Zinc in PDB 8p7i: 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: 8p7i was solved by O.Dym, N.Aggarwal, 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) 39.18 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.23, 81.249, 70.666, 90, 94.8, 90
R / Rfree (%) 15.1 / 18.1

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 8p7i). 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: 8p7i:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8p7i

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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:20.2
occ:1.00
 OAF A:X3E404 2.0 19.4 1.0
NE2 A:HIS57 2.0 16.3 1.0
NE2 A:HIS55 2.1 18.0 1.0
O2 A:FMT401 2.3 19.6 1.0
OD1 A:ASP301 2.3 18.0 1.0
CE1 A:HIS57 3.0 17.1 1.0
CD2 A:HIS55 3.0 18.1 1.0
CD2 A:HIS57 3.0 18.8 1.0
CAL A:X3E404 3.1 18.7 1.0
CG A:ASP301 3.1 17.9 1.0
C A:FMT401 3.2 19.1 1.0
CE1 A:HIS55 3.2 19.3 1.0
CAH A:X3E404 3.2 21.2 1.0
OD2 A:ASP301 3.4 19.5 1.0
O1 A:FMT401 3.6 19.0 1.0
ZN A:ZN403 3.8 20.9 1.0
CAI A:X3E404 3.9 30.5 1.0
O A:X3E404 3.9 23.1 1.0
CG2 A:VAL101 4.1 18.1 1.0
CE1 A:HIS230 4.1 18.3 1.0
ND1 A:HIS57 4.1 17.6 1.0
OAJ A:X3E404 4.1 28.3 1.0
CG A:HIS57 4.2 17.0 1.0
NZ A:LYS169 4.2 19.5 1.0
CG A:HIS55 4.2 17.6 1.0
ND1 A:HIS55 4.2 15.3 1.0
NE2 A:HIS230 4.4 17.8 1.0
CB A:ASP301 4.4 18.2 1.0
CAE A:X3E404 4.7 25.8 1.0
CAK A:X3E404 4.8 28.0 1.0
CAA A:X3E404 4.8 25.8 1.0
OAG A:X3E404 4.9 40.2 1.0
CA A:ASP301 4.9 17.5 1.0

Zinc binding site 2 out of 4 in 8p7i

Go back to Zinc Binding Sites List in 8p7i
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:20.9
occ:1.00
 O1 A:FMT401 1.9 19.0 1.0
NE2 A:HIS230 2.0 17.8 1.0
O A:X3E404 2.0 23.1 1.0
ND1 A:HIS201 2.1 23.2 1.0
OAF A:X3E404 2.6 19.4 1.0
CAL A:X3E404 2.8 18.7 1.0
C A:FMT401 3.0 19.1 1.0
CD2 A:HIS230 3.0 18.6 1.0
CE1 A:HIS201 3.0 25.3 1.0
CE1 A:HIS230 3.0 18.3 1.0
CG A:HIS201 3.1 20.9 1.0
O2 A:FMT401 3.4 19.6 1.0
CB A:HIS201 3.5 18.2 1.0
OAJ A:X3E404 3.7 28.3 1.0
CAH A:X3E404 3.8 21.2 1.0
ZN A:ZN402 3.8 20.2 1.0
NE1 A:TRP131 3.9 23.6 1.0
ND1 A:HIS230 4.1 20.0 1.0
CG A:HIS230 4.1 18.4 1.0
NE2 A:HIS201 4.1 25.8 1.0
CD2 A:HIS201 4.2 22.7 1.0
CE1 A:HIS55 4.3 19.3 1.0
NZ A:LYS169 4.3 19.5 1.0
NE2 A:HIS55 4.3 18.0 1.0
CA A:HIS201 4.3 17.8 1.0
O A:HOH537 4.3 30.5 1.0
CD1 A:TRP131 4.5 22.1 1.0
CE A:LYS169 4.6 18.6 1.0
OD2 A:ASP301 4.7 19.5 1.0

Zinc binding site 3 out of 4 in 8p7i

Go back to Zinc Binding Sites List in 8p7i
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:23.4
occ:1.00
 O B:X3E404 1.9 24.8 1.0
NE2 B:HIS57 2.0 21.9 1.0
NE2 B:HIS55 2.1 18.5 1.0
OD1 B:ASP301 2.2 23.5 1.0
O1 B:FMT401 2.3 23.8 1.0
CE1 B:HIS57 3.0 21.2 1.0
CD2 B:HIS55 3.0 19.9 1.0
CD2 B:HIS57 3.0 21.1 1.0
CG B:ASP301 3.1 24.9 1.0
CAL B:X3E404 3.1 26.6 1.0
C B:FMT401 3.2 24.2 1.0
CE1 B:HIS55 3.2 21.4 1.0
OAJ B:X3E404 3.2 42.6 1.0
OD2 B:ASP301 3.4 23.2 1.0
O2 B:FMT401 3.6 23.6 1.0
CAH B:X3E404 3.7 44.0 1.0
ZN B:ZN403 3.8 25.0 1.0
CAK B:X3E404 3.8 40.3 1.0
CE1 B:HIS230 4.1 24.8 1.0
CG2 B:VAL101 4.1 19.0 1.0
ND1 B:HIS57 4.1 19.9 1.0
OAF B:X3E404 4.1 31.3 1.0
CG B:HIS57 4.2 18.6 1.0
CG B:HIS55 4.2 19.1 1.0
NZ B:LYS169 4.2 22.8 1.0
ND1 B:HIS55 4.3 20.0 1.0
NE2 B:HIS230 4.3 21.7 1.0
CB B:ASP301 4.4 19.8 1.0
CAI B:X3E404 4.8 43.3 1.0
OAG B:X3E404 4.8 54.2 1.0
CA B:ASP301 4.9 18.4 1.0
CAE B:X3E404 4.9 38.1 1.0

Zinc binding site 4 out of 4 in 8p7i

Go back to Zinc Binding Sites List in 8p7i
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:25.0
occ:1.00
 O2 B:FMT401 2.0 23.6 1.0
NE2 B:HIS230 2.0 21.7 1.0
ND1 B:HIS201 2.1 27.9 1.0
OAF B:X3E404 2.2 31.3 1.0
O B:X3E404 2.4 24.8 1.0
CAL B:X3E404 2.8 26.6 1.0
C B:FMT401 3.0 24.2 1.0
CD2 B:HIS230 3.0 23.2 1.0
CE1 B:HIS201 3.0 26.8 1.0
CE1 B:HIS230 3.0 24.8 1.0
CG B:HIS201 3.2 25.7 1.0
O1 B:FMT401 3.3 23.8 1.0
CB B:HIS201 3.5 21.9 1.0
OAJ B:X3E404 3.8 42.6 1.0
ZN B:ZN402 3.8 23.4 1.0
CAH B:X3E404 3.8 44.0 1.0
NE1 B:TRP131 3.9 24.7 1.0
ND1 B:HIS230 4.1 24.5 1.0
CG B:HIS230 4.1 20.1 1.0
NE2 B:HIS201 4.2 30.6 1.0
CD2 B:HIS201 4.3 27.1 1.0
CE1 B:HIS55 4.3 21.4 1.0
NZ B:LYS169 4.3 22.8 1.0
NE2 B:HIS55 4.3 18.5 1.0
CA B:HIS201 4.4 22.5 1.0
CD1 B:TRP131 4.5 22.3 1.0
CE B:LYS169 4.6 22.8 1.0
OD2 B:ASP301 4.8 23.2 1.0

Reference:

O.Dym, N.Aggarwal, Y.Ashani, H.Leader, S.Albeck, T.Unger, S.Hamer Rogotner, I.Silman, D.S.Tawfik, J.L.Sussman. The Impact of Molecular Variants, Crystallization Conditions and the Space Group on Ligand–Protein Complexes: A Case Study on Bacterial Phosphotriesterase Acta Crystallogr. V. 79 2023.
ISSN: ISSN 0365-110X
DOI: 10.1107/S2059798323007672
Page generated: Thu Oct 31 09:08:33 2024

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