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp

All present enzymatic activity of Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp:
2.7.9.3;

Protein crystallography data

The structure of Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp, PDB code: 2yye was solved by Y.Itoh, S.Sekine, E.Matsumoto, S.Yokoyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.47 / 2.10
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.536, 80.536, 160.641, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 22.5

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp (pdb code 2yye). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 10 binding sites of Cobalt where determined in the Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp, PDB code: 2yye:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 10 in 2yye

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Cobalt binding site 1 out of 10 in the Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp


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Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co702

b:27.1
occ:1.00
 O2B A:APC501 2.0 28.0 1.0
OD2 A:ASP83 2.0 27.2 1.0
O A:HOH859 2.1 15.2 1.0
OD1 A:ASP219 2.1 25.4 1.0
O A:HOH918 2.2 23.6 1.0
OD2 A:ASP44 2.2 18.9 1.0
CG A:ASP219 3.0 21.5 1.0
CG A:ASP83 3.1 28.3 1.0
PB A:APC501 3.2 22.7 1.0
OD2 A:ASP219 3.3 22.1 1.0
CG A:ASP44 3.3 23.1 1.0
OD1 A:ASP83 3.5 27.7 1.0
CO A:CO703 3.7 25.4 1.0
CB A:ASP44 3.7 18.8 1.0
O3B A:APC501 3.8 26.3 1.0
O1B A:APC501 3.9 22.8 1.0
O A:HOH833 4.0 29.3 1.0
OG1 A:THR221 4.1 24.6 1.0
CA A:ASP44 4.2 24.1 1.0
O A:ASP219 4.2 21.8 1.0
OD1 A:ASP44 4.3 25.3 1.0
N A:ASP219 4.4 19.2 1.0
CB A:ASP219 4.4 19.9 1.0
CB A:ASP83 4.4 19.2 1.0
OG1 A:THR218 4.5 25.8 1.0
O1G A:APC501 4.6 23.7 1.0
C3A A:APC501 4.6 21.2 1.0
O A:HOH932 4.7 31.5 1.0
CA A:ASP219 4.8 22.2 1.0
CA A:ASP83 4.8 17.2 1.0
C A:ASP219 4.8 20.9 1.0
PG A:APC501 4.8 24.7 1.0
O A:HOH809 4.9 27.3 1.0
O A:ASP44 4.9 19.2 1.0

Cobalt binding site 2 out of 10 in 2yye

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Cobalt binding site 2 out of 10 in the Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp


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Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co703

b:25.4
occ:1.00
 OD2 A:ASP60 2.1 25.3 1.0
OD1 A:ASP83 2.1 27.7 1.0
O1G A:APC501 2.2 23.7 1.0
O A:HOH932 2.2 31.5 1.0
O1B A:APC501 2.2 22.8 1.0
O A:HOH859 2.3 15.2 1.0
CG A:ASP60 3.1 24.2 1.0
PB A:APC501 3.1 22.7 1.0
CG A:ASP83 3.1 28.3 1.0
PG A:APC501 3.2 24.7 1.0
O3B A:APC501 3.4 26.3 1.0
O2B A:APC501 3.4 28.0 1.0
OD1 A:ASP60 3.5 23.7 1.0
OD2 A:ASP83 3.5 27.2 1.0
CO A:CO702 3.7 27.1 1.0
CO B:CO701 3.8 24.2 1.0
CO A:CO704 3.8 35.6 1.0
O3G A:APC501 3.9 29.5 1.0
O A:HOH928 4.1 31.4 1.0
O A:HOH805 4.3 17.8 1.0
OG1 A:THR221 4.3 24.6 1.0
OD2 A:ASP219 4.3 22.1 1.0
CB A:ASP60 4.3 22.0 1.0
CB A:ASP83 4.5 19.2 1.0
O A:HOH931 4.6 19.0 1.0
O2G A:APC501 4.6 27.1 1.0
O A:ASN79 4.6 19.7 1.0
CG2 A:THR221 4.7 22.7 1.0
C3A A:APC501 4.8 21.2 1.0
CB A:THR221 4.9 24.8 1.0
O A:HOH918 5.0 23.6 1.0
OD1 A:ASP219 5.0 25.4 1.0

Cobalt binding site 3 out of 10 in 2yye

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Cobalt binding site 3 out of 10 in the Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co704

b:35.6
occ:1.00
 OG1 A:THR58 2.6 17.7 1.0
O A:HOH860 2.7 24.1 1.0
O A:HOH804 2.8 13.9 1.0
O A:ASP44 2.8 19.2 1.0
O1B A:APC501 2.8 22.8 1.0
OD1 A:ASP83 2.9 27.7 1.0
O A:HOH931 3.0 19.0 1.0
CG A:ASP83 3.3 28.3 1.0
OD2 A:ASP60 3.7 25.3 1.0
PB A:APC501 3.8 22.7 1.0
CB A:THR58 3.8 17.0 1.0
CO A:CO703 3.8 25.4 1.0
O A:HOH805 3.8 17.8 1.0
CB A:ASP83 3.9 19.2 1.0
O A:VAL59 3.9 18.9 1.0
C A:ASP44 3.9 23.5 1.0
OD2 A:ASP83 4.0 27.2 1.0
O2B A:APC501 4.0 28.0 1.0
CO B:CO701 4.2 24.2 1.0
N A:VAL59 4.2 15.3 1.0
C3A A:APC501 4.3 21.2 1.0
O A:HOH806 4.3 16.8 1.0
CG A:ASP60 4.4 24.2 1.0
CA A:THR58 4.5 18.3 1.0
CA A:ASP44 4.6 24.1 1.0
OD1 A:ASP60 4.6 23.7 1.0
O B:GLY131 4.7 19.4 1.0
C A:VAL59 4.7 15.1 1.0
O1A A:APC501 4.8 23.4 1.0
C A:THR58 4.8 16.6 1.0
O2' A:APC501 4.9 20.9 1.0
N A:ALA45 4.9 18.5 1.0
CG2 A:THR58 5.0 15.8 1.0

Cobalt binding site 4 out of 10 in 2yye

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Cobalt binding site 4 out of 10 in the Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp


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Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co705

b:38.1
occ:1.00
 O A:CYS217 2.6 23.8 1.0
OD1 A:ASP43 2.8 31.1 1.0
O A:ALA86 2.8 22.4 1.0
O A:ILE155 2.8 29.1 1.0
OD1 A:ASP44 2.9 25.3 1.0
SD A:MET87 3.2 24.6 1.0
C A:CYS217 3.6 28.0 1.0
C A:ALA86 3.7 24.5 1.0
C A:ILE155 3.9 30.5 1.0
CG A:ASP44 3.9 23.1 1.0
CG A:ASP43 3.9 41.2 1.0
C A:THR156 3.9 27.8 1.0
CA A:THR156 3.9 30.7 1.0
CA A:MET87 4.2 27.8 1.0
CB A:ASP44 4.2 18.8 1.0
N A:GLN157 4.2 31.2 1.0
CG A:GLN157 4.3 31.9 1.0
N A:MET87 4.3 23.1 1.0
O A:THR156 4.3 32.5 1.0
CE A:MET87 4.3 30.5 1.0
N A:THR156 4.4 26.1 1.0
CA A:THR218 4.4 29.7 1.0
N A:THR218 4.4 26.6 1.0
OD2 A:ASP43 4.4 47.3 1.0
CB A:ALA86 4.4 17.8 1.0
CG A:MET87 4.5 29.7 1.0
CA A:CYS217 4.6 25.6 1.0
CA A:ALA86 4.7 23.9 1.0
CB A:CYS217 4.7 26.7 1.0
N A:ASP44 4.7 27.6 1.0
N A:CYS217 4.8 22.8 1.0
CB A:MET87 4.9 25.8 1.0
NE2 A:GLN157 4.9 34.7 1.0
CA A:GLN157 4.9 33.8 1.0

Cobalt binding site 5 out of 10 in 2yye

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Cobalt binding site 5 out of 10 in the Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co801

b:26.9
occ:1.00
 O1A B:APC601 2.1 30.9 1.0
O B:HOH991 2.1 19.8 1.0
O3G B:APC601 2.1 27.7 1.0
OD1 B:ASP60 2.1 30.5 1.0
ND1 A:HIS132 2.3 17.7 1.0
O1B B:APC601 2.5 23.3 1.0
CE1 A:HIS132 3.0 20.1 1.0
CG B:ASP60 3.2 33.4 1.0
PG B:APC601 3.2 29.8 1.0
PA B:APC601 3.3 28.1 1.0
CG A:HIS132 3.4 19.4 1.0
PB B:APC601 3.4 26.1 1.0
O1G B:APC601 3.6 25.4 1.0
OD2 B:ASP60 3.6 30.2 1.0
O3B B:APC601 3.6 33.1 1.0
CO B:CO803 3.8 28.6 1.0
CB A:HIS132 3.8 18.9 1.0
C3A B:APC601 3.8 22.4 1.0
O B:VAL59 3.9 19.0 1.0
O A:HOH929 4.0 18.6 1.0
O B:HOH944 4.1 38.2 1.0
O2A B:APC601 4.2 30.8 1.0
NE2 A:HIS132 4.2 24.9 1.0
CO B:CO804 4.2 38.6 1.0
CA A:HIS132 4.3 22.2 1.0
CD2 A:HIS132 4.3 18.0 1.0
O A:GLY131 4.5 21.4 1.0
CB B:ASP60 4.5 21.1 1.0
O5' B:APC601 4.5 29.2 1.0
O2G B:APC601 4.6 32.2 1.0
O B:HOH935 4.6 30.3 1.0
CA B:ASP60 4.7 12.6 1.0
O2B B:APC601 4.8 28.4 1.0
OD1 B:ASP83 5.0 24.7 1.0

Cobalt binding site 6 out of 10 in 2yye

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Cobalt binding site 6 out of 10 in the Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co701

b:24.2
occ:1.00
 O1A A:APC501 2.0 23.4 1.0
O3G A:APC501 2.1 29.5 1.0
O A:HOH931 2.2 19.0 1.0
OD1 A:ASP60 2.2 23.7 1.0
ND1 B:HIS132 2.2 17.5 1.0
O1B A:APC501 2.5 22.8 1.0
CE1 B:HIS132 2.9 13.2 1.0
PG A:APC501 3.2 24.7 1.0
CG A:ASP60 3.2 24.2 1.0
PA A:APC501 3.3 26.0 1.0
CG B:HIS132 3.3 20.6 1.0
PB A:APC501 3.4 22.7 1.0
OD2 A:ASP60 3.5 25.3 1.0
O1G A:APC501 3.5 23.7 1.0
O3B A:APC501 3.7 26.3 1.0
CO A:CO703 3.8 25.4 1.0
C3A A:APC501 3.8 21.2 1.0
CB B:HIS132 3.9 16.4 1.0
O A:VAL59 4.0 18.9 1.0
NZ A:LYS16 4.1 16.4 0.5
O B:HOH1048 4.1 22.2 1.0
NE2 B:HIS132 4.1 24.8 1.0
O2A A:APC501 4.1 28.8 1.0
CO A:CO704 4.2 35.6 1.0
CD2 B:HIS132 4.3 17.7 1.0
CA B:HIS132 4.4 18.4 1.0
O B:GLY131 4.4 19.4 1.0
O5' A:APC501 4.4 26.5 1.0
CB A:ASP60 4.5 22.0 1.0
O2G A:APC501 4.5 27.1 1.0
O A:HOH928 4.7 31.4 1.0
O2B A:APC501 4.8 28.0 1.0
CA A:ASP60 4.8 18.7 1.0

Cobalt binding site 7 out of 10 in 2yye

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Cobalt binding site 7 out of 10 in the Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co802

b:29.6
occ:1.00
 O2B B:APC601 2.0 28.4 1.0
OD2 B:ASP83 2.1 18.4 1.0
O B:HOH1049 2.1 15.2 1.0
OD1 B:ASP219 2.1 25.5 1.0
O B:HOH902 2.2 28.7 1.0
OD2 B:ASP44 2.4 20.4 1.0
CG B:ASP219 3.0 24.8 1.0
CG B:ASP83 3.1 22.9 1.0
OD2 B:ASP219 3.3 24.9 1.0
PB B:APC601 3.3 26.1 1.0
CG B:ASP44 3.4 24.2 1.0
OD1 B:ASP83 3.5 24.7 1.0
CO B:CO803 3.6 28.6 1.0
CB B:ASP44 3.8 18.4 1.0
O3B B:APC601 3.9 33.1 1.0
O B:HOH949 3.9 40.4 1.0
O1B B:APC601 3.9 23.3 1.0
OG1 B:THR221 4.1 26.5 1.0
O B:ASP219 4.2 18.5 1.0
CA B:ASP44 4.3 21.3 1.0
N B:ASP219 4.4 18.7 1.0
CB B:ASP219 4.4 16.4 1.0
OD1 B:ASP44 4.4 22.4 1.0
CB B:ASP83 4.4 17.1 1.0
OG1 B:THR218 4.5 20.2 1.0
O1G B:APC601 4.5 25.4 1.0
O B:HOH1027 4.7 29.9 1.0
C3A B:APC601 4.7 22.4 1.0
CA B:ASP219 4.8 17.4 1.0
C B:ASP219 4.8 18.6 1.0
CA B:ASP83 4.8 21.9 1.0
PG B:APC601 4.8 29.8 1.0
O B:ASP44 4.9 19.9 1.0
CO B:CO804 5.0 38.6 1.0

Cobalt binding site 8 out of 10 in 2yye

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Cobalt binding site 8 out of 10 in the Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co803

b:28.6
occ:1.00
 O1G B:APC601 2.1 25.4 1.0
OD2 B:ASP60 2.2 30.2 1.0
O B:HOH1049 2.2 15.2 1.0
OD1 B:ASP83 2.3 24.7 1.0
O1B B:APC601 2.3 23.3 1.0
O B:HOH1027 2.3 29.9 1.0
CG B:ASP60 3.0 33.4 1.0
PB B:APC601 3.1 26.1 1.0
PG B:APC601 3.1 29.8 1.0
CG B:ASP83 3.2 22.9 1.0
OD1 B:ASP60 3.3 30.5 1.0
O2B B:APC601 3.4 28.4 1.0
O3B B:APC601 3.4 33.1 1.0
OD2 B:ASP83 3.5 18.4 1.0
CO B:CO802 3.6 29.6 1.0
CO A:CO801 3.8 26.9 1.0
CO B:CO804 3.9 38.6 1.0
O3G B:APC601 3.9 27.7 1.0
O B:HOH935 4.1 30.3 1.0
O B:HOH912 4.2 22.9 1.0
OG1 B:THR221 4.2 26.5 1.0
CB B:ASP60 4.3 21.1 1.0
OD2 B:ASP219 4.4 24.9 1.0
O B:HOH991 4.5 19.8 1.0
O2G B:APC601 4.5 32.2 1.0
CG2 B:THR221 4.5 29.7 1.0
CB B:ASP83 4.5 17.1 1.0
O B:ASN79 4.7 22.1 1.0
C3A B:APC601 4.8 22.4 1.0
O B:HOH902 4.8 28.7 1.0
CB B:THR221 4.8 24.0 1.0

Cobalt binding site 9 out of 10 in 2yye

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Cobalt binding site 9 out of 10 in the Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co804

b:38.6
occ:1.00
 OG1 B:THR58 2.5 14.7 1.0
O B:HOH917 2.7 24.1 1.0
OD1 B:ASP83 2.7 24.7 1.0
O1B B:APC601 2.8 23.3 1.0
O B:ASP44 2.8 19.9 1.0
O B:HOH903 2.9 16.2 1.0
O B:HOH991 2.9 19.8 1.0
CG B:ASP83 3.3 22.9 1.0
OD2 B:ASP60 3.5 30.2 1.0
PB B:APC601 3.7 26.1 1.0
O B:VAL59 3.8 19.0 1.0
O B:HOH912 3.8 22.9 1.0
CB B:THR58 3.8 21.1 1.0
CB B:ASP83 3.8 17.1 1.0
CO B:CO803 3.9 28.6 1.0
C B:ASP44 3.9 22.0 1.0
O2B B:APC601 4.0 28.4 1.0
OD2 B:ASP83 4.0 18.4 1.0
C3A B:APC601 4.2 22.4 1.0
CO A:CO801 4.2 26.9 1.0
N B:VAL59 4.2 15.1 1.0
CG B:ASP60 4.3 33.4 1.0
O B:HOH908 4.4 18.4 1.0
CA B:THR58 4.5 18.5 1.0
OD1 B:ASP60 4.5 30.5 1.0
CA B:ASP44 4.6 21.3 1.0
C B:VAL59 4.6 16.7 1.0
O A:GLY131 4.7 21.4 1.0
O1A B:APC601 4.8 30.9 1.0
C B:THR58 4.9 22.7 1.0
O2' B:APC601 4.9 18.0 1.0
N B:ALA45 4.9 18.0 1.0
CG2 B:THR58 4.9 14.7 1.0
CO B:CO802 5.0 29.6 1.0

Cobalt binding site 10 out of 10 in 2yye

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Cobalt binding site 10 out of 10 in the Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co805

b:38.1
occ:1.00
 O B:CYS217 2.7 25.1 1.0
O B:ILE155 2.8 20.4 1.0
OD1 B:ASP43 2.8 26.5 1.0
O B:ALA86 2.8 21.1 1.0
OD1 B:ASP44 2.9 22.4 1.0
SD B:MET87 3.2 24.1 1.0
C B:CYS217 3.6 26.8 1.0
C B:ALA86 3.7 20.4 1.0
C B:ILE155 3.8 23.8 1.0
CA B:THR156 3.9 23.9 1.0
CG B:ASP43 3.9 35.1 1.0
CG B:ASP44 3.9 24.2 1.0
C B:THR156 3.9 24.6 1.0
CB B:ASP44 4.1 18.4 1.0
CA B:MET87 4.1 22.2 1.0
CE B:MET87 4.2 25.7 1.0
O B:THR156 4.2 25.7 1.0
CA B:THR218 4.3 26.5 1.0
N B:MET87 4.3 15.2 1.0
N B:GLN157 4.3 20.7 1.0
N B:THR156 4.3 23.8 1.0
N B:THR218 4.3 26.8 1.0
OD2 B:ASP43 4.3 33.6 1.0
CG B:GLN157 4.4 27.9 1.0
CG B:MET87 4.5 28.0 1.0
CB B:ALA86 4.6 14.3 1.0
N B:ASP44 4.6 17.3 1.0
CA B:CYS217 4.6 23.7 1.0
CB B:CYS217 4.7 22.7 1.0
CA B:ALA86 4.8 20.4 1.0
N B:CYS217 4.8 22.1 1.0
CB B:MET87 4.8 27.4 1.0
CB B:THR218 4.9 27.6 1.0
NE2 B:GLN157 5.0 24.3 1.0

Reference:

Y.Itoh, S.Sekine, E.Matsumoto, R.Akasaka, C.Takemoto, M.Shirouzu, S.Yokoyama. Structure of Selenophosphate Synthetase Essential For Selenium Incorporation Into Proteins and Rnas J.Mol.Biol. V. 385 1456 2009.
ISSN: ISSN 0022-2836
PubMed: 18773910
DOI: 10.1016/J.JMB.2008.08.042
Page generated: Tue Jul 30 15:42:18 2024

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