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Cobalt in PDB 1qw7: Structure of An Engineered Organophosphorous Hydrolase with Increased Activity Toward Hydrolysis of Phosphothiolate Bonds

Enzymatic activity of Structure of An Engineered Organophosphorous Hydrolase with Increased Activity Toward Hydrolysis of Phosphothiolate Bonds

All present enzymatic activity of Structure of An Engineered Organophosphorous Hydrolase with Increased Activity Toward Hydrolysis of Phosphothiolate Bonds:
3.1.8.1;

Protein crystallography data

The structure of Structure of An Engineered Organophosphorous Hydrolase with Increased Activity Toward Hydrolysis of Phosphothiolate Bonds, PDB code: 1qw7 was solved by A.D.Mesecar, J.K.Grimsley, T.Holton, J.R.Wild, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.50 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 126.719, 89.879, 68.337, 90.00, 91.73, 90.00
R / Rfree (%) 17.9 / 23

Other elements in 1qw7:

The structure of Structure of An Engineered Organophosphorous Hydrolase with Increased Activity Toward Hydrolysis of Phosphothiolate Bonds also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of An Engineered Organophosphorous Hydrolase with Increased Activity Toward Hydrolysis of Phosphothiolate Bonds (pdb code 1qw7). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Structure of An Engineered Organophosphorous Hydrolase with Increased Activity Toward Hydrolysis of Phosphothiolate Bonds, PDB code: 1qw7:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 1qw7

Go back to Cobalt Binding Sites List in 1qw7
Cobalt binding site 1 out of 4 in the Structure of An Engineered Organophosphorous Hydrolase with Increased Activity Toward Hydrolysis of Phosphothiolate Bonds


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of An Engineered Organophosphorous Hydrolase with Increased Activity Toward Hydrolysis of Phosphothiolate Bonds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co601

b:15.0
occ:1.00
 O A:HOH802 1.8 9.1 1.0
OQ1 A:KCX169 1.9 23.2 1.0
O A:HOH826 2.0 28.4 1.0
ND1 A:HIS201 2.1 10.4 1.0
NE2 A:HIS230 2.2 19.8 1.0
CX A:KCX169 2.9 29.7 1.0
CE1 A:HIS201 3.0 17.2 1.0
OQ2 A:KCX169 3.1 28.5 1.0
CE1 A:HIS230 3.1 22.9 1.0
CD2 A:HIS230 3.2 24.7 1.0
CG A:HIS201 3.2 15.6 1.0
NH2 A:ARG254 3.4 21.2 1.0
CB A:HIS201 3.6 16.2 1.0
CO A:CO602 3.6 11.3 1.0
O A:HOH805 3.9 30.0 1.0
NE1 A:TRP131 4.1 20.4 1.0
NZ A:KCX169 4.1 24.1 1.0
CE1 A:HIS55 4.1 18.1 1.0
CZ A:ARG254 4.2 26.8 1.0
NE2 A:HIS201 4.2 16.5 1.0
NE2 A:HIS55 4.2 10.8 1.0
ND1 A:HIS230 4.3 15.7 1.0
CD2 A:HIS201 4.3 16.6 1.0
CG A:HIS230 4.3 20.8 1.0
OD1 A:ASP301 4.4 18.0 1.0
CA A:HIS201 4.4 15.0 1.0
NE A:ARG254 4.6 24.9 1.0
CD1 A:TRP131 4.7 19.6 1.0
CE A:KCX169 4.7 19.1 1.0
NH1 A:ARG254 5.0 32.2 1.0

Cobalt binding site 2 out of 4 in 1qw7

Go back to Cobalt Binding Sites List in 1qw7
Cobalt binding site 2 out of 4 in the Structure of An Engineered Organophosphorous Hydrolase with Increased Activity Toward Hydrolysis of Phosphothiolate Bonds


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of An Engineered Organophosphorous Hydrolase with Increased Activity Toward Hydrolysis of Phosphothiolate Bonds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co602

b:11.3
occ:1.00
 O A:HOH802 2.1 9.1 1.0
NE2 A:HIS57 2.1 15.8 1.0
OQ2 A:KCX169 2.1 28.5 1.0
NE2 A:HIS55 2.2 10.8 1.0
OD2 A:ASP301 2.3 26.1 1.0
CE1 A:HIS57 3.0 16.4 1.0
CD2 A:HIS57 3.1 16.8 1.0
CD2 A:HIS55 3.2 14.7 1.0
CG A:ASP301 3.2 23.4 1.0
CX A:KCX169 3.2 29.7 1.0
CE1 A:HIS55 3.2 18.1 1.0
OD1 A:ASP301 3.4 18.0 1.0
O A:HOH805 3.5 30.0 1.0
CO A:CO601 3.6 15.0 1.0
OQ1 A:KCX169 3.7 23.2 1.0
O A:HOH914 3.9 32.3 1.0
O A:HOH826 3.9 28.4 1.0
ND1 A:HIS57 4.1 13.3 1.0
CE1 A:HIS230 4.2 22.9 1.0
NZ A:KCX169 4.2 24.1 1.0
CG A:HIS57 4.2 17.5 1.0
CG2 A:VAL101 4.3 17.5 1.0
ND1 A:HIS55 4.3 14.4 1.0
CG A:HIS55 4.3 14.8 1.0
NE2 A:HIS230 4.4 19.8 1.0
CB A:ASP301 4.5 20.3 1.0
CA A:ASP301 5.0 20.2 1.0

Cobalt binding site 3 out of 4 in 1qw7

Go back to Cobalt Binding Sites List in 1qw7
Cobalt binding site 3 out of 4 in the Structure of An Engineered Organophosphorous Hydrolase with Increased Activity Toward Hydrolysis of Phosphothiolate Bonds


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of An Engineered Organophosphorous Hydrolase with Increased Activity Toward Hydrolysis of Phosphothiolate Bonds within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co603

b:14.6
occ:1.00
 NE2 B:HIS57 2.0 21.0 1.0
NE2 B:HIS55 2.1 12.4 1.0
OQ2 B:KCX169 2.3 23.2 1.0
OD2 B:ASP301 2.4 25.4 1.0
O B:HOH774 2.4 8.4 1.0
CE1 B:HIS57 2.9 23.9 1.0
CD2 B:HIS55 3.0 16.4 1.0
CD2 B:HIS57 3.1 19.7 1.0
CG B:ASP301 3.1 23.8 1.0
CE1 B:HIS55 3.2 16.9 1.0
OD1 B:ASP301 3.2 22.2 1.0
CX B:KCX169 3.3 21.5 1.0
CO B:CO604 3.6 16.6 1.0
OQ1 B:KCX169 3.9 21.7 1.0
O B:HOH776 3.9 16.7 1.0
ND1 B:HIS57 4.0 21.7 1.0
O B:HOH764 4.0 35.2 1.0
CE1 B:HIS230 4.1 29.0 1.0
CG B:HIS57 4.1 19.8 1.0
CG B:HIS55 4.2 15.3 1.0
CG2 B:VAL101 4.2 16.7 1.0
ND1 B:HIS55 4.2 17.1 1.0
NZ B:KCX169 4.2 20.0 1.0
NE2 B:HIS230 4.3 31.6 1.0
CB B:ASP301 4.5 22.4 1.0

Cobalt binding site 4 out of 4 in 1qw7

Go back to Cobalt Binding Sites List in 1qw7
Cobalt binding site 4 out of 4 in the Structure of An Engineered Organophosphorous Hydrolase with Increased Activity Toward Hydrolysis of Phosphothiolate Bonds


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of An Engineered Organophosphorous Hydrolase with Increased Activity Toward Hydrolysis of Phosphothiolate Bonds within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co604

b:16.6
occ:1.00
 O B:HOH774 1.6 8.4 1.0
O B:HOH776 1.9 16.7 1.0
NE2 B:HIS230 2.1 31.6 1.0
OQ1 B:KCX169 2.1 21.7 1.0
ND1 B:HIS201 2.2 27.5 1.0
OQ2 B:KCX169 2.9 23.2 1.0
CX B:KCX169 2.9 21.5 1.0
CE1 B:HIS201 3.0 29.6 1.0
CE1 B:HIS230 3.1 29.0 1.0
CD2 B:HIS230 3.1 25.9 1.0
CG B:HIS201 3.2 28.2 1.0
NH2 B:ARG254 3.4 41.3 1.0
CO B:CO603 3.6 14.6 1.0
CB B:HIS201 3.7 18.5 1.0
CE1 B:HIS55 4.0 16.9 1.0
NE1 B:TRP131 4.1 24.3 1.0
NE2 B:HIS55 4.1 12.4 1.0
NE2 B:HIS201 4.2 30.9 1.0
NZ B:KCX169 4.2 20.0 1.0
ND1 B:HIS230 4.2 25.8 1.0
CG B:HIS230 4.3 28.7 1.0
CZ B:ARG254 4.3 46.2 1.0
CD2 B:HIS201 4.3 27.3 1.0
OD1 B:ASP301 4.4 22.2 1.0
CA B:HIS201 4.5 22.6 1.0
NE B:ARG254 4.7 41.1 1.0
CD1 B:TRP131 4.8 26.5 1.0
CE B:KCX169 4.9 18.9 1.0

Reference:

J.K.Grimsley, B.Calamini, J.R.Wild, A.D.Mesecar. Structural and Mutational Studies of Organophosphorus Hydrolase Reveal A Cryptic and Functional Allosteric-Binding Site. Arch.Biochem.Biophys. V. 442 169 2005.
ISSN: ISSN 0003-9861
PubMed: 16188223
DOI: 10.1016/J.ABB.2005.08.012
Page generated: Tue Jul 30 14:32:08 2024

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