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Zinc in PDB 8p7k: The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes

Enzymatic activity of The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes

All present enzymatic activity of The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes:
3.1.8.1;

Protein crystallography data

The structure of The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes, PDB code: 8p7k was solved by O.Dym, N.Aggawal, Y.Ashani, S.Albeck, T.Unger, S.Hamer Rogotner, I.Silman, J.L.Sussman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.70 / 1.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.034, 81.488, 70.81, 90, 95, 90
R / Rfree (%) 16 / 21.2

Zinc Binding Sites:

The binding sites of Zinc atom in the The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes (pdb code 8p7k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes, PDB code: 8p7k:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8p7k

Go back to Zinc Binding Sites List in 8p7k
Zinc binding site 1 out of 4 in the The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:23.1
occ:1.00
 O41 A:E5N404 1.9 20.8 1.0
NE2 A:HIS57 2.0 18.7 1.0
NE2 A:HIS55 2.1 24.4 1.0
OD1 A:ASP301 2.2 20.5 1.0
O1 A:FMT401 2.4 18.8 1.0
C4 A:E5N404 2.8 24.2 1.0
CD2 A:HIS55 2.9 18.9 1.0
CD2 A:HIS57 3.0 19.7 1.0
CE1 A:HIS57 3.1 18.9 1.0
CG A:ASP301 3.1 21.4 1.0
CE1 A:HIS55 3.2 20.5 1.0
C A:FMT401 3.3 23.6 1.0
C41 A:E5N404 3.4 22.2 1.0
OD2 A:ASP301 3.4 21.4 1.0
C32 A:E5N404 3.5 25.3 1.0
O2 A:FMT401 3.6 23.9 1.0
O42 A:E5N404 3.8 24.8 1.0
ZN A:ZN403 3.9 24.3 1.0
CG2 A:VAL101 4.0 18.7 1.0
CE1 A:HIS230 4.1 18.3 1.0
C31 A:E5N404 4.1 30.6 1.0
CG A:HIS57 4.1 21.1 1.0
CG A:HIS55 4.1 20.2 1.0
ND1 A:HIS57 4.1 21.1 1.0
ND1 A:HIS55 4.2 19.6 1.0
NZ A:LYS169 4.3 21.0 1.0
CB A:ASP301 4.4 19.6 1.0
NE2 A:HIS230 4.4 17.5 1.0
CA A:ASP301 4.8 19.9 1.0

Zinc binding site 2 out of 4 in 8p7k

Go back to Zinc Binding Sites List in 8p7k
Zinc binding site 2 out of 4 in the The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:24.3
occ:1.00
 O2 A:FMT401 1.9 23.9 1.0
O42 A:E5N404 2.0 24.8 1.0
NE2 A:HIS230 2.0 17.5 1.0
ND1 A:HIS201 2.1 21.9 1.0
C4 A:E5N404 2.6 24.2 1.0
O41 A:E5N404 2.6 20.8 1.0
C A:FMT401 2.9 23.6 1.0
CD2 A:HIS230 3.0 19.4 1.0
CE1 A:HIS230 3.1 18.3 1.0
CE1 A:HIS201 3.1 23.1 1.0
CG A:HIS201 3.1 17.9 1.0
O1 A:FMT401 3.3 18.8 1.0
CB A:HIS201 3.4 17.0 1.0
ZN A:ZN402 3.9 23.1 1.0
NE1 A:TRP131 3.9 24.9 1.0
C41 A:E5N404 4.0 22.2 1.0
CG A:HIS230 4.2 18.5 1.0
ND1 A:HIS230 4.2 20.9 1.0
NZ A:LYS169 4.2 21.0 1.0
NE2 A:HIS201 4.2 24.9 1.0
CD2 A:HIS201 4.2 25.9 1.0
CE1 A:HIS55 4.3 20.5 1.0
CA A:HIS201 4.3 19.2 1.0
NE2 A:HIS55 4.3 24.4 1.0
O A:HOH642 4.5 40.0 1.0
CD1 A:TRP131 4.6 22.9 1.0
CE A:LYS169 4.7 22.5 1.0
OD2 A:ASP301 4.8 21.4 1.0
O31 A:E5N404 4.8 58.4 1.0

Zinc binding site 3 out of 4 in 8p7k

Go back to Zinc Binding Sites List in 8p7k
Zinc binding site 3 out of 4 in the The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:26.0
occ:1.00
 O42 B:E5N404 1.9 21.3 0.9
NE2 B:HIS57 2.1 26.5 1.0
NE2 B:HIS55 2.2 25.7 1.0
OD1 B:ASP301 2.2 23.1 1.0
O1 B:FMT401 2.5 26.5 1.0
C4 B:E5N404 2.9 27.8 0.9
CD2 B:HIS55 2.9 26.3 1.0
CE1 B:HIS57 3.0 25.1 1.0
CG B:ASP301 3.1 29.4 1.0
CD2 B:HIS57 3.1 25.9 1.0
C B:FMT401 3.2 27.1 1.0
CE1 B:HIS55 3.3 25.3 1.0
OD2 B:ASP301 3.4 24.1 1.0
C32 B:E5N404 3.6 26.8 0.9
C41 B:E5N404 3.6 28.9 0.9
O2 B:FMT401 3.7 25.4 1.0
ZN B:ZN403 3.9 30.9 1.0
C31 B:E5N404 3.9 35.6 0.9
O41 B:E5N404 3.9 27.6 0.9
CE1 B:HIS230 4.0 26.4 1.0
CG2 B:VAL101 4.0 22.9 1.0
ND1 B:HIS57 4.1 24.2 1.0
CG B:HIS55 4.2 24.8 1.0
CG B:HIS57 4.2 19.3 1.0
ND1 B:HIS55 4.3 27.3 1.0
NE2 B:HIS230 4.3 27.2 1.0
CB B:ASP301 4.3 17.2 1.0
NZ B:LYS169 4.5 26.1 1.0
CA B:ASP301 4.8 22.9 1.0
C22 B:E5N404 4.8 38.0 0.9

Zinc binding site 4 out of 4 in 8p7k

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Zinc binding site 4 out of 4 in the The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:30.9
occ:1.00
 O41 B:E5N404 2.1 27.6 0.9
NE2 B:HIS230 2.1 27.2 1.0
ND1 B:HIS201 2.1 30.6 1.0
O2 B:FMT401 2.1 25.4 1.0
O42 B:E5N404 2.6 21.3 0.9
C4 B:E5N404 2.6 27.8 0.9
CD2 B:HIS230 3.0 28.8 1.0
CE1 B:HIS201 3.0 31.8 1.0
C B:FMT401 3.1 27.1 1.0
CG B:HIS201 3.1 26.3 1.0
CE1 B:HIS230 3.1 26.4 1.0
O1 B:FMT401 3.3 26.5 1.0
CB B:HIS201 3.5 24.6 1.0
ZN B:ZN402 3.9 26.0 1.0
NE1 B:TRP131 3.9 27.5 1.0
NE2 B:HIS201 4.1 38.3 1.0
C41 B:E5N404 4.1 28.9 0.9
CG B:HIS230 4.1 31.0 1.0
NZ B:LYS169 4.2 26.1 1.0
CD2 B:HIS201 4.2 33.2 1.0
ND1 B:HIS230 4.2 28.4 1.0
CE1 B:HIS55 4.3 25.3 1.0
NE2 B:HIS55 4.3 25.7 1.0
CA B:HIS201 4.4 26.1 1.0
CD1 B:TRP131 4.5 28.1 1.0
CE B:LYS169 4.6 22.6 1.0
OD2 B:ASP301 4.8 24.1 1.0

Reference:

O.Dym, N.Aggawal, Y.Ashani, S.Albeck, T.Unger, S.Hamer Rogotner, I.Silman, J.L.Sussman. The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes To Be Published.
Page generated: Fri Jul 28 07:23:30 2023

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