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Cobalt in PDB 1rvg: Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y

Enzymatic activity of Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y

All present enzymatic activity of Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y:
4.1.2.13;

Protein crystallography data

The structure of Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y, PDB code: 1rvg was solved by T.Izard, J.Sygusch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.00
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.860, 57.550, 138.617, 90.00, 90.26, 90.00
R / Rfree (%) 22.5 / 25.9

Other elements in 1rvg:

The structure of Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y also contains other interesting chemical elements:

Yttrium (Y) 1 atom
Sodium (Na) 4 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y (pdb code 1rvg). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 5 binding sites of Cobalt where determined in the Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y, PDB code: 1rvg:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5;

Cobalt binding site 1 out of 5 in 1rvg

Go back to Cobalt Binding Sites List in 1rvg
Cobalt binding site 1 out of 5 in the Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1703

b:23.0
occ:0.50
CO A:CO1709 1.8 60.4 0.5
O A:HOH1944 2.1 39.0 1.0
NE2 A:HIS81 2.2 22.7 0.5
ND1 A:HIS208 2.3 25.5 0.5
NE2 A:HIS178 2.3 34.3 0.5
NE2 A:HIS178 2.3 34.6 0.5
NE2 A:HIS81 2.3 22.7 0.5
O A:HOH2027 2.6 49.3 1.0
CE1 A:HIS81 2.7 22.6 0.5
ND1 A:HIS208 2.8 25.4 0.5
CE1 A:HIS178 2.8 34.6 0.5
CD2 A:HIS178 2.8 34.5 0.5
CD2 A:HIS81 2.9 22.7 0.5
CE1 A:HIS208 3.1 25.3 0.5
CG A:HIS208 3.3 25.5 0.5
CE1 A:HIS81 3.3 22.6 0.5
CD2 A:HIS178 3.3 34.6 0.5
CB A:HIS208 3.5 25.5 0.5
CG A:HIS208 3.5 25.4 0.5
CE1 A:HIS178 3.5 34.3 0.5
CD2 A:HIS81 3.6 22.4 0.5
CB A:HIS208 3.7 25.6 0.5
CE1 A:HIS208 3.8 25.2 0.5
ND1 A:HIS178 3.9 34.6 0.5
ND1 A:HIS81 3.9 22.4 0.5
O A:HOH1885 4.0 33.5 1.0
ND2 A:ASN251 4.1 23.5 1.0
CG A:HIS178 4.1 34.4 0.5
CG A:HIS178 4.2 34.6 0.5
CG A:HIS81 4.2 22.6 0.5
NE2 A:HIS208 4.2 25.4 0.5
ND1 A:HIS81 4.3 22.6 0.5
CD2 A:HIS208 4.3 25.3 0.5
OD2 A:ASP80 4.4 21.9 0.5
CG A:HIS81 4.4 22.5 0.5
OD2 A:ASP80 4.4 21.4 0.5
ND1 A:HIS178 4.4 34.4 0.5
CA A:HIS208 4.5 26.0 0.5
CA A:HIS208 4.5 26.0 0.5
N A:GLY209 4.5 27.1 0.5
N A:GLY209 4.6 27.1 0.5
O A:HOH1964 4.6 41.1 1.0
CD2 A:HIS208 4.7 25.3 0.5
OD1 A:ASP80 4.7 22.0 0.5
O A:HOH2016 4.8 48.4 1.0
OD1 A:ASP80 4.8 21.3 0.5
NE2 A:HIS208 4.8 25.3 0.5
CG A:ASP80 5.0 21.9 0.5

Cobalt binding site 2 out of 5 in 1rvg

Go back to Cobalt Binding Sites List in 1rvg
Cobalt binding site 2 out of 5 in the Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1709

b:60.4
occ:0.50
CO A:CO1703 1.8 23.0 0.5
NE2 A:HIS178 2.2 34.3 0.5
NE2 A:HIS81 2.2 22.7 0.5
NE2 A:HIS178 2.2 34.6 0.5
ND1 A:HIS208 2.3 25.4 0.5
ND1 A:HIS208 2.3 25.5 0.5
CE1 A:HIS178 2.6 34.6 0.5
CE1 A:HIS81 2.6 22.6 0.5
CE1 A:HIS81 2.6 22.6 0.5
CG A:HIS208 2.7 25.5 0.5
CE1 A:HIS178 2.8 34.3 0.5
O A:HOH1964 2.9 41.1 1.0
CG A:HIS208 2.9 25.4 0.5
CB A:HIS208 3.0 25.5 0.5
CE1 A:HIS208 3.0 25.3 0.5
CB A:HIS208 3.1 25.6 0.5
NE2 A:HIS81 3.1 22.7 0.5
CE1 A:HIS208 3.4 25.2 0.5
CD2 A:HIS178 3.4 34.5 0.5
CD2 A:HIS208 3.5 25.3 0.5
CD2 A:HIS81 3.5 22.7 0.5
CD2 A:HIS178 3.5 34.6 0.5
CD1 A:LEU136 3.7 32.5 0.5
NE2 A:HIS208 3.7 25.4 0.5
OE1 A:GLU132 3.8 26.7 0.5
O A:HOH1944 3.8 39.0 1.0
ND1 A:HIS81 3.8 22.4 0.5
O A:HOH2027 3.9 49.3 1.0
ND1 A:HIS178 3.9 34.6 0.5
ND1 A:HIS81 3.9 22.6 0.5
ND1 A:HIS178 4.0 34.4 0.5
CD2 A:HIS208 4.1 25.3 0.5
NE2 A:HIS208 4.3 25.3 0.5
CG A:HIS178 4.3 34.4 0.5
CG A:HIS178 4.4 34.6 0.5
CG A:HIS81 4.4 22.6 0.5
CA A:HIS208 4.4 26.0 0.5
CA A:HIS208 4.4 26.0 0.5
OE1 A:GLU132 4.4 26.1 0.5
CD2 A:HIS81 4.5 22.4 0.5
O A:HOH2006 4.7 46.1 1.0
OE2 A:GLU132 4.8 25.6 0.5
O A:HOH1879 4.8 32.4 1.0
CG A:HIS81 4.8 22.5 0.5
CD A:GLU132 4.9 26.7 0.5
N A:GLY209 4.9 27.1 0.5
CD A:GLU132 4.9 25.8 0.5
N A:GLY209 4.9 27.1 0.5
ND2 A:ASN251 5.0 23.5 1.0

Cobalt binding site 3 out of 5 in 1rvg

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Cobalt binding site 3 out of 5 in the Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1701

b:43.1
occ:1.00
NE2 B:HIS178 2.1 43.4 1.0
NE2 B:HIS81 2.3 25.1 1.0
OE2 B:GLU132 2.4 33.0 1.0
OE1 B:GLU132 2.5 33.1 1.0
ND1 B:HIS208 2.5 33.5 1.0
CD B:GLU132 2.8 32.6 1.0
CD2 B:HIS178 2.9 43.3 1.0
CE1 B:HIS178 3.2 43.4 1.0
CE1 B:HIS81 3.3 24.8 1.0
CD2 B:HIS81 3.3 24.9 1.0
CE1 B:HIS208 3.3 33.4 1.0
CG B:HIS208 3.6 33.5 1.0
CB B:HIS208 3.9 33.5 1.0
O B:HOH1913 4.0 52.7 1.0
OD1 B:ASP102 4.1 33.0 1.0
CG B:HIS178 4.1 43.3 1.0
ND1 B:HIS178 4.3 43.5 1.0
CG B:GLU132 4.3 32.5 1.0
ND1 B:HIS81 4.4 25.1 1.0
CG B:HIS81 4.4 24.7 1.0
CE B:MET100 4.5 30.9 1.0
NE2 B:HIS208 4.5 33.4 1.0
O B:HOH1924 4.5 55.1 1.0
CD2 B:HIS208 4.6 33.3 1.0
CG B:ASP102 4.7 32.4 1.0

Cobalt binding site 4 out of 5 in 1rvg

Go back to Cobalt Binding Sites List in 1rvg
Cobalt binding site 4 out of 5 in the Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co1705

b:27.4
occ:1.00
NE2 C:HIS178 2.2 32.1 1.0
OE1 C:GLU132 2.2 26.6 1.0
NE2 C:HIS81 2.2 24.2 1.0
OE2 C:GLU132 2.3 27.3 1.0
ND1 C:HIS208 2.3 28.3 1.0
O C:HOH1715 2.5 21.4 1.0
CD C:GLU132 2.6 26.8 1.0
CE1 C:HIS208 3.0 28.1 1.0
CD2 C:HIS178 3.0 32.2 1.0
CE1 C:HIS81 3.2 24.3 1.0
CD2 C:HIS81 3.3 24.2 1.0
CE1 C:HIS178 3.3 32.0 1.0
CG C:HIS208 3.4 28.6 1.0
CB C:HIS208 3.9 28.8 1.0
CG C:GLU132 4.1 26.9 1.0
OD1 C:ASP102 4.2 26.1 1.0
NE2 C:HIS208 4.2 28.2 1.0
CG C:HIS178 4.2 32.5 1.0
ND1 C:HIS178 4.3 32.2 1.0
ND1 C:HIS81 4.3 24.4 1.0
CG C:HIS81 4.4 24.1 1.0
CD2 C:HIS208 4.4 28.2 1.0
O C:HOH1760 4.5 30.8 1.0
CE C:MET100 4.6 26.9 1.0
CG C:ASP102 4.7 26.2 1.0
O C:HOH1886 4.7 45.2 1.0
O C:HOH1814 4.8 37.4 1.0
CB C:GLU132 4.9 27.0 1.0

Cobalt binding site 5 out of 5 in 1rvg

Go back to Cobalt Binding Sites List in 1rvg
Cobalt binding site 5 out of 5 in the Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Strcuture of Class II Fructose-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Y within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co1707

b:39.2
occ:1.00
NE2 D:HIS178 2.2 44.0 1.0
NE2 D:HIS81 2.4 27.7 1.0
OE2 D:GLU132 2.4 34.2 1.0
OE1 D:GLU132 2.4 34.1 1.0
O D:HOH1729 2.4 27.0 1.0
ND1 D:HIS208 2.5 38.4 1.0
CD D:GLU132 2.7 33.5 1.0
CD2 D:HIS178 2.8 44.2 1.0
CE1 D:HIS81 3.2 27.8 1.0
CE1 D:HIS208 3.4 38.4 1.0
CD2 D:HIS81 3.4 27.1 1.0
CE1 D:HIS178 3.4 44.2 1.0
CG D:HIS208 3.6 38.4 1.0
CB D:HIS208 3.9 38.5 1.0
CG D:HIS178 4.1 44.4 1.0
OD1 D:ASP102 4.2 29.9 1.0
CG D:GLU132 4.2 32.9 1.0
ND1 D:HIS178 4.3 44.4 1.0
ND1 D:HIS81 4.4 27.5 1.0
CG D:HIS81 4.5 27.0 1.0
NE2 D:HIS208 4.5 38.0 1.0
CD2 D:HIS208 4.7 38.3 1.0
CG D:ASP102 4.7 29.7 1.0
CE D:MET100 4.9 28.8 1.0
CB D:GLU132 5.0 32.4 1.0
O D:HOH1898 5.0 52.0 1.0

Reference:

T.Izard, J.Sygusch. Induced Fit Movements and Metal Cofactor Selectivity of Class II Aldolases: Structure of Thermus Aquaticus Fructose-1,6-Bisphosphate Aldolase. J.Biol.Chem. V. 279 11825 2004.
ISSN: ISSN 0021-9258
PubMed: 14699122
DOI: 10.1074/JBC.M311375200
Page generated: Sun Dec 13 10:36:01 2020

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