Atomistry » Cobalt » PDB 3mdl-3r61 » 3ood
Atomistry »
  Cobalt »
    PDB 3mdl-3r61 »
      3ood »

Cobalt in PDB 3ood: Structure of Opda Y257F Mutant Soaked with Diethyl 4-Methoxyphenyl Phosphate For 20 Hours.

Enzymatic activity of Structure of Opda Y257F Mutant Soaked with Diethyl 4-Methoxyphenyl Phosphate For 20 Hours.

All present enzymatic activity of Structure of Opda Y257F Mutant Soaked with Diethyl 4-Methoxyphenyl Phosphate For 20 Hours.:
3.1.8.1;

Protein crystallography data

The structure of Structure of Opda Y257F Mutant Soaked with Diethyl 4-Methoxyphenyl Phosphate For 20 Hours., PDB code: 3ood was solved by F.Ely, L.W.Guddat, D.L.Ollis, G.Schenk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.27 / 1.89
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.000, 109.000, 62.000, 90.00, 90.00, 120.00
R / Rfree (%) 15.5 / 19.5

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of Opda Y257F Mutant Soaked with Diethyl 4-Methoxyphenyl Phosphate For 20 Hours. (pdb code 3ood). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Structure of Opda Y257F Mutant Soaked with Diethyl 4-Methoxyphenyl Phosphate For 20 Hours., PDB code: 3ood:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 3ood

Go back to Cobalt Binding Sites List in 3ood
Cobalt binding site 1 out of 2 in the Structure of Opda Y257F Mutant Soaked with Diethyl 4-Methoxyphenyl Phosphate For 20 Hours.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Opda Y257F Mutant Soaked with Diethyl 4-Methoxyphenyl Phosphate For 20 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co800

b:12.3
occ:1.00
O1 A:EPL702 1.8 17.3 0.6
NE2 A:HIS57 2.1 9.0 1.0
NE2 A:HIS55 2.1 10.3 1.0
OQ1 A:KCX169 2.1 4.5 0.8
O A:HOH500 2.2 4.1 0.4
OD1 A:ASP301 2.2 9.8 1.0
O A:HOH434 2.8 7.4 0.4
CD2 A:HIS55 3.0 10.1 1.0
CE1 A:HIS57 3.0 10.2 1.0
CX A:KCX169 3.0 7.5 0.8
CG A:ASP301 3.1 8.9 1.0
CD2 A:HIS57 3.1 8.6 1.0
CE1 A:HIS55 3.2 8.9 1.0
P A:EPL702 3.2 11.6 0.6
OD2 A:ASP301 3.4 10.5 1.0
OQ2 A:KCX169 3.4 7.6 0.8
C10 A:EPL702 3.7 19.8 0.6
CO A:CO801 3.7 14.2 1.0
O4 A:EPL702 3.9 18.6 0.6
O A:HOH602 4.0 14.2 0.5
NZ A:KCX169 4.1 9.3 1.0
CG2 A:VAL101 4.1 7.5 1.0
ND1 A:HIS57 4.2 9.2 1.0
CE1 A:HIS230 4.2 9.2 1.0
O3 A:EPL702 4.2 9.9 0.3
O2 A:EPL702 4.2 26.6 0.4
CG A:HIS55 4.2 8.7 1.0
C11 A:EPL702 4.2 22.0 0.6
CG A:HIS57 4.2 9.7 1.0
ND1 A:HIS55 4.3 9.7 1.0
C11 A:EPL702 4.3 25.7 0.4
O2 A:EPL702 4.3 18.4 0.6
NE2 A:HIS230 4.4 9.9 1.0
CB A:ASP301 4.4 8.8 1.0
C8 A:EPL702 4.5 18.4 0.6
CA A:ASP301 4.8 8.6 1.0
O1 A:EPL702 4.9 26.1 0.4
C10 A:EPL702 4.9 25.2 0.4
O A:HOH435 4.9 16.3 0.5

Cobalt binding site 2 out of 2 in 3ood

Go back to Cobalt Binding Sites List in 3ood
Cobalt binding site 2 out of 2 in the Structure of Opda Y257F Mutant Soaked with Diethyl 4-Methoxyphenyl Phosphate For 20 Hours.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Opda Y257F Mutant Soaked with Diethyl 4-Methoxyphenyl Phosphate For 20 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co801

b:14.2
occ:1.00
OQ2 A:KCX169 1.9 7.6 0.8
NE2 A:HIS230 2.0 9.9 1.0
ND1 A:HIS201 2.1 8.6 1.0
O A:HOH500 2.1 4.1 0.4
O3 A:EPL702 2.3 9.9 0.3
O1 A:EPL702 2.9 17.3 0.6
P A:EPL702 3.0 11.6 0.6
CD2 A:HIS230 3.0 8.2 1.0
CX A:KCX169 3.0 7.5 0.8
CE1 A:HIS201 3.0 9.3 1.0
CE1 A:HIS230 3.0 9.2 1.0
CG A:HIS201 3.1 10.4 1.0
OQ1 A:KCX169 3.4 4.5 0.8
O1 A:EPL702 3.5 26.1 0.4
CB A:HIS201 3.5 10.2 1.0
NH2 A:ARG254 3.7 5.8 0.5
CO A:CO800 3.7 12.3 1.0
NE1 A:TRP131 3.9 11.1 1.0
O2 A:EPL702 4.0 18.4 0.6
ND1 A:HIS230 4.1 8.2 1.0
CE1 A:HIS55 4.1 8.9 1.0
NE2 A:HIS201 4.1 9.9 1.0
CG A:HIS230 4.1 10.0 1.0
NZ A:KCX169 4.1 9.3 1.0
NE2 A:HIS55 4.2 10.3 1.0
CD2 A:HIS201 4.2 9.0 1.0
CA A:HIS201 4.3 9.7 1.0
OD2 A:ASP301 4.3 10.5 1.0
O4 A:EPL702 4.4 18.6 0.6
CD1 A:TRP131 4.5 11.3 1.0
CZ A:ARG254 4.5 8.0 0.5
C8 A:EPL702 4.5 18.4 0.6
O A:HOH434 4.6 7.4 0.4
O A:HOH515 4.6 37.4 1.0
CE A:KCX169 4.6 10.3 1.0
O2 A:EPL702 4.7 26.6 0.4
P A:EPL702 4.7 25.1 0.4
NE A:ARG254 5.0 7.8 0.5

Reference:

F.Ely, K.S.Hadler, L.R.Gahan, L.W.Guddat, D.L.Ollis, G.Schenk. The Organophosphate-Degrading Enzyme From Agrobacterium Radiobacter Displays Mechanistic Flexibility For Catalysis. Biochem.J. V. 432 565 2010.
ISSN: ISSN 0264-6021
PubMed: 20868365
DOI: 10.1042/BJ20101054
Page generated: Sun Dec 13 10:41:48 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