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Cobalt in PDB 3urb: Crystal Structure of Pte Mutant H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/R67H

Enzymatic activity of Crystal Structure of Pte Mutant H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/R67H

All present enzymatic activity of Crystal Structure of Pte Mutant H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/R67H:
3.1.8.1;

Protein crystallography data

The structure of Crystal Structure of Pte Mutant H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/R67H, PDB code: 3urb was solved by P.Tsai, N.G.Fox, Y.Li, D.P.Barondeau, F.M.Raushel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.77
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 85.468, 86.396, 88.118, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 23.4

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Pte Mutant H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/R67H (pdb code 3urb). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of Pte Mutant H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/R67H, PDB code: 3urb:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 3urb

Go back to Cobalt Binding Sites List in 3urb
Cobalt binding site 1 out of 4 in the Crystal Structure of Pte Mutant H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/R67H


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Pte Mutant H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/R67H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co801

b:22.7
occ:1.00
 ND1 A:HIS201 2.0 24.4 1.0
OQ2 A:KCX169 2.0 20.1 1.0
NE2 A:HIS230 2.0 19.9 1.0
O2 A:DPF903 2.1 32.0 1.0
O4 A:DPF903 2.7 30.0 1.0
P1 A:DPF903 2.8 33.4 1.0
CE1 A:HIS201 2.9 25.2 1.0
CE1 A:HIS230 3.0 21.5 1.0
CD2 A:HIS230 3.0 20.9 1.0
CX A:KCX169 3.0 20.4 1.0
CG A:HIS201 3.1 24.2 1.0
OQ1 A:KCX169 3.5 18.1 1.0
CB A:HIS201 3.5 22.0 1.0
O1 A:DPF903 3.7 35.9 1.0
CO A:CO802 3.9 19.0 1.0
NE1 A:TRP131 3.9 24.0 1.0
NE2 A:HIS201 4.0 26.8 1.0
ND1 A:HIS230 4.1 22.3 1.0
O3 A:DPF903 4.1 34.0 1.0
CD2 A:HIS201 4.1 24.9 1.0
CG A:HIS230 4.1 20.5 1.0
NZ A:KCX169 4.2 18.2 1.0
NE2 A:HIS55 4.3 18.8 1.0
CA A:HIS201 4.3 19.2 1.0
CE1 A:HIS55 4.5 17.3 1.0
CD1 A:TRP131 4.5 22.3 1.0
CE A:KCX169 4.6 19.4 1.0
OD2 A:ASP301 4.6 20.1 1.0
C2 A:DPF903 4.8 40.4 1.0

Cobalt binding site 2 out of 4 in 3urb

Go back to Cobalt Binding Sites List in 3urb
Cobalt binding site 2 out of 4 in the Crystal Structure of Pte Mutant H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/R67H


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Pte Mutant H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/R67H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co802

b:19.0
occ:1.00
 NE2 A:HIS57 2.0 17.1 1.0
O4 A:DPF903 2.0 30.0 1.0
OQ1 A:KCX169 2.2 18.1 1.0
OD1 A:ASP301 2.3 17.2 1.0
NE2 A:HIS55 2.3 18.8 1.0
CD2 A:HIS57 3.0 15.9 1.0
CD2 A:HIS55 3.0 16.7 1.0
CE1 A:HIS57 3.0 17.6 1.0
CX A:KCX169 3.1 20.4 1.0
CG A:ASP301 3.1 18.8 1.0
P1 A:DPF903 3.3 33.4 1.0
OD2 A:ASP301 3.4 20.1 1.0
C1 A:DPF903 3.4 35.2 1.0
CE1 A:HIS55 3.4 17.3 1.0
OQ2 A:KCX169 3.5 20.1 1.0
O3 A:DPF903 3.6 34.0 1.0
CO A:CO801 3.9 22.7 1.0
CG2 A:VAL101 4.0 15.7 1.0
NZ A:KCX169 4.1 18.2 1.0
ND1 A:HIS57 4.1 17.8 1.0
CG A:HIS57 4.1 15.2 1.0
O2 A:DPF903 4.1 32.0 1.0
CE1 A:HIS230 4.2 21.5 1.0
CG A:HIS55 4.3 16.4 1.0
ND1 A:HIS55 4.4 16.6 1.0
O1 A:DPF903 4.5 35.9 1.0
CB A:ASP301 4.5 18.5 1.0
NE2 A:HIS230 4.5 19.9 1.0
C2 A:DPF903 4.6 40.4 1.0
C4 A:DPF903 4.6 34.0 1.0
O A:HOH1436 4.7 57.5 1.0
CA A:ASP301 4.9 16.8 1.0

Cobalt binding site 3 out of 4 in 3urb

Go back to Cobalt Binding Sites List in 3urb
Cobalt binding site 3 out of 4 in the Crystal Structure of Pte Mutant H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/R67H


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Pte Mutant H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/R67H within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co803

b:24.9
occ:1.00
 NE2 B:HIS57 2.1 23.6 1.0
OQ2 B:KCX169 2.2 23.9 1.0
OD1 B:ASP301 2.3 25.6 1.0
O2 B:DPF902 2.3 38.1 1.0
NE2 B:HIS55 2.4 27.9 1.0
CD2 B:HIS55 3.0 27.3 1.0
CD2 B:HIS57 3.0 24.7 1.0
CE1 B:HIS57 3.1 24.1 1.0
CX B:KCX169 3.1 24.3 1.0
CG B:ASP301 3.2 25.5 1.0
P1 B:DPF902 3.4 32.9 1.0
OD2 B:ASP301 3.4 24.1 1.0
CE1 B:HIS55 3.5 27.2 1.0
O3 B:DPF902 3.6 39.5 1.0
OQ1 B:KCX169 3.6 23.9 1.0
C4 B:DPF902 3.8 39.2 1.0
CO B:CO804 3.8 26.0 1.0
CG2 B:VAL101 4.0 23.3 1.0
NZ B:KCX169 4.1 24.2 1.0
CE1 B:HIS230 4.1 25.5 1.0
O4 B:DPF902 4.1 37.4 1.0
ND1 B:HIS57 4.1 24.6 1.0
CG B:HIS57 4.2 23.6 1.0
C1 B:DPF902 4.2 38.7 1.0
CG B:HIS55 4.3 27.3 1.0
NE2 B:HIS230 4.4 27.1 1.0
ND1 B:HIS55 4.5 26.5 1.0
CB B:ASP301 4.5 25.0 1.0
O1 B:DPF902 4.7 39.7 1.0
CA B:ASP301 4.9 26.0 1.0

Cobalt binding site 4 out of 4 in 3urb

Go back to Cobalt Binding Sites List in 3urb
Cobalt binding site 4 out of 4 in the Crystal Structure of Pte Mutant H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/R67H


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Pte Mutant H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/R67H within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co804

b:26.0
occ:1.00
 OQ1 B:KCX169 2.0 23.9 1.0
ND1 B:HIS201 2.0 26.1 1.0
NE2 B:HIS230 2.1 27.1 1.0
O4 B:DPF902 2.3 37.4 1.0
O2 B:DPF902 2.8 38.1 1.0
CE1 B:HIS201 2.8 24.7 1.0
P1 B:DPF902 3.0 32.9 1.0
CX B:KCX169 3.0 24.3 1.0
CD2 B:HIS230 3.0 26.8 1.0
CE1 B:HIS230 3.1 25.5 1.0
CG B:HIS201 3.1 25.1 1.0
OQ2 B:KCX169 3.3 23.9 1.0
CB B:HIS201 3.6 25.1 1.0
NE1 B:TRP131 3.7 31.5 1.0
CO B:CO803 3.8 24.9 1.0
NE2 B:HIS201 4.0 25.5 1.0
O1 B:DPF902 4.1 39.7 1.0
ND1 B:HIS230 4.1 25.7 1.0
CD2 B:HIS201 4.2 27.2 1.0
CG B:HIS230 4.2 26.3 1.0
NZ B:KCX169 4.2 24.2 1.0
C2 B:DPF902 4.2 41.6 1.0
O3 B:DPF902 4.2 39.5 1.0
NE2 B:HIS55 4.2 27.9 1.0
CA B:HIS201 4.4 25.2 1.0
CD1 B:TRP131 4.5 29.5 1.0
CE1 B:HIS55 4.5 27.2 1.0
OD2 B:ASP301 4.6 24.1 1.0
CE B:KCX169 4.6 23.8 1.0
C3 B:DPF902 4.7 43.8 1.0
O B:HOH1499 4.8 49.2 1.0
CE2 B:TRP131 4.8 31.6 1.0

Reference:

P.C.Tsai, N.Fox, A.N.Bigley, S.P.Harvey, D.P.Barondeau, F.M.Raushel. Enzymes For the Homeland Defense: Optimizing Phosphotriesterase For the Hydrolysis of Organophosphate Nerve Agents. Biochemistry V. 51 6463 2012.
ISSN: ISSN 0006-2960
PubMed: 22809162
DOI: 10.1021/BI300811T
Page generated: Tue Jul 30 16:46:10 2024

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