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Zinc in PDB 1hzy: High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta

Enzymatic activity of High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta

All present enzymatic activity of High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta:
3.1.8.1;

Protein crystallography data

The structure of High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta, PDB code: 1hzy was solved by H.M.Holden, M.M.Benning, F.M.Raushel, H.Shim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 128.400, 90.030, 68.400, 90.00, 91.70, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1hzy:

The structure of High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta (pdb code 1hzy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta, PDB code: 1hzy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1hzy

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Zinc binding site 1 out of 4 in the High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:12.3
occ:1.00
NE2 A:HIS55 1.8 9.5 1.0
O A:HOH876 2.0 10.6 1.0
NE2 A:HIS57 2.1 11.4 1.0
O1 A:FMT369 2.1 10.4 1.0
OD2 A:ASP301 2.2 12.6 1.0
CD2 A:HIS55 2.8 10.7 1.0
C A:FMT369 2.9 9.8 1.0
CE1 A:HIS55 2.9 10.6 1.0
CE1 A:HIS57 3.1 12.1 1.0
CG A:ASP301 3.1 14.2 1.0
CD2 A:HIS57 3.1 11.0 1.0
OD1 A:ASP301 3.4 14.4 1.0
O2 A:FMT369 3.4 12.3 1.0
ZN A:ZN402 3.4 14.4 1.0
O2 A:EDO408 3.6 21.0 1.0
C2 A:EDO408 3.8 15.6 1.0
CG A:HIS55 4.0 10.7 1.0
CG2 A:VAL101 4.0 11.2 1.0
ND1 A:HIS55 4.0 10.1 1.0
CE1 A:HIS230 4.0 20.9 1.0
NZ A:LYS169 4.1 11.6 1.0
ND1 A:HIS57 4.2 11.0 1.0
CG A:HIS57 4.2 13.0 1.0
O A:HOH897 4.2 13.4 1.0
NE2 A:HIS230 4.3 20.2 1.0
O1 A:EDO425 4.3 35.6 1.0
CB A:ASP301 4.3 10.0 1.0
CA A:ASP301 4.9 12.8 1.0

Zinc binding site 2 out of 4 in 1hzy

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Zinc binding site 2 out of 4 in the High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:14.4
occ:1.00
O2 A:FMT369 2.0 12.3 1.0
O A:HOH876 2.0 10.6 1.0
NE2 A:HIS230 2.0 20.2 1.0
O A:HOH897 2.1 13.4 1.0
ND1 A:HIS201 2.2 16.3 1.0
C A:FMT369 3.0 9.8 1.0
CE1 A:HIS230 3.0 20.9 1.0
CE1 A:HIS201 3.1 15.1 1.0
CD2 A:HIS230 3.1 18.2 1.0
CG A:HIS201 3.2 13.5 1.0
O1 A:FMT369 3.3 10.4 1.0
ZN A:ZN401 3.4 12.3 1.0
CB A:HIS201 3.6 12.3 1.0
O2 A:EDO408 3.8 21.0 1.0
CE1 A:HIS55 3.9 10.6 1.0
NE2 A:HIS55 3.9 9.5 1.0
NE1 A:TRP131 4.0 12.4 1.0
ND1 A:HIS230 4.2 15.8 1.0
NZ A:LYS169 4.2 11.6 1.0
NE2 A:HIS201 4.2 18.3 1.0
CG A:HIS230 4.2 17.4 1.0
OD1 A:ASP301 4.2 14.4 1.0
CD2 A:HIS201 4.3 18.9 1.0
CA A:HIS201 4.4 11.1 1.0
CD1 A:TRP131 4.7 10.3 1.0
CE A:LYS169 4.7 12.4 1.0
OD2 A:ASP301 4.8 12.6 1.0
C2 A:EDO408 4.9 15.6 1.0
CG A:ASP301 4.9 14.2 1.0

Zinc binding site 3 out of 4 in 1hzy

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Zinc binding site 3 out of 4 in the High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:9.8
occ:1.00
O B:HOH831 2.0 9.7 1.0
NE2 B:HIS57 2.1 9.9 1.0
NE2 B:HIS55 2.1 9.4 1.0
O1 B:FMT369 2.1 9.5 1.0
OD2 B:ASP301 2.2 10.3 1.0
C B:FMT369 2.9 10.9 1.0
CE1 B:HIS57 3.0 8.4 1.0
CD2 B:HIS55 3.0 8.1 1.0
CE1 B:HIS55 3.1 10.0 1.0
CD2 B:HIS57 3.1 8.2 1.0
CG B:ASP301 3.1 11.2 1.0
OD1 B:ASP301 3.3 9.6 1.0
O2 B:FMT369 3.4 11.0 1.0
ZN B:ZN402 3.5 10.6 1.0
O1 B:EDO407 3.7 16.7 1.0
C1 B:EDO407 3.7 19.8 1.0
O2 B:EDO423 4.0 31.6 1.0
CG2 B:VAL101 4.1 9.3 1.0
NZ B:LYS169 4.1 11.2 1.0
CE1 B:HIS230 4.1 10.3 1.0
ND1 B:HIS57 4.1 8.5 1.0
CG B:HIS57 4.2 9.6 1.0
CG B:HIS55 4.2 8.9 1.0
ND1 B:HIS55 4.2 8.2 1.0
NE2 B:HIS230 4.3 8.6 1.0
CB B:ASP301 4.3 10.5 1.0
O B:HOH919 4.3 12.3 1.0
C2 B:EDO423 4.8 27.7 1.0
CA B:ASP301 4.9 8.3 1.0

Zinc binding site 4 out of 4 in 1hzy

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Zinc binding site 4 out of 4 in the High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:10.6
occ:1.00
O B:HOH831 2.0 9.7 1.0
O2 B:FMT369 2.0 11.0 1.0
NE2 B:HIS230 2.1 8.6 1.0
ND1 B:HIS201 2.1 10.7 1.0
O B:HOH919 2.4 12.3 1.0
C B:FMT369 3.0 10.9 1.0
CE1 B:HIS230 3.0 10.3 1.0
CE1 B:HIS201 3.0 11.3 1.0
CD2 B:HIS230 3.1 8.7 1.0
CG B:HIS201 3.2 12.3 1.0
O1 B:FMT369 3.3 9.5 1.0
ZN B:ZN401 3.5 9.8 1.0
O B:HOH1124 3.6 52.4 1.0
CB B:HIS201 3.6 10.1 1.0
O1 B:EDO407 3.8 16.7 1.0
NE1 B:TRP131 4.0 11.2 1.0
CE1 B:HIS55 4.1 10.0 1.0
NE2 B:HIS55 4.1 9.4 1.0
NZ B:LYS169 4.2 11.2 1.0
ND1 B:HIS230 4.2 10.4 1.0
NE2 B:HIS201 4.2 11.7 1.0
OD1 B:ASP301 4.2 9.6 1.0
CG B:HIS230 4.2 8.5 1.0
CD2 B:HIS201 4.3 10.8 1.0
CA B:HIS201 4.4 7.6 1.0
O2 B:EDO423 4.6 31.6 1.0
O B:HOH920 4.6 37.2 1.0
CD1 B:TRP131 4.6 9.0 1.0
CE B:LYS169 4.7 9.1 1.0
C1 B:EDO407 4.8 19.8 1.0
OD2 B:ASP301 4.9 10.3 1.0
CG B:ASP301 4.9 11.2 1.0

Reference:

M.M.Benning, H.Shim, F.M.Raushel, H.M.Holden. High Resolution X-Ray Structures of Different Metal-Substituted Forms of Phosphotriesterase From Pseudomonas Diminuta. Biochemistry V. 40 2712 2001.
ISSN: ISSN 0006-2960
PubMed: 11258882
DOI: 10.1021/BI002661E
Page generated: Wed Dec 16 02:52:10 2020

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