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
![](/pictures/ZN/pdb/p7/8p7k-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/p7/8p7k-ZN-sphere_01_stereo.jpg) 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
![](/pictures/ZN/pdb/p7/8p7k-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/p7/8p7k-ZN-sphere_02_stereo.jpg) 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
![](/pictures/ZN/pdb/p7/8p7k-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/p7/8p7k-ZN-sphere_03_stereo.jpg) 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
Go back to
Zinc Binding Sites List in 8p7k
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
![](/pictures/ZN/pdb/p7/8p7k-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/p7/8p7k-ZN-sphere_04_stereo.jpg) 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
|