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Cobalt in PDB 4lk8: Crystal Structure of Cyay Protein From Psychromonas Ingrahamii in Complex with Co(II)

Protein crystallography data

The structure of Crystal Structure of Cyay Protein From Psychromonas Ingrahamii in Complex with Co(II), PDB code: 4lk8 was solved by M.E.Noguera, E.A.Roman, A.Cousido-Siah, A.Mitschler, A.Podjarny, J.Santos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.43 / 1.49
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.891, 50.564, 46.310, 90.00, 90.77, 90.00
R / Rfree (%) 18.4 / 21.1

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Cyay Protein From Psychromonas Ingrahamii in Complex with Co(II) (pdb code 4lk8). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Crystal Structure of Cyay Protein From Psychromonas Ingrahamii in Complex with Co(II), PDB code: 4lk8:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in 4lk8

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Cobalt binding site 1 out of 6 in the Crystal Structure of Cyay Protein From Psychromonas Ingrahamii in Complex with Co(II)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Cyay Protein From Psychromonas Ingrahamii in Complex with Co(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co201

b:61.9
occ:1.00
NE2 A:HIS44 2.4 39.0 1.0
CE1 A:HIS44 3.2 43.8 1.0
HE1 A:HIS44 3.2 43.8 1.0
CD2 A:HIS44 3.5 38.6 1.0
HD2 A:HIS44 3.7 38.6 1.0
ND1 A:HIS44 4.4 43.3 1.0
CG A:HIS44 4.6 39.9 1.0
O A:GLU42 4.7 36.6 1.0

Cobalt binding site 2 out of 6 in 4lk8

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Cobalt binding site 2 out of 6 in the Crystal Structure of Cyay Protein From Psychromonas Ingrahamii in Complex with Co(II)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Cyay Protein From Psychromonas Ingrahamii in Complex with Co(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co202

b:20.7
occ:0.24
OE2 A:GLU5 2.1 35.4 1.0
CD A:GLU5 3.0 34.0 1.0
OE1 A:GLU5 3.2 31.6 1.0
HD21 A:ASN2 4.3 35.5 1.0
ND2 A:ASN2 4.3 35.5 1.0
HD22 A:ASN2 4.4 35.5 1.0
CG A:GLU5 4.4 27.4 1.0
H A:ASN2 4.5 30.3 1.0
HG3 A:GLU5 4.6 27.4 1.0
CG A:ASN2 4.6 28.6 1.0
HB3 A:ASN2 4.7 30.1 1.0
HG2 A:GLU5 4.7 27.4 1.0
HA A:MET1 4.9 34.4 1.0

Cobalt binding site 3 out of 6 in 4lk8

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Cobalt binding site 3 out of 6 in the Crystal Structure of Cyay Protein From Psychromonas Ingrahamii in Complex with Co(II)


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 Cyay Protein From Psychromonas Ingrahamii in Complex with Co(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co203

b:31.5
occ:0.31
O A:HOH351 3.8 36.1 1.0
O A:GLU23 3.8 30.5 1.0
HA A:SER24 4.1 28.8 1.0
O A:SER24 4.6 31.4 1.0
C A:SER24 4.9 26.5 1.0
CA A:SER24 4.9 28.8 1.0
C A:GLU23 4.9 25.5 1.0

Cobalt binding site 4 out of 6 in 4lk8

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Cobalt binding site 4 out of 6 in the Crystal Structure of Cyay Protein From Psychromonas Ingrahamii in Complex with Co(II)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Cyay Protein From Psychromonas Ingrahamii in Complex with Co(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co201

b:19.8
occ:0.57
H B:TRP76 2.5 17.1 1.0
H B:LEU86 2.6 13.8 1.0
HB3 B:PHE85 2.9 16.0 1.0
O B:HOH322 3.0 27.2 1.0
HG B:LEU86 3.1 17.4 1.0
HB3 B:GLU84 3.2 20.1 1.0
HD2 B:LYS75 3.2 30.1 1.0
HA B:LYS75 3.3 19.5 1.0
H B:PHE85 3.3 17.8 1.0
N B:TRP76 3.3 17.1 1.0
O B:HOH305 3.3 19.1 1.0
HD12 B:LEU86 3.3 17.2 1.0
N B:LEU86 3.4 13.8 1.0
HB2 B:TRP76 3.4 17.1 1.0
HB2 B:LEU86 3.4 16.2 1.0
HB3 B:LYS75 3.5 21.6 1.0
N B:PHE85 3.6 17.8 1.0
HD1 B:TRP76 3.7 16.4 1.0
CG B:LEU86 3.8 17.4 1.0
CB B:PHE85 3.8 16.0 1.0
CA B:LYS75 3.9 19.5 1.0
O B:TRP76 3.9 19.0 1.0
CD1 B:LEU86 4.0 17.2 1.0
CB B:LEU86 4.0 16.2 1.0
HD3 B:LYS75 4.0 30.1 1.0
CD B:LYS75 4.0 30.1 1.0
CA B:PHE85 4.1 16.1 1.0
C B:LYS75 4.1 20.0 1.0
CB B:GLU84 4.1 20.1 1.0
CB B:LYS75 4.1 21.6 1.0
HB2 B:PHE85 4.2 16.0 1.0
CB B:TRP76 4.2 17.1 1.0
CA B:TRP76 4.2 17.2 1.0
HD11 B:LEU86 4.2 17.2 1.0
C B:PHE85 4.2 14.8 1.0
C B:GLU84 4.3 18.5 1.0
HA B:GLU84 4.3 19.5 1.0
CA B:LEU86 4.3 16.8 1.0
HD13 B:LEU13 4.3 15.3 1.0
C B:TRP76 4.5 19.8 1.0
CD1 B:TRP76 4.5 16.4 1.0
CA B:GLU84 4.5 19.5 1.0
HD1 B:PHE85 4.6 19.9 1.0
HG2 B:GLU84 4.6 23.8 1.0
HB2 B:GLU84 4.7 20.1 1.0
H B:THR87 4.7 16.7 1.0
CG B:LYS75 4.7 26.2 1.0
HD11 B:LEU13 4.8 15.3 1.0
CG B:TRP76 4.8 16.3 1.0
HD13 B:LEU86 4.8 17.2 1.0
OE1 B:GLU84 4.8 30.4 1.0
CG B:GLU84 4.8 23.8 1.0
HB3 B:LEU86 4.9 16.2 1.0
CG B:PHE85 4.9 17.8 1.0
HA B:LEU86 4.9 16.8 1.0
HB3 B:TRP76 5.0 17.1 1.0
CD1 B:LEU13 5.0 15.3 1.0
HB2 B:LYS75 5.0 21.6 1.0

Cobalt binding site 5 out of 6 in 4lk8

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Cobalt binding site 5 out of 6 in the Crystal Structure of Cyay Protein From Psychromonas Ingrahamii in Complex with Co(II)


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 Cyay Protein From Psychromonas Ingrahamii in Complex with Co(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co202

b:20.4
occ:0.36
O B:HOH388 2.0 18.9 1.0
OD2 B:ASP102 2.0 24.8 1.0
O B:HOH372 2.4 25.3 1.0
O B:HOH351 2.4 41.5 1.0
CO B:CO203 3.1 17.4 0.6
CG B:ASP102 3.1 21.1 1.0
HG1 B:THR104 3.5 26.4 1.0
OG1 B:THR104 3.8 26.4 1.0
HB3 B:ASP102 3.8 21.2 1.0
OD1 B:ASP102 3.9 22.4 1.0
CB B:ASP102 4.0 21.2 1.0
O B:HOH368 4.1 18.8 1.0
HB2 B:ASP102 4.3 21.2 1.0
O B:HOH370 4.8 22.2 1.0
O B:HOH373 5.0 25.2 1.0

Cobalt binding site 6 out of 6 in 4lk8

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Cobalt binding site 6 out of 6 in the Crystal Structure of Cyay Protein From Psychromonas Ingrahamii in Complex with Co(II)


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 Cyay Protein From Psychromonas Ingrahamii in Complex with Co(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co203

b:17.4
occ:0.57
O B:HOH388 1.9 18.9 1.0
O B:HOH368 2.1 18.8 1.0
O B:HOH370 2.1 22.2 1.0
O B:HOH372 2.1 25.3 1.0
O B:HOH373 2.2 25.2 1.0
CO B:CO202 3.1 20.4 0.4
HZ2 B:LYS20 3.3 20.9 1.0
O B:THR104 3.7 23.2 1.0
NZ B:LYS20 4.1 20.9 1.0
OD2 B:ASP102 4.2 24.8 1.0
HG1 B:THR104 4.2 26.4 1.0
HZ1 B:LYS20 4.3 20.9 1.0
HB3 B:ASP102 4.3 21.2 1.0
OE1 B:GLU23 4.4 20.8 1.0
HZ3 B:LYS20 4.4 20.9 1.0
OG1 B:THR104 4.4 26.4 1.0
HA B:GLU105 4.5 44.8 1.0
CG B:ASP102 4.5 21.1 1.0
O B:GLU105 4.7 53.0 1.0
C B:THR104 4.7 28.6 1.0
O B:ASP102 4.8 19.2 1.0
HD2 B:LYS20 4.9 15.6 1.0
O B:HOH351 4.9 41.5 1.0
CB B:ASP102 5.0 21.2 1.0

Reference:

M.E.Noguera, E.A.Roman, A.Cousido-Siah, A.Mitschler, A.Podjarny, J.Santos. Crystal Structures of Frataxin From Psychromonas Ingrahamii in Complex with Co(II) and Eu(III): Insights Into the Metal Binding Properties and Conformational Flexibility To Be Published.
Page generated: Sun Dec 13 10:45:10 2020

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