Zinc in PDB 8p7n: 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: 8p7n 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) 77.87 / 3.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.89, 119.9, 161.49, 90, 90, 90
R / Rfree (%) 18.2 / 25.6

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 8p7n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 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: 8p7n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8p7n

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Zinc binding site 1 out of 8 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:36.6
occ:1.00
 O1 A:FMT401 2.0 34.6 1.0
NE2 A:HIS57 2.2 46.8 1.0
NE2 A:HIS55 2.2 41.4 1.0
OD1 A:ASP301 2.6 48.3 1.0
C A:FMT401 2.8 38.5 1.0
CE1 A:HIS57 3.0 43.6 1.0
O2 A:FMT401 3.0 34.7 1.0
CD2 A:HIS55 3.2 40.2 1.0
CE1 A:HIS55 3.2 38.4 1.0
CG A:ASP301 3.3 57.4 1.0
CD2 A:HIS57 3.3 48.2 1.0
ZN A:ZN403 3.3 42.4 1.0
OD2 A:ASP301 3.4 52.3 1.0
NZ A:LYS169 3.8 33.9 1.0
CE1 A:HIS230 4.0 54.0 1.0
NE2 A:HIS230 4.1 58.6 1.0
ND1 A:HIS57 4.2 47.3 1.0
ND1 A:HIS55 4.3 45.0 1.0
CG A:HIS57 4.4 47.5 1.0
CG A:HIS55 4.4 42.3 1.0
CG2 A:VAL101 4.4 35.5 1.0
CB A:ASP301 4.6 54.7 1.0
CE A:LYS169 5.0 33.1 1.0

Zinc binding site 2 out of 8 in 8p7n

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Zinc binding site 2 out of 8 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:42.4
occ:1.00
 O2 A:FMT401 2.0 34.7 1.0
ND1 A:HIS201 2.2 46.8 1.0
NE2 A:HIS230 2.2 58.6 1.0
CE1 A:HIS201 2.9 50.2 1.0
C A:FMT401 3.1 38.5 1.0
CE1 A:HIS230 3.1 54.0 1.0
CD2 A:HIS230 3.2 53.8 1.0
CG A:HIS201 3.3 49.8 1.0
ZN A:ZN402 3.3 36.6 1.0
O1 A:FMT401 3.6 34.6 1.0
NE1 A:TRP131 3.7 45.7 1.0
CB A:HIS201 3.8 38.1 1.0
NE2 A:HIS201 4.1 48.5 1.0
ND1 A:HIS230 4.2 59.6 1.0
CG A:HIS230 4.2 51.6 1.0
OD2 A:ASP301 4.2 52.3 1.0
CD2 A:HIS201 4.3 50.7 1.0
NE2 A:HIS55 4.4 41.4 1.0
NZ A:LYS169 4.5 33.9 1.0
CE1 A:HIS55 4.5 38.4 1.0
CD1 A:TRP131 4.5 41.7 1.0
CE2 A:TRP131 4.7 50.4 1.0
CE A:LYS169 4.8 33.1 1.0
CA A:HIS201 4.8 39.9 1.0
CZ2 A:TRP131 4.9 53.5 1.0

Zinc binding site 3 out of 8 in 8p7n

Go back to Zinc Binding Sites List in 8p7n
Zinc binding site 3 out of 8 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:24.8
occ:1.00
 NE2 B:HIS55 2.1 29.4 1.0
NE2 B:HIS57 2.1 33.7 1.0
O2 B:FMT401 2.3 24.9 1.0
OD1 B:ASP301 2.3 30.8 1.0
CE1 B:HIS55 3.0 30.4 1.0
CD2 B:HIS57 3.0 32.2 1.0
CG B:ASP301 3.0 33.1 1.0
OD2 B:ASP301 3.1 31.9 1.0
CD2 B:HIS55 3.1 29.1 1.0
CE1 B:HIS57 3.2 35.9 1.0
C B:FMT401 3.2 25.8 1.0
ZN B:ZN403 3.5 34.7 1.0
O1 B:FMT401 3.5 21.4 1.0
CE1 B:HIS230 4.1 34.0 1.0
ND1 B:HIS55 4.1 34.9 1.0
CG B:HIS57 4.2 31.5 1.0
CG2 B:VAL101 4.2 23.8 1.0
ND1 B:HIS57 4.2 34.8 1.0
CG B:HIS55 4.2 30.5 1.0
NE2 B:HIS230 4.2 30.8 1.0
NZ B:LYS169 4.3 25.1 1.0
CB B:ASP301 4.5 31.3 1.0

Zinc binding site 4 out of 8 in 8p7n

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Zinc binding site 4 out of 8 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:34.7
occ:1.00
 NE2 B:HIS230 2.0 30.8 1.0
O1 B:FMT401 2.0 21.4 1.0
ND1 B:HIS201 2.3 28.7 1.0
CE1 B:HIS230 2.9 34.0 1.0
CE1 B:HIS201 3.0 30.5 1.0
C B:FMT401 3.0 25.8 1.0
CD2 B:HIS230 3.0 31.6 1.0
O2 B:FMT401 3.4 24.9 1.0
ZN B:ZN402 3.5 24.8 1.0
CG B:HIS201 3.5 26.1 1.0
NE1 B:TRP131 3.6 29.8 1.0
CB B:HIS201 4.0 24.7 1.0
ND1 B:HIS230 4.0 32.2 1.0
CG B:HIS230 4.1 36.4 1.0
NE2 B:HIS201 4.2 27.5 1.0
OD2 B:ASP301 4.2 31.9 1.0
CE1 B:HIS55 4.2 30.4 1.0
NZ B:LYS169 4.3 25.1 1.0
NE2 B:HIS55 4.3 29.4 1.0
CD1 B:TRP131 4.5 30.5 1.0
CD2 B:HIS201 4.5 28.2 1.0
CE2 B:TRP131 4.6 35.2 1.0
CE B:LYS169 4.7 22.7 1.0
CA B:HIS201 4.9 25.9 1.0
CZ2 B:TRP131 4.9 45.0 1.0

Zinc binding site 5 out of 8 in 8p7n

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Zinc binding site 5 out of 8 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 5 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
C:Zn402

b:20.3
occ:1.00
 NE2 C:HIS57 2.0 29.9 1.0
O2 C:FMT401 2.1 32.7 1.0
NE2 C:HIS55 2.3 27.9 1.0
OD1 C:ASP301 2.4 39.5 1.0
CE1 C:HIS57 2.9 28.6 1.0
C C:FMT401 2.9 35.4 1.0
CD2 C:HIS55 3.1 27.5 1.0
CD2 C:HIS57 3.1 31.3 1.0
CG C:ASP301 3.2 41.4 1.0
O1 C:FMT401 3.3 34.3 1.0
ZN C:ZN403 3.5 37.3 1.0
CE1 C:HIS55 3.5 28.8 1.0
OD2 C:ASP301 3.5 48.0 1.0
NZ C:LYS169 4.0 34.6 1.0
CG2 C:VAL101 4.1 31.3 1.0
ND1 C:HIS57 4.1 29.5 1.0
CE1 C:HIS230 4.1 39.6 1.0
CG C:HIS57 4.2 28.9 1.0
NE2 C:HIS230 4.2 37.5 1.0
CG C:HIS55 4.3 29.6 1.0
ND1 C:HIS55 4.5 31.1 1.0
CB C:ASP301 4.6 27.0 1.0

Zinc binding site 6 out of 8 in 8p7n

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Zinc binding site 6 out of 8 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 6 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
C:Zn403

b:37.3
occ:1.00
 O1 C:FMT401 1.9 34.3 1.0
NE2 C:HIS230 2.1 37.5 1.0
ND1 C:HIS201 2.1 39.7 1.0
C C:FMT401 2.9 35.4 1.0
CE1 C:HIS201 2.9 41.6 1.0
CE1 C:HIS230 3.1 39.6 1.0
CD2 C:HIS230 3.1 39.4 1.0
O2 C:FMT401 3.2 32.7 1.0
CG C:HIS201 3.3 39.4 1.0
ZN C:ZN402 3.5 20.3 1.0
CB C:HIS201 3.7 33.2 1.0
NE1 C:TRP131 3.8 45.2 1.0
NE2 C:HIS201 4.1 42.8 1.0
NZ C:LYS169 4.1 34.6 1.0
ND1 C:HIS230 4.2 45.9 1.0
CG C:HIS230 4.2 44.8 1.0
CD2 C:HIS201 4.3 41.0 1.0
NE2 C:HIS55 4.3 27.9 1.0
OD2 C:ASP301 4.5 48.0 1.0
CE1 C:HIS55 4.6 28.8 1.0
CD1 C:TRP131 4.6 32.1 1.0
CE2 C:TRP131 4.7 37.9 1.0
CA C:HIS201 4.8 33.1 1.0
CE C:LYS169 4.9 26.1 1.0
CZ2 C:TRP131 4.9 34.0 1.0

Zinc binding site 7 out of 8 in 8p7n

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Zinc binding site 7 out of 8 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 7 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
D:Zn402

b:29.6
occ:1.00
 O1 D:FMT401 2.0 35.1 1.0
OD1 D:ASP301 2.1 40.0 1.0
NE2 D:HIS55 2.1 34.8 1.0
NE2 D:HIS57 2.2 36.8 1.0
CG D:ASP301 2.8 42.2 1.0
OD2 D:ASP301 3.0 29.4 1.0
C D:FMT401 3.0 36.3 1.0
CE1 D:HIS55 3.0 40.5 1.0
CD2 D:HIS55 3.1 38.5 1.0
CD2 D:HIS57 3.2 32.8 1.0
CE1 D:HIS57 3.3 36.2 1.0
O2 D:FMT401 3.4 30.1 1.0
ZN D:ZN403 3.4 33.9 1.0
CE1 D:HIS230 3.9 41.3 1.0
NE2 D:HIS230 4.1 39.1 1.0
ND1 D:HIS55 4.2 37.6 1.0
CB D:ASP301 4.2 45.5 1.0
CG D:HIS55 4.3 36.0 1.0
CG D:HIS57 4.3 29.1 1.0
NZ D:LYS169 4.3 26.5 1.0
ND1 D:HIS57 4.4 32.0 1.0
CG2 D:VAL101 4.6 27.6 1.0
CA D:ASP301 4.8 37.7 1.0

Zinc binding site 8 out of 8 in 8p7n

Go back to Zinc Binding Sites List in 8p7n
Zinc binding site 8 out of 8 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 8 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
D:Zn403

b:33.9
occ:1.00
 NE2 D:HIS230 2.0 39.1 1.0
O2 D:FMT401 2.1 30.1 1.0
ND1 D:HIS201 2.1 41.9 1.0
C D:FMT401 2.9 36.3 1.0
CE1 D:HIS201 2.9 45.3 1.0
CE1 D:HIS230 3.0 41.3 1.0
CD2 D:HIS230 3.1 43.0 1.0
CG D:HIS201 3.2 41.1 1.0
O1 D:FMT401 3.3 35.1 1.0
ZN D:ZN402 3.4 29.6 1.0
NE1 D:TRP131 3.5 37.6 1.0
CB D:HIS201 3.6 38.3 1.0
NZ D:LYS169 3.9 26.5 1.0
NE2 D:HIS201 4.1 48.2 1.0
OD2 D:ASP301 4.1 29.4 1.0
ND1 D:HIS230 4.1 38.8 1.0
CG D:HIS230 4.2 41.8 1.0
CD2 D:HIS201 4.2 44.0 1.0
CE1 D:HIS55 4.3 40.5 1.0
CD1 D:TRP131 4.4 33.6 1.0
NE2 D:HIS55 4.5 34.8 1.0
CE2 D:TRP131 4.5 37.7 1.0
CA D:HIS201 4.5 39.0 1.0
CE D:LYS169 4.6 28.1 1.0
CZ2 D:TRP131 4.8 48.0 1.0
CG D:ASP301 4.9 42.2 1.0
OD1 D:ASP301 5.0 40.0 1.0

Reference:

O.Dym, N.Aggarwal, Y.Ashani, S.Albeck, H.Leader, 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 09:10:46 2024

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