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Zinc in PDB 1dpm: Three-Dimensional Structure of the Zinc-Containing Phosphotriesterase with Bound Substrate Analog Diethyl 4- Methylbenzylphosphonate

Protein crystallography data

The structure of Three-Dimensional Structure of the Zinc-Containing Phosphotriesterase with Bound Substrate Analog Diethyl 4- Methylbenzylphosphonate, PDB code: 1dpm was solved by J.L.Vanhooke, M.M.Benning, F.M.Raushel, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 129.600, 91.400, 69.400, 90.00, 91.90, 90.00
R / Rfree (%) n/a / n/a

Zinc Binding Sites:

The binding sites of Zinc atom in the Three-Dimensional Structure of the Zinc-Containing Phosphotriesterase with Bound Substrate Analog Diethyl 4- Methylbenzylphosphonate (pdb code 1dpm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Three-Dimensional Structure of the Zinc-Containing Phosphotriesterase with Bound Substrate Analog Diethyl 4- Methylbenzylphosphonate, PDB code: 1dpm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1dpm

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Zinc binding site 1 out of 4 in the Three-Dimensional Structure of the Zinc-Containing Phosphotriesterase with Bound Substrate Analog Diethyl 4- Methylbenzylphosphonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Three-Dimensional Structure of the Zinc-Containing Phosphotriesterase with Bound Substrate Analog Diethyl 4- Methylbenzylphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn800

b:18.6
occ:1.00
NE2 A:HIS55 1.8 6.0 1.0
NE2 A:HIS57 1.9 15.7 1.0
O A:HOH909 1.9 18.0 1.0
O2 A:FMT902 2.4 15.9 1.0
OD1 A:ASP301 2.4 18.5 1.0
CE1 A:HIS57 2.8 20.1 1.0
CD2 A:HIS55 2.8 9.0 1.0
CE1 A:HIS55 2.9 4.6 1.0
CD2 A:HIS57 3.1 14.8 1.0
CG A:ASP301 3.1 19.9 1.0
C A:FMT902 3.1 23.9 1.0
OD2 A:ASP301 3.2 19.3 1.0
O1 A:FMT902 3.3 13.5 1.0
ZN A:ZN801 3.3 21.4 1.0
C11 A:EBP900 3.9 37.8 1.0
ND1 A:HIS57 4.0 6.8 1.0
CG A:HIS55 4.0 3.1 1.0
ND1 A:HIS55 4.0 7.7 1.0
CG2 A:VAL101 4.0 10.4 1.0
CG A:HIS57 4.1 14.7 1.0
CE1 A:HIS230 4.2 17.0 1.0
NZ A:LYS169 4.3 23.4 1.0
NE2 A:HIS230 4.4 17.6 1.0
CB A:ASP301 4.4 18.4 1.0
C2 A:EBP900 4.5 80.1 1.0
O2 A:EBP900 4.7 59.6 1.0
C12 A:EBP900 4.8 19.6 1.0
C7 A:EBP900 4.9 61.8 1.0

Zinc binding site 2 out of 4 in 1dpm

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Zinc binding site 2 out of 4 in the Three-Dimensional Structure of the Zinc-Containing Phosphotriesterase with Bound Substrate Analog Diethyl 4- Methylbenzylphosphonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Three-Dimensional Structure of the Zinc-Containing Phosphotriesterase with Bound Substrate Analog Diethyl 4- Methylbenzylphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:21.4
occ:1.00
O1 A:FMT902 1.8 13.5 1.0
O A:HOH909 1.9 18.0 1.0
NE2 A:HIS230 2.0 17.6 1.0
ND1 A:HIS201 2.1 40.0 1.0
C A:FMT902 2.8 23.9 1.0
CE1 A:HIS230 2.9 17.0 1.0
CG A:HIS201 3.1 17.2 1.0
CE1 A:HIS201 3.1 17.2 1.0
CD2 A:HIS230 3.1 13.8 1.0
O2 A:FMT902 3.3 15.9 1.0
ZN A:ZN800 3.3 18.6 1.0
CB A:HIS201 3.4 19.5 1.0
O3 A:EBP900 3.5 72.5 1.0
CE1 A:HIS55 3.6 4.6 1.0
NE2 A:HIS55 3.7 6.0 1.0
OD2 A:ASP301 4.1 19.3 1.0
ND1 A:HIS230 4.1 16.6 1.0
NZ A:LYS169 4.1 23.4 1.0
C7 A:EBP900 4.2 61.8 1.0
NE2 A:HIS201 4.2 30.2 1.0
CG A:HIS230 4.2 21.5 1.0
CD2 A:HIS201 4.2 20.1 1.0
NE1 A:TRP131 4.3 15.2 1.0
P A:EBP900 4.3 52.3 1.0
CA A:HIS201 4.4 17.8 1.0
C11 A:EBP900 4.6 37.8 1.0
CG A:ASP301 4.8 19.9 1.0
CE A:LYS169 4.8 19.7 1.0
ND1 A:HIS55 4.9 7.7 1.0
CD1 A:TRP131 4.9 13.7 1.0
O2 A:EBP900 4.9 59.6 1.0
OD1 A:ASP301 5.0 18.5 1.0

Zinc binding site 3 out of 4 in 1dpm

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Zinc binding site 3 out of 4 in the Three-Dimensional Structure of the Zinc-Containing Phosphotriesterase with Bound Substrate Analog Diethyl 4- Methylbenzylphosphonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Three-Dimensional Structure of the Zinc-Containing Phosphotriesterase with Bound Substrate Analog Diethyl 4- Methylbenzylphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:13.9
occ:1.00
NE2 B:HIS55 1.9 3.5 1.0
O B:HOH924 2.0 12.3 1.0
NE2 B:HIS57 2.0 14.8 1.0
O1 B:FMT904 2.2 18.6 1.0
OD1 B:ASP301 2.3 10.2 1.0
CE1 B:HIS55 2.9 15.0 1.0
CE1 B:HIS57 3.0 18.0 1.0
CD2 B:HIS55 3.0 17.3 1.0
C B:FMT904 3.1 11.2 1.0
CD2 B:HIS57 3.1 7.0 1.0
CG B:ASP301 3.1 16.4 1.0
OD2 B:ASP301 3.3 16.6 1.0
ZN B:ZN803 3.3 18.3 1.0
O2 B:FMT904 3.4 22.6 1.0
CG2 B:VAL101 4.0 2.5 1.0
ND1 B:HIS55 4.0 6.1 1.0
CG B:HIS55 4.1 3.7 1.0
ND1 B:HIS57 4.1 10.6 1.0
C11 B:EBP902 4.1 27.5 1.0
CG B:HIS57 4.2 17.5 1.0
CE1 B:HIS230 4.3 11.8 1.0
NZ B:LYS169 4.4 35.5 1.0
CB B:ASP301 4.4 19.9 1.0
NE2 B:HIS230 4.5 16.9 1.0
C2 B:EBP902 4.6 54.3 1.0
C12 B:EBP902 4.6 31.5 1.0
C7 B:EBP902 4.7 62.0 1.0
O2 B:EBP902 5.0 61.9 1.0

Zinc binding site 4 out of 4 in 1dpm

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Zinc binding site 4 out of 4 in the Three-Dimensional Structure of the Zinc-Containing Phosphotriesterase with Bound Substrate Analog Diethyl 4- Methylbenzylphosphonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Three-Dimensional Structure of the Zinc-Containing Phosphotriesterase with Bound Substrate Analog Diethyl 4- Methylbenzylphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn803

b:18.3
occ:1.00
O2 B:FMT904 1.8 22.6 1.0
ND1 B:HIS201 2.0 10.3 1.0
O B:HOH924 2.0 12.3 1.0
NE2 B:HIS230 2.1 16.9 1.0
C B:FMT904 2.8 11.2 1.0
CE1 B:HIS201 2.9 18.8 1.0
CE1 B:HIS230 3.0 11.8 1.0
O1 B:FMT904 3.0 18.6 1.0
CG B:HIS201 3.1 19.1 1.0
CD2 B:HIS230 3.2 20.2 1.0
ZN B:ZN802 3.3 13.9 1.0
O3 B:EBP902 3.4 53.9 1.0
CB B:HIS201 3.5 13.0 1.0
CE1 B:HIS55 3.8 15.0 1.0
NE2 B:HIS55 4.0 3.5 1.0
NZ B:LYS169 4.0 35.5 1.0
NE2 B:HIS201 4.1 22.6 1.0
C7 B:EBP902 4.1 62.0 1.0
OD2 B:ASP301 4.1 16.6 1.0
CD2 B:HIS201 4.1 9.1 1.0
ND1 B:HIS230 4.2 17.5 1.0
P B:EBP902 4.3 49.1 1.0
CG B:HIS230 4.3 21.0 1.0
NE1 B:TRP131 4.3 11.3 1.0
CA B:HIS201 4.4 14.1 1.0
C11 B:EBP902 4.6 27.5 1.0
CE B:LYS169 4.7 22.3 1.0
CG B:ASP301 4.8 16.4 1.0
OD1 B:ASP301 4.9 10.2 1.0
CD1 B:TRP131 4.9 12.5 1.0
ND1 B:HIS55 5.0 6.1 1.0
O2 B:EBP902 5.0 61.9 1.0

Reference:

J.L.Vanhooke, M.M.Benning, F.M.Raushel, H.M.Holden. Three-Dimensional Structure of the Zinc-Containing Phosphotriesterase with the Bound Substrate Analog Diethyl 4-Methylbenzylphosphonate. Biochemistry V. 35 6020 1996.
ISSN: ISSN 0006-2960
PubMed: 8634243
DOI: 10.1021/BI960325L
Page generated: Wed Dec 16 02:47:25 2020

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