Zinc in PDB 1njf: Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit
Enzymatic activity of Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit
All present enzymatic activity of Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit:
2.7.7.7;
Protein crystallography data
The structure of Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit, PDB code: 1njf
was solved by
M.Podobnik,
T.F.Weitze,
M.O'donnell,
J.Kuriyan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
82.84 /
2.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
71.708,
113.347,
121.355,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21 /
24.8
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit
(pdb code 1njf). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit, PDB code: 1njf:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 1njf
Go back to
Zinc Binding Sites List in 1njf
Zinc binding site 1 out
of 4 in the Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:38.7
occ:1.00
|
SG
|
A:CYS64
|
2.4
|
15.0
|
1.0
|
SG
|
A:CYS73
|
2.4
|
21.3
|
1.0
|
SG
|
A:CYS76
|
2.4
|
19.3
|
1.0
|
SG
|
A:CYS79
|
2.5
|
26.5
|
1.0
|
CB
|
A:CYS76
|
3.4
|
19.0
|
1.0
|
CB
|
A:CYS79
|
3.4
|
18.8
|
1.0
|
CB
|
A:CYS64
|
3.5
|
18.4
|
1.0
|
N
|
A:CYS73
|
3.6
|
20.4
|
1.0
|
CB
|
A:CYS73
|
3.6
|
18.2
|
1.0
|
N
|
A:GLY74
|
3.6
|
22.8
|
1.0
|
CA
|
A:CYS64
|
3.8
|
18.6
|
1.0
|
N
|
A:CYS76
|
3.9
|
21.6
|
1.0
|
CA
|
A:CYS73
|
4.0
|
19.5
|
1.0
|
N
|
A:GLU65
|
4.1
|
23.9
|
1.0
|
CA
|
A:CYS76
|
4.2
|
21.0
|
1.0
|
C
|
A:CYS73
|
4.3
|
20.9
|
1.0
|
C
|
A:CYS64
|
4.4
|
21.7
|
1.0
|
N
|
A:CYS79
|
4.4
|
20.0
|
1.0
|
CA
|
A:CYS79
|
4.5
|
22.5
|
1.0
|
O
|
A:HOH514
|
4.5
|
17.2
|
1.0
|
C
|
A:PRO72
|
4.5
|
20.8
|
1.0
|
N
|
A:VAL75
|
4.5
|
24.0
|
1.0
|
CA
|
A:GLY74
|
4.6
|
23.6
|
1.0
|
N
|
A:THR66
|
4.8
|
22.4
|
1.0
|
CA
|
A:PRO72
|
4.8
|
20.6
|
1.0
|
O
|
A:CYS76
|
4.9
|
21.1
|
1.0
|
C
|
A:CYS76
|
4.9
|
21.8
|
1.0
|
C
|
A:GLY74
|
5.0
|
25.5
|
1.0
|
CB
|
A:PRO72
|
5.0
|
22.1
|
1.0
|
CB
|
A:THR66
|
5.0
|
23.3
|
1.0
|
|
Zinc binding site 2 out
of 4 in 1njf
Go back to
Zinc Binding Sites List in 1njf
Zinc binding site 2 out
of 4 in the Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn301
b:43.7
occ:1.00
|
SG
|
B:CYS73
|
2.3
|
32.3
|
1.0
|
SG
|
B:CYS76
|
2.4
|
33.3
|
1.0
|
SG
|
B:CYS64
|
2.4
|
24.5
|
1.0
|
SG
|
B:CYS79
|
2.6
|
32.1
|
1.0
|
CB
|
B:CYS76
|
3.3
|
35.3
|
1.0
|
CB
|
B:CYS73
|
3.4
|
31.5
|
1.0
|
CB
|
B:CYS79
|
3.5
|
32.6
|
1.0
|
N
|
B:CYS73
|
3.5
|
27.8
|
1.0
|
CB
|
B:CYS64
|
3.6
|
28.8
|
1.0
|
N
|
B:GLY74
|
3.8
|
32.5
|
1.0
|
CA
|
B:CYS73
|
3.8
|
30.3
|
1.0
|
CA
|
B:CYS64
|
3.9
|
28.8
|
1.0
|
N
|
B:CYS76
|
3.9
|
32.9
|
1.0
|
N
|
B:GLU65
|
4.0
|
31.5
|
1.0
|
CA
|
B:CYS76
|
4.2
|
35.3
|
1.0
|
C
|
B:CYS73
|
4.3
|
31.6
|
1.0
|
C
|
B:CYS64
|
4.4
|
30.9
|
1.0
|
N
|
B:CYS79
|
4.5
|
34.1
|
1.0
|
C
|
B:PRO72
|
4.5
|
27.1
|
1.0
|
CA
|
B:CYS79
|
4.6
|
34.8
|
1.0
|
N
|
B:VAL75
|
4.6
|
32.5
|
1.0
|
O
|
B:CYS76
|
4.8
|
37.0
|
1.0
|
C
|
B:CYS76
|
4.8
|
36.8
|
1.0
|
CA
|
B:GLY74
|
4.9
|
31.7
|
1.0
|
CG2
|
B:THR66
|
4.9
|
27.8
|
1.0
|
CA
|
B:PRO72
|
4.9
|
25.6
|
1.0
|
N
|
B:THR66
|
4.9
|
33.1
|
1.0
|
|
Zinc binding site 3 out
of 4 in 1njf
Go back to
Zinc Binding Sites List in 1njf
Zinc binding site 3 out
of 4 in the Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn301
b:46.5
occ:1.00
|
SG
|
C:CYS73
|
2.4
|
33.9
|
1.0
|
SG
|
C:CYS76
|
2.4
|
39.5
|
1.0
|
SG
|
C:CYS79
|
2.5
|
32.2
|
1.0
|
SG
|
C:CYS64
|
2.5
|
31.4
|
1.0
|
CB
|
C:CYS79
|
3.4
|
30.4
|
1.0
|
CB
|
C:CYS76
|
3.4
|
37.1
|
1.0
|
CB
|
C:CYS64
|
3.4
|
27.3
|
1.0
|
N
|
C:CYS73
|
3.6
|
37.5
|
1.0
|
CB
|
C:CYS73
|
3.7
|
36.4
|
1.0
|
N
|
C:GLY74
|
3.8
|
37.5
|
1.0
|
CA
|
C:CYS64
|
3.8
|
28.5
|
1.0
|
N
|
C:CYS76
|
3.9
|
38.4
|
1.0
|
CA
|
C:CYS73
|
4.0
|
36.8
|
1.0
|
N
|
C:GLU65
|
4.0
|
32.2
|
1.0
|
CA
|
C:CYS76
|
4.2
|
36.1
|
1.0
|
N
|
C:CYS79
|
4.3
|
28.8
|
1.0
|
C
|
C:CYS73
|
4.3
|
36.5
|
1.0
|
C
|
C:CYS64
|
4.3
|
29.9
|
1.0
|
CA
|
C:CYS79
|
4.4
|
30.3
|
1.0
|
N
|
C:VAL75
|
4.4
|
38.8
|
1.0
|
C
|
C:PRO72
|
4.6
|
36.6
|
1.0
|
CG2
|
C:THR66
|
4.7
|
39.6
|
1.0
|
CA
|
C:GLY74
|
4.7
|
36.9
|
1.0
|
O
|
C:CYS76
|
4.7
|
32.4
|
1.0
|
C
|
C:CYS76
|
4.8
|
34.6
|
1.0
|
CA
|
C:PRO72
|
4.9
|
35.7
|
1.0
|
N
|
C:THR66
|
5.0
|
39.0
|
1.0
|
|
Zinc binding site 4 out
of 4 in 1njf
Go back to
Zinc Binding Sites List in 1njf
Zinc binding site 4 out
of 4 in the Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn301
b:48.8
occ:1.00
|
SG
|
D:CYS79
|
2.3
|
25.7
|
1.0
|
SG
|
D:CYS64
|
2.4
|
24.1
|
1.0
|
SG
|
D:CYS73
|
2.5
|
29.9
|
1.0
|
SG
|
D:CYS76
|
2.6
|
26.4
|
1.0
|
CB
|
D:CYS64
|
3.4
|
25.5
|
1.0
|
CB
|
D:CYS79
|
3.4
|
26.7
|
1.0
|
CB
|
D:CYS76
|
3.4
|
27.3
|
1.0
|
N
|
D:CYS73
|
3.5
|
32.2
|
1.0
|
CB
|
D:CYS73
|
3.6
|
30.1
|
1.0
|
CA
|
D:CYS64
|
3.7
|
26.4
|
1.0
|
N
|
D:GLY74
|
3.7
|
31.6
|
1.0
|
CA
|
D:CYS73
|
3.9
|
31.9
|
1.0
|
N
|
D:GLU65
|
4.0
|
30.0
|
1.0
|
N
|
D:CYS76
|
4.1
|
30.5
|
1.0
|
C
|
D:CYS73
|
4.3
|
32.3
|
1.0
|
C
|
D:CYS64
|
4.3
|
28.0
|
1.0
|
CA
|
D:CYS76
|
4.3
|
28.6
|
1.0
|
O
|
D:HOH417
|
4.4
|
22.4
|
1.0
|
N
|
D:CYS79
|
4.4
|
24.2
|
1.0
|
C
|
D:PRO72
|
4.4
|
30.7
|
1.0
|
CA
|
D:CYS79
|
4.5
|
25.9
|
1.0
|
N
|
D:VAL75
|
4.6
|
31.6
|
1.0
|
CG2
|
D:THR66
|
4.7
|
37.1
|
1.0
|
CA
|
D:PRO72
|
4.7
|
30.9
|
1.0
|
CA
|
D:GLY74
|
4.7
|
30.7
|
1.0
|
CB
|
D:PRO72
|
4.8
|
31.5
|
1.0
|
N
|
D:THR66
|
4.9
|
33.9
|
1.0
|
N
|
D:CYS64
|
4.9
|
23.1
|
1.0
|
O
|
D:CYS76
|
4.9
|
26.8
|
1.0
|
C
|
D:CYS76
|
5.0
|
27.5
|
1.0
|
|
Reference:
M.Podobnik,
T.F.Weitze,
M.O'donnell,
J.Kuriyan.
Nucleotide-Induced Conformational Changes in An Isolated Escherichia Coli Dna Polymerase III Clamp Loader Subunit Structure V. 11 253 2003.
ISSN: ISSN 0969-2126
PubMed: 12623013
DOI: 10.1016/S0969-2126(03)00027-3
Page generated: Wed Oct 16 17:16:58 2024
|