Zinc in PDB 6p1z: Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain
Enzymatic activity of Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain
All present enzymatic activity of Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain:
3.2.1.17;
Protein crystallography data
The structure of Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain, PDB code: 6p1z
was solved by
S.A.Buth,
M.M.Shneider,
P.G.Leiman,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.60 /
2.10
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.275,
69.123,
77.802,
90.00,
102.48,
90.00
|
R / Rfree (%)
|
18.8 /
25.1
|
Other elements in 6p1z:
The structure of Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain
(pdb code 6p1z). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the
Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain, PDB code: 6p1z:
Jump to Zinc binding site number:
1;
2;
Zinc binding site 1 out
of 2 in 6p1z
Go back to
Zinc Binding Sites List in 6p1z
Zinc binding site 1 out
of 2 in the Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn101
b:14.8
occ:1.00
|
ND1
|
D:HIS76
|
2.0
|
27.7
|
1.0
|
NE2
|
D:HIS41
|
2.0
|
10.5
|
1.0
|
ND1
|
D:HIS46
|
2.0
|
13.3
|
1.0
|
SG
|
D:CYS74
|
2.2
|
21.5
|
1.0
|
CE1
|
D:HIS76
|
2.8
|
30.6
|
1.0
|
HB2
|
D:CYS74
|
2.8
|
21.4
|
1.0
|
CE1
|
D:HIS46
|
2.9
|
23.0
|
1.0
|
HE1
|
D:HIS76
|
2.9
|
36.7
|
1.0
|
CD2
|
D:HIS41
|
3.0
|
10.6
|
1.0
|
CE1
|
D:HIS41
|
3.0
|
10.8
|
1.0
|
HE1
|
D:HIS46
|
3.1
|
27.6
|
1.0
|
HB2
|
D:HIS76
|
3.1
|
20.7
|
1.0
|
CG
|
D:HIS76
|
3.1
|
23.2
|
1.0
|
CG
|
D:HIS46
|
3.1
|
31.2
|
1.0
|
HB3
|
D:HIS46
|
3.1
|
17.4
|
1.0
|
CB
|
D:CYS74
|
3.1
|
17.9
|
1.0
|
HD2
|
D:HIS41
|
3.2
|
12.7
|
1.0
|
HE1
|
D:HIS41
|
3.2
|
12.9
|
1.0
|
HA
|
D:HIS46
|
3.4
|
17.0
|
1.0
|
H
|
D:HIS76
|
3.5
|
24.8
|
1.0
|
CB
|
D:HIS46
|
3.5
|
14.5
|
1.0
|
HA3
|
D:GLY13
|
3.5
|
20.4
|
1.0
|
CB
|
D:HIS76
|
3.6
|
17.3
|
1.0
|
HB3
|
D:CYS74
|
3.6
|
21.4
|
1.0
|
NE2
|
D:HIS76
|
4.0
|
24.5
|
1.0
|
CA
|
D:HIS46
|
4.0
|
14.2
|
1.0
|
NE2
|
D:HIS46
|
4.1
|
28.4
|
1.0
|
ND1
|
D:HIS41
|
4.1
|
10.9
|
1.0
|
CD2
|
D:HIS76
|
4.1
|
34.0
|
1.0
|
CG
|
D:HIS41
|
4.1
|
14.9
|
1.0
|
O
|
D:ALA12
|
4.2
|
20.5
|
1.0
|
CD2
|
D:HIS46
|
4.2
|
26.3
|
1.0
|
N
|
D:HIS76
|
4.2
|
20.6
|
1.0
|
HB3
|
D:HIS76
|
4.3
|
20.7
|
1.0
|
O
|
D:CYS74
|
4.3
|
25.0
|
1.0
|
CA
|
D:CYS74
|
4.4
|
19.9
|
1.0
|
C
|
D:CYS74
|
4.4
|
31.9
|
1.0
|
HB2
|
D:HIS46
|
4.4
|
17.4
|
1.0
|
CA
|
D:GLY13
|
4.5
|
17.0
|
1.0
|
CA
|
D:HIS76
|
4.5
|
21.1
|
1.0
|
HE2
|
D:HIS76
|
4.7
|
29.5
|
1.0
|
HB2
|
D:ALA49
|
4.8
|
31.9
|
1.0
|
O
|
D:HOH269
|
4.8
|
30.0
|
1.0
|
HA2
|
D:GLY13
|
4.8
|
20.4
|
1.0
|
HE2
|
D:HIS46
|
4.8
|
34.0
|
1.0
|
H
|
D:CYS74
|
4.9
|
23.8
|
1.0
|
N
|
D:HIS46
|
4.9
|
19.9
|
1.0
|
HD1
|
D:HIS41
|
4.9
|
13.1
|
1.0
|
N
|
D:GLY75
|
5.0
|
20.0
|
1.0
|
HA
|
D:HIS76
|
5.0
|
25.3
|
1.0
|
HD2
|
D:HIS76
|
5.0
|
40.9
|
1.0
|
|
Zinc binding site 2 out
of 2 in 6p1z
Go back to
Zinc Binding Sites List in 6p1z
Zinc binding site 2 out
of 2 in the Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C- Terminal Part of the T4 GP5 Beta-Helical Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn101
b:24.2
occ:1.00
|
NE2
|
H:HIS41
|
2.0
|
27.0
|
1.0
|
ND1
|
H:HIS46
|
2.0
|
42.5
|
1.0
|
ND1
|
H:HIS76
|
2.0
|
41.2
|
1.0
|
SG
|
H:CYS74
|
2.3
|
26.4
|
1.0
|
HB2
|
H:CYS74
|
2.8
|
32.4
|
1.0
|
CE1
|
H:HIS76
|
2.8
|
21.7
|
1.0
|
CE1
|
H:HIS46
|
2.9
|
31.3
|
1.0
|
HE1
|
H:HIS76
|
2.9
|
26.0
|
1.0
|
CE1
|
H:HIS41
|
3.0
|
31.7
|
1.0
|
HE1
|
H:HIS46
|
3.0
|
37.6
|
1.0
|
CD2
|
H:HIS41
|
3.1
|
33.4
|
1.0
|
HB2
|
H:HIS76
|
3.1
|
30.9
|
1.0
|
CB
|
H:CYS74
|
3.1
|
27.0
|
1.0
|
CG
|
H:HIS76
|
3.1
|
37.3
|
1.0
|
CG
|
H:HIS46
|
3.1
|
46.1
|
1.0
|
HE1
|
H:HIS41
|
3.1
|
38.0
|
1.0
|
HB3
|
H:HIS46
|
3.2
|
35.0
|
1.0
|
HD2
|
H:HIS41
|
3.3
|
40.0
|
1.0
|
HA
|
H:HIS46
|
3.4
|
48.0
|
1.0
|
H
|
H:HIS76
|
3.6
|
24.9
|
1.0
|
CB
|
H:HIS46
|
3.6
|
29.2
|
1.0
|
HB3
|
H:CYS74
|
3.6
|
32.4
|
1.0
|
CB
|
H:HIS76
|
3.6
|
25.7
|
1.0
|
HA3
|
H:GLY13
|
3.7
|
31.7
|
1.0
|
NE2
|
H:HIS76
|
4.0
|
53.1
|
1.0
|
CA
|
H:HIS46
|
4.0
|
40.0
|
1.0
|
NE2
|
H:HIS46
|
4.1
|
36.4
|
1.0
|
ND1
|
H:HIS41
|
4.1
|
27.7
|
1.0
|
CD2
|
H:HIS76
|
4.1
|
29.9
|
1.0
|
CG
|
H:HIS41
|
4.2
|
28.1
|
1.0
|
CD2
|
H:HIS46
|
4.2
|
35.8
|
1.0
|
O
|
H:ALA12
|
4.2
|
41.5
|
1.0
|
N
|
H:HIS76
|
4.3
|
20.8
|
1.0
|
O
|
H:CYS74
|
4.3
|
20.8
|
1.0
|
HB3
|
H:HIS76
|
4.3
|
30.9
|
1.0
|
CA
|
H:CYS74
|
4.3
|
26.3
|
1.0
|
C
|
H:CYS74
|
4.4
|
28.5
|
1.0
|
HB2
|
H:HIS46
|
4.5
|
35.0
|
1.0
|
CA
|
H:HIS76
|
4.6
|
30.1
|
1.0
|
CA
|
H:GLY13
|
4.6
|
26.4
|
1.0
|
O
|
H:HOH275
|
4.7
|
41.5
|
1.0
|
HE2
|
H:HIS76
|
4.7
|
63.8
|
1.0
|
HE2
|
H:HIS46
|
4.8
|
43.6
|
1.0
|
O
|
H:HOH225
|
4.8
|
34.2
|
1.0
|
HB2
|
H:ALA49
|
4.8
|
32.2
|
1.0
|
H
|
H:CYS74
|
4.9
|
27.8
|
1.0
|
HD1
|
H:HIS41
|
4.9
|
33.2
|
1.0
|
N
|
H:HIS46
|
4.9
|
37.0
|
1.0
|
HA2
|
H:GLY13
|
5.0
|
31.7
|
1.0
|
HA
|
H:CYS74
|
5.0
|
31.5
|
1.0
|
|
Reference:
S.A.Buth,
M.M.Shneider,
P.G.Leiman.
Bacteriophage Phikz GP163.1 Paar Repeat Protein in Complex with the C-Terminal Part of the T4 GP5 Beta-Helical Domain To Be Published.
Page generated: Wed Dec 16 12:28:38 2020
|