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Cobalt in PDB 1rv8: Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt

Enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt

All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt:
4.1.2.13;

Protein crystallography data

The structure of Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt, PDB code: 1rv8 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) 40.43 / 2.30
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.354, 57.629, 138.577, 90.00, 90.23, 90.00
R / Rfree (%) 21.1 / 25.2

Other elements in 1rv8:

The structure of Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt (pdb code 1rv8). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 5 binding sites of Cobalt where determined in the Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt, PDB code: 1rv8:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5;

Cobalt binding site 1 out of 5 in 1rv8

Go back to Cobalt Binding Sites List in 1rv8
Cobalt binding site 1 out of 5 in the Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1703

b:37.7
occ:0.50
 NE2 A:HIS178 2.1 40.4 0.5
ND1 A:HIS208 2.2 31.5 0.5
NE2 A:HIS81 2.3 24.3 0.5
O A:HOH1918 2.3 55.1 1.0
CE1 A:HIS178 2.4 40.5 0.5
CO A:CO1709 2.5 53.6 0.5
ND1 A:HIS208 2.5 31.8 0.5
CE1 A:HIS178 2.6 40.4 0.5
CE1 A:HIS81 2.6 24.3 0.5
NE2 A:HIS81 2.8 23.8 0.5
CG A:HIS208 2.9 31.8 0.5
CB A:HIS208 2.9 31.8 0.5
CG A:HIS208 3.0 31.6 0.5
NE2 A:HIS178 3.0 40.6 0.5
CB A:HIS208 3.1 31.6 0.5
O A:HOH1868 3.1 45.3 1.0
CE1 A:HIS208 3.3 31.5 0.5
CD2 A:HIS178 3.4 40.4 0.5
ND1 A:HIS178 3.4 40.5 0.5
CE1 A:HIS208 3.5 31.8 0.5
CE1 A:HIS81 3.5 23.7 0.5
CD2 A:HIS81 3.6 23.7 0.5
CD2 A:HIS81 3.6 24.1 0.5
ND2 A:ASN251 3.9 24.7 1.0
ND1 A:HIS178 3.9 40.4 0.5
CD2 A:HIS208 3.9 31.8 0.5
CA A:HIS208 3.9 31.8 0.5
ND1 A:HIS81 3.9 24.2 0.5
CA A:HIS208 4.0 31.7 0.5
O A:HOH1736 4.1 29.2 1.0
NE2 A:HIS208 4.2 31.8 0.5
CD2 A:HIS208 4.2 31.6 0.5
N A:GLY209 4.2 32.4 0.5
CD2 A:HIS178 4.2 40.5 0.5
N A:GLY209 4.2 32.3 0.5
CG A:HIS178 4.3 40.4 0.5
OD2 A:ASP80 4.3 23.4 0.5
NE2 A:HIS208 4.3 31.5 0.5
OD2 A:ASP80 4.4 23.0 0.5
CD1 A:LEU136 4.4 45.2 0.5
CG A:HIS178 4.4 40.5 0.5
CG A:HIS81 4.5 24.1 0.5
C A:HIS208 4.5 32.1 0.5
ND1 A:HIS81 4.5 23.6 0.5
CG A:HIS81 4.6 23.6 0.5
C A:HIS208 4.6 31.9 0.5
OD1 A:ASP80 4.8 23.3 0.5
OD1 A:ASP80 4.9 22.8 0.5
CG A:ASN251 4.9 25.0 1.0
CG A:ASP80 5.0 23.2 0.5

Cobalt binding site 2 out of 5 in 1rv8

Go back to Cobalt Binding Sites List in 1rv8
Cobalt binding site 2 out of 5 in the Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1709

b:53.6
occ:0.50
 NE2 A:HIS178 2.4 40.6 0.5
ND1 A:HIS208 2.4 31.8 0.5
CE1 A:HIS81 2.4 23.7 0.5
CO A:CO1703 2.5 37.7 0.5
NE2 A:HIS81 2.5 23.8 0.5
CE1 A:HIS178 2.6 40.4 0.5
CD1 A:LEU136 2.6 45.2 0.5
ND1 A:HIS208 2.7 31.5 0.5
NE2 A:HIS81 2.8 24.3 0.5
CE1 A:HIS178 2.8 40.5 0.5
O A:HOH1937 2.8 63.9 1.0
NE2 A:HIS178 3.3 40.4 0.5
CG A:HIS208 3.3 31.8 0.5
CG A:HIS208 3.3 31.6 0.5
CB A:HIS208 3.4 31.8 0.5
CE1 A:HIS208 3.5 31.8 0.5
CB A:HIS208 3.5 31.6 0.5
OE2 A:GLU132 3.5 33.6 0.5
CD2 A:HIS81 3.6 24.1 0.5
CE1 A:HIS208 3.6 31.5 0.5
CE1 A:HIS81 3.6 24.3 0.5
ND1 A:HIS178 3.7 40.4 0.5
CD2 A:HIS178 3.7 40.5 0.5
ND1 A:HIS81 3.7 23.6 0.5
CD2 A:HIS81 3.8 23.7 0.5
CG A:LEU136 4.0 45.3 0.5
OE1 A:GLU132 4.1 33.8 0.5
ND1 A:HIS178 4.1 40.5 0.5
OE2 A:GLU132 4.1 33.8 0.5
CD A:GLU132 4.2 33.6 0.5
CD2 A:HIS208 4.3 31.6 0.5
NE2 A:HIS208 4.4 31.5 0.5
CG A:HIS81 4.4 23.6 0.5
CD2 A:HIS208 4.5 31.8 0.5
NE2 A:HIS208 4.5 31.8 0.5
CD2 A:HIS178 4.6 40.4 0.5
CG A:HIS178 4.6 40.5 0.5
OE1 A:GLU132 4.6 33.8 0.5
CD A:GLU132 4.6 33.7 0.5
CG A:HIS81 4.6 24.1 0.5
OD1 A:ASP102 4.6 27.6 1.0
ND1 A:HIS81 4.6 24.2 0.5
O A:HOH1918 4.7 55.1 1.0
CG A:HIS178 4.8 40.4 0.5
CD2 A:LEU136 4.8 45.2 0.5
CA A:HIS208 4.9 31.8 0.5
CA A:HIS208 5.0 31.7 0.5

Cobalt binding site 3 out of 5 in 1rv8

Go back to Cobalt Binding Sites List in 1rv8
Cobalt binding site 3 out of 5 in the Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1701

b:32.5
occ:1.00
 NE2 B:HIS178 2.0 42.2 1.0
OE2 B:GLU132 2.2 34.4 1.0
NE2 B:HIS81 2.2 25.6 1.0
ND1 B:HIS208 2.3 37.9 1.0
O B:HOH1750 2.4 32.5 1.0
OE1 B:GLU132 2.5 34.3 1.0
CD B:GLU132 2.6 34.2 1.0
CE1 B:HIS178 3.0 42.2 1.0
CD2 B:HIS178 3.0 42.1 1.0
CE1 B:HIS208 3.1 38.0 1.0
CE1 B:HIS81 3.1 25.4 1.0
CD2 B:HIS81 3.2 25.3 1.0
CG B:HIS208 3.5 38.0 1.0
CB B:HIS208 3.9 38.0 1.0
ND1 B:HIS178 4.1 42.2 1.0
CG B:GLU132 4.1 33.9 1.0
CG B:HIS178 4.1 42.2 1.0
OD1 B:ASP102 4.2 33.3 1.0
ND1 B:HIS81 4.3 25.4 1.0
NE2 B:HIS208 4.3 38.1 1.0
O B:HOH1819 4.3 42.0 1.0
CG B:HIS81 4.4 25.2 1.0
CE B:MET100 4.4 31.2 1.0
CD2 B:HIS208 4.5 38.0 1.0
O B:HOH1936 4.6 75.4 1.0
CG B:ASP102 4.7 33.4 1.0
CB B:GLU132 4.8 33.7 1.0

Cobalt binding site 4 out of 5 in 1rv8

Go back to Cobalt Binding Sites List in 1rv8
Cobalt binding site 4 out of 5 in the Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co1707

b:35.0
occ:1.00
 NE2 C:HIS178 2.1 42.7 1.0
OE2 C:GLU132 2.2 33.6 1.0
OE1 C:GLU132 2.3 33.9 1.0
O C:HOH1729 2.3 25.0 1.0
NE2 C:HIS81 2.3 26.3 1.0
ND1 C:HIS208 2.4 43.4 1.0
CD C:GLU132 2.6 33.6 1.0
CD2 C:HIS178 2.8 42.8 1.0
CE1 C:HIS208 3.2 43.4 1.0
CE1 C:HIS81 3.2 26.2 1.0
CE1 C:HIS178 3.3 42.8 1.0
CD2 C:HIS81 3.3 26.0 1.0
CG C:HIS208 3.5 43.5 1.0
CB C:HIS208 3.9 43.5 1.0
CG C:HIS178 4.1 42.9 1.0
CG C:GLU132 4.1 33.6 1.0
OD1 C:ASP102 4.2 30.5 1.0
ND1 C:HIS178 4.2 42.8 1.0
ND1 C:HIS81 4.4 26.0 1.0
NE2 C:HIS208 4.4 43.3 1.0
CG C:HIS81 4.4 25.8 1.0
CD2 C:HIS208 4.6 43.4 1.0
CG C:ASP102 4.7 30.6 1.0
CE C:MET100 4.7 29.6 1.0
CB C:GLU132 4.8 33.6 1.0
OD2 C:ASP102 4.9 30.7 1.0

Cobalt binding site 5 out of 5 in 1rv8

Go back to Cobalt Binding Sites List in 1rv8
Cobalt binding site 5 out of 5 in the Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Class II Fructose-1,6-Bisphosphate Aldolase From Thermus Aquaticus in Complex with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co1705

b:27.7
occ:1.00
 OE1 D:GLU132 2.2 27.4 1.0
NE2 D:HIS178 2.2 34.1 1.0
OE2 D:GLU132 2.3 27.9 1.0
NE2 D:HIS81 2.3 23.1 1.0
ND1 D:HIS208 2.3 33.7 1.0
O D:HOH1751 2.4 28.5 1.0
CD D:GLU132 2.5 27.7 1.0
CD2 D:HIS178 2.9 33.9 1.0
CE1 D:HIS208 3.0 33.7 1.0
CE1 D:HIS81 3.2 23.0 1.0
CD2 D:HIS81 3.3 23.2 1.0
CE1 D:HIS178 3.3 34.1 1.0
CG D:HIS208 3.5 33.9 1.0
CB D:HIS208 3.9 34.1 1.0
CG D:GLU132 4.0 27.8 1.0
CG D:HIS178 4.1 34.1 1.0
OD1 D:ASP102 4.1 26.7 1.0
NE2 D:HIS208 4.2 33.7 1.0
ND1 D:HIS178 4.3 34.1 1.0
ND1 D:HIS81 4.3 23.1 1.0
CG D:HIS81 4.4 23.1 1.0
O D:HOH1780 4.5 32.2 1.0
CD2 D:HIS208 4.5 33.7 1.0
O D:HOH1830 4.5 45.0 1.0
CE D:MET100 4.6 27.0 1.0
CG D:ASP102 4.6 26.9 1.0
O D:HOH1828 4.7 39.9 1.0
CB D:GLU132 4.8 28.2 1.0
OD2 D:ASP102 4.9 26.9 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: Tue Jul 30 14:37:12 2024

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