Atomistry » Cobalt » PDB 1rrk-1vlx » 1rvg
Atomistry »
  Cobalt »
    PDB 1rrk-1vlx »
      1rvg »

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

Go back to Cobalt Binding Sites List in 1rvg
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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy