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Cobalt in PDB 4b5u: Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate and Succinic Semialdehyde

Enzymatic activity of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate and Succinic Semialdehyde

All present enzymatic activity of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate and Succinic Semialdehyde:
4.1.2.20;

Protein crystallography data

The structure of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate and Succinic Semialdehyde, PDB code: 4b5u was solved by M.Coincon, W.Wang, S.Y.K.Seah, J.Sygusch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.92 / 1.91
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 151.130, 151.130, 151.130, 90.00, 90.00, 90.00
R / Rfree (%) 13 / 15.4

Other elements in 4b5u:

The structure of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate and Succinic Semialdehyde also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate and Succinic Semialdehyde (pdb code 4b5u). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate and Succinic Semialdehyde, PDB code: 4b5u:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 4b5u

Go back to Cobalt Binding Sites List in 4b5u
Cobalt binding site 1 out of 2 in the Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate and Succinic Semialdehyde


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate and Succinic Semialdehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1000

b:19.2
occ:0.70
 MG A:MG1001 0.1 19.6 0.3
OE1 A:GLU149 2.1 17.8 1.0
O3 A:PYR4000 2.1 19.7 1.0
OD2 A:ASP175 2.2 19.4 1.0
O A:HOH2125 2.2 14.5 1.0
O A:HOH2131 2.3 20.3 1.0
O1 A:PYR4000 2.3 19.4 1.0
C2 A:PYR4000 2.9 21.9 1.0
C1 A:PYR4000 2.9 23.3 1.0
HE22 A:GLN147 3.0 27.5 1.0
HB2 A:ASP175 3.1 19.8 1.0
CD A:GLU149 3.1 28.7 1.0
CG A:ASP175 3.2 22.7 1.0
HH12 A:ARG70 3.4 20.0 1.0
OE2 A:GLU149 3.5 20.1 1.0
CB A:ASP175 3.6 16.5 1.0
NE2 A:GLN147 3.7 22.9 1.0
H A:ASP175 3.8 19.5 1.0
O A:HOH2126 3.8 17.5 1.0
HE21 A:GLN147 3.8 27.5 1.0
HA3 A:GLY172 3.8 19.8 1.0
NH1 A:ARG70 4.1 16.6 1.0
HE3 A:MET94 4.2 37.7 1.0
O2 A:PYR4000 4.2 19.5 1.0
O A:HOH2171 4.2 37.5 0.3
HB3 A:GLU149 4.2 32.3 1.0
HB3 A:ASP175 4.3 19.8 1.0
HH11 A:ARG70 4.3 20.0 1.0
OD1 A:ASP175 4.3 19.6 1.0
C3 A:PYR4000 4.3 19.1 1.0
O4 A:SSN4002 4.3 38.1 0.3
HE2 A:HIS45 4.4 15.5 1.0
O4 A:SSN4002 4.4 40.2 0.3
CG A:GLU149 4.4 23.3 1.0
N A:ASP175 4.5 16.3 1.0
OE1 A:GLU44 4.5 14.7 1.0
HG2 A:GLU149 4.6 28.0 1.0
C4 A:SSN4002 4.6 37.0 0.3
HB1 A:ALA174 4.6 27.1 1.0
HH22 A:ARG70 4.7 14.8 1.0
CA A:ASP175 4.7 15.6 1.0
HD2 A:HIS45 4.7 12.5 1.0
CA A:GLY172 4.7 16.5 1.0
CD A:GLN147 4.8 16.3 1.0
CB A:GLU149 4.9 26.9 1.0
HA2 A:GLY172 4.9 19.8 1.0
NE2 A:HIS45 5.0 12.9 1.0
CZ A:ARG70 5.0 15.6 1.0

Cobalt binding site 2 out of 2 in 4b5u

Go back to Cobalt Binding Sites List in 4b5u
Cobalt binding site 2 out of 2 in the Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate and Succinic Semialdehyde


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate and Succinic Semialdehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1000

b:17.3
occ:0.70
 MG B:MG1001 0.1 18.3 0.3
OE1 B:GLU149 2.1 16.9 1.0
OD2 B:ASP175 2.1 20.8 1.0
O3 B:PYR4000 2.2 20.9 1.0
O A:HOH2436 2.2 18.0 1.0
O1 B:PYR4000 2.3 17.3 1.0
O B:HOH2097 2.3 14.6 1.0
C2 B:PYR4000 2.9 21.6 1.0
C1 B:PYR4000 2.9 24.4 1.0
HE22 B:GLN147 3.0 32.3 1.0
HB2 B:ASP175 3.1 24.1 1.0
CD B:GLU149 3.2 27.5 1.0
CG B:ASP175 3.2 18.6 1.0
HH12 B:ARG70 3.4 17.6 1.0
OE2 B:GLU149 3.5 18.1 1.0
CB B:ASP175 3.6 20.1 1.0
NE2 B:GLN147 3.7 26.9 1.0
H B:ASP175 3.8 17.5 1.0
O B:HOH2098 3.8 18.0 1.0
HA3 B:GLY172 3.9 20.1 1.0
HE21 B:GLN147 3.9 32.3 1.0
NH1 B:ARG70 4.0 14.7 1.0
O B:HOH2143 4.1 32.5 0.3
O4 B:SSN4002 4.2 32.5 0.3
O2 B:PYR4000 4.2 20.0 1.0
HH11 B:ARG70 4.2 17.6 1.0
OD1 B:ASP175 4.3 16.6 1.0
HB3 B:ASP175 4.3 24.1 1.0
HE3 B:MET94 4.3 37.3 1.0
C3 B:PYR4000 4.3 16.4 1.0
O4 B:SSN4002 4.4 37.5 0.3
HB2 B:GLU149 4.5 42.7 1.0
N B:ASP175 4.5 14.6 1.0
HB3 B:GLU149 4.5 42.7 1.0
C4 B:SSN4002 4.5 32.5 0.3
CG B:GLU149 4.5 25.5 1.0
OE1 B:GLU44 4.5 15.0 1.0
HB1 B:ALA174 4.5 24.1 1.0
HH22 B:ARG70 4.6 14.6 1.0
CA B:ASP175 4.7 16.9 1.0
HD2 B:HIS45 4.7 14.6 1.0
CB B:GLU149 4.7 35.6 1.0
CA B:GLY172 4.8 16.8 1.0
CD B:GLN147 4.8 18.0 1.0
NE2 B:HIS45 4.9 13.8 1.0
HG3 B:GLU149 4.9 30.6 1.0
CZ B:ARG70 4.9 15.2 1.0
HA2 B:GLY172 5.0 20.1 1.0

Reference:

M.Coincon, W.Wang, J.Sygusch, S.Y.K.Seah. Crystal Structure of Reaction Intermediates in Pyruvate Class II Aldolase: Substrate Cleavage, Enolate Stabilization and Substrate Specificity J.Biol.Chem. V. 287 36208 2012.
ISSN: ISSN 0021-9258
PubMed: 22908224
DOI: 10.1074/JBC.M112.400705
Page generated: Sun Dec 13 10:43:49 2020

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