Zinc in PDB 8gj3: E. Coli Clamp Loader on Primed Template Dna
Enzymatic activity of E. Coli Clamp Loader on Primed Template Dna
All present enzymatic activity of E. Coli Clamp Loader on Primed Template Dna:
2.7.7.7;
Other elements in 8gj3:
The structure of E. Coli Clamp Loader on Primed Template Dna also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the E. Coli Clamp Loader on Primed Template Dna
(pdb code 8gj3). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
E. Coli Clamp Loader on Primed Template Dna, PDB code: 8gj3:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8gj3
Go back to
Zinc Binding Sites List in 8gj3
Zinc binding site 1 out
of 4 in the E. Coli Clamp Loader on Primed Template Dna
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of E. Coli Clamp Loader on Primed Template Dna within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn704
b:225.6
occ:1.00
|
SG
|
B:CYS76
|
2.3
|
165.5
|
1.0
|
|
SG
|
B:CYS79
|
2.3
|
140.5
|
1.0
|
|
SG
|
B:CYS73
|
2.3
|
156.0
|
1.0
|
|
SG
|
B:CYS64
|
2.3
|
132.8
|
1.0
|
|
H
|
B:GLY74
|
3.1
|
146.5
|
1.0
|
|
H
|
B:CYS76
|
3.2
|
156.6
|
1.0
|
|
HB2
|
B:CYS79
|
3.4
|
143.3
|
1.0
|
|
HB3
|
B:CYS76
|
3.4
|
156.6
|
1.0
|
|
H
|
B:GLU65
|
3.4
|
144.4
|
1.0
|
|
H
|
B:CYS73
|
3.5
|
150.5
|
1.0
|
|
CB
|
B:CYS76
|
3.5
|
157.1
|
1.0
|
|
CB
|
B:CYS79
|
3.5
|
143.5
|
1.0
|
|
H
|
B:CYS79
|
3.7
|
143.0
|
1.0
|
|
CB
|
B:CYS64
|
3.7
|
127.1
|
1.0
|
|
HA
|
B:CYS64
|
3.8
|
128.1
|
1.0
|
|
CB
|
B:CYS73
|
3.8
|
150.9
|
1.0
|
|
HB2
|
B:CYS64
|
3.8
|
127.7
|
1.0
|
|
H
|
B:VAL75
|
3.8
|
153.7
|
1.0
|
|
N
|
B:GLY74
|
3.9
|
147.7
|
1.0
|
|
N
|
B:CYS76
|
3.9
|
155.1
|
1.0
|
|
HB3
|
B:CYS73
|
4.0
|
150.9
|
1.0
|
|
N
|
B:CYS73
|
4.1
|
152.4
|
1.0
|
|
N
|
B:GLU65
|
4.2
|
144.0
|
1.0
|
|
HB3
|
B:CYS79
|
4.2
|
142.8
|
1.0
|
|
CA
|
B:CYS64
|
4.2
|
126.7
|
1.0
|
|
CA
|
B:CYS76
|
4.3
|
157.1
|
1.0
|
|
HB2
|
B:CYS76
|
4.3
|
156.3
|
1.0
|
|
N
|
B:CYS79
|
4.3
|
141.5
|
1.0
|
|
HB2
|
B:GLU65
|
4.3
|
144.5
|
1.0
|
|
CA
|
B:CYS73
|
4.4
|
151.9
|
1.0
|
|
H
|
B:THR66
|
4.4
|
135.3
|
1.0
|
|
CA
|
B:CYS79
|
4.5
|
143.4
|
1.0
|
|
HB3
|
B:CYS64
|
4.5
|
127.7
|
1.0
|
|
N
|
B:VAL75
|
4.5
|
153.5
|
1.0
|
|
HB2
|
B:ASN78
|
4.5
|
141.2
|
1.0
|
|
HB2
|
B:CYS73
|
4.5
|
150.7
|
1.0
|
|
HB3
|
B:PRO72
|
4.6
|
127.2
|
1.0
|
|
C
|
B:CYS73
|
4.6
|
151.6
|
1.0
|
|
HA2
|
B:GLY74
|
4.6
|
146.0
|
1.0
|
|
HG2
|
B:GLU65
|
4.7
|
145.0
|
1.0
|
|
HA
|
B:CYS79
|
4.7
|
142.6
|
1.0
|
|
CA
|
B:GLY74
|
4.7
|
146.2
|
1.0
|
|
C
|
B:CYS64
|
4.7
|
129.0
|
1.0
|
|
C
|
B:CYS76
|
4.9
|
157.8
|
1.0
|
|
O
|
B:CYS76
|
4.9
|
154.8
|
1.0
|
|
HA
|
B:PRO72
|
5.0
|
126.5
|
1.0
|
|
HG12
|
B:VAL75
|
5.0
|
153.6
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8gj3
Go back to
Zinc Binding Sites List in 8gj3
Zinc binding site 2 out
of 4 in the E. Coli Clamp Loader on Primed Template Dna
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of E. Coli Clamp Loader on Primed Template Dna within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn704
b:220.8
occ:1.00
|
SG
|
C:CYS76
|
2.3
|
141.2
|
1.0
|
|
SG
|
C:CYS73
|
2.3
|
142.8
|
1.0
|
|
SG
|
C:CYS79
|
2.3
|
135.8
|
1.0
|
|
SG
|
C:CYS64
|
2.3
|
121.7
|
1.0
|
|
H
|
C:GLY74
|
3.2
|
131.9
|
1.0
|
|
H
|
C:CYS76
|
3.2
|
138.9
|
1.0
|
|
HB2
|
C:CYS79
|
3.3
|
132.3
|
1.0
|
|
HB3
|
C:CYS76
|
3.3
|
139.1
|
1.0
|
|
H
|
C:CYS73
|
3.3
|
136.5
|
1.0
|
|
H
|
C:GLU65
|
3.4
|
128.9
|
1.0
|
|
CB
|
C:CYS76
|
3.5
|
139.3
|
1.0
|
|
CB
|
C:CYS79
|
3.5
|
133.6
|
1.0
|
|
HA
|
C:CYS64
|
3.6
|
117.2
|
1.0
|
|
CB
|
C:CYS64
|
3.7
|
122.0
|
1.0
|
|
H
|
C:CYS79
|
3.7
|
131.9
|
1.0
|
|
CB
|
C:CYS73
|
3.8
|
137.5
|
1.0
|
|
HB2
|
C:CYS64
|
3.9
|
117.5
|
1.0
|
|
N
|
C:GLY74
|
3.9
|
133.3
|
1.0
|
|
H
|
C:VAL75
|
3.9
|
134.2
|
1.0
|
|
N
|
C:CYS76
|
3.9
|
138.3
|
1.0
|
|
N
|
C:CYS73
|
4.0
|
139.8
|
1.0
|
|
HB3
|
C:CYS73
|
4.0
|
136.9
|
1.0
|
|
CA
|
C:CYS64
|
4.1
|
118.2
|
1.0
|
|
HB3
|
C:CYS79
|
4.1
|
131.6
|
1.0
|
|
N
|
C:GLU65
|
4.1
|
128.1
|
1.0
|
|
HB2
|
C:CYS76
|
4.2
|
138.6
|
1.0
|
|
CA
|
C:CYS76
|
4.2
|
138.2
|
1.0
|
|
N
|
C:CYS79
|
4.3
|
132.0
|
1.0
|
|
CA
|
C:CYS73
|
4.3
|
136.9
|
1.0
|
|
H
|
C:THR66
|
4.4
|
120.5
|
1.0
|
|
HB2
|
C:GLU65
|
4.4
|
128.8
|
1.0
|
|
CA
|
C:CYS79
|
4.4
|
130.4
|
1.0
|
|
HB3
|
C:CYS64
|
4.5
|
117.3
|
1.0
|
|
HB3
|
C:PRO72
|
4.5
|
111.8
|
1.0
|
|
HB2
|
C:CYS73
|
4.5
|
136.8
|
1.0
|
|
N
|
C:VAL75
|
4.6
|
134.1
|
1.0
|
|
HB2
|
C:ASN78
|
4.6
|
126.2
|
1.0
|
|
C
|
C:CYS73
|
4.6
|
135.9
|
1.0
|
|
C
|
C:CYS64
|
4.7
|
116.5
|
1.0
|
|
HA
|
C:CYS79
|
4.7
|
130.6
|
1.0
|
|
HA2
|
C:GLY74
|
4.7
|
131.3
|
1.0
|
|
HA
|
C:PRO72
|
4.8
|
110.9
|
1.0
|
|
CA
|
C:GLY74
|
4.8
|
132.6
|
1.0
|
|
HG2
|
C:GLU65
|
4.8
|
129.2
|
1.0
|
|
C
|
C:CYS76
|
4.8
|
140.6
|
1.0
|
|
O
|
C:CYS76
|
4.9
|
140.3
|
1.0
|
|
C
|
C:PRO72
|
4.9
|
115.6
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8gj3
Go back to
Zinc Binding Sites List in 8gj3
Zinc binding site 3 out
of 4 in the E. Coli Clamp Loader on Primed Template Dna
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of E. Coli Clamp Loader on Primed Template Dna within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn704
b:197.6
occ:1.00
|
SG
|
D:CYS76
|
2.3
|
158.1
|
1.0
|
|
SG
|
D:CYS73
|
2.3
|
146.6
|
1.0
|
|
SG
|
D:CYS79
|
2.3
|
139.9
|
1.0
|
|
SG
|
D:CYS64
|
2.3
|
121.7
|
1.0
|
|
H
|
D:GLY74
|
3.1
|
132.7
|
1.0
|
|
HB3
|
D:CYS76
|
3.2
|
145.8
|
1.0
|
|
HB2
|
D:CYS79
|
3.2
|
132.1
|
1.0
|
|
H
|
D:CYS76
|
3.3
|
145.8
|
1.0
|
|
H
|
D:CYS73
|
3.3
|
138.0
|
1.0
|
|
CB
|
D:CYS76
|
3.4
|
146.8
|
1.0
|
|
CB
|
D:CYS79
|
3.5
|
134.7
|
1.0
|
|
H
|
D:GLU65
|
3.5
|
125.3
|
1.0
|
|
HA
|
D:CYS64
|
3.6
|
116.3
|
1.0
|
|
CB
|
D:CYS64
|
3.7
|
117.8
|
1.0
|
|
H
|
D:CYS79
|
3.7
|
131.5
|
1.0
|
|
CB
|
D:CYS73
|
3.8
|
140.0
|
1.0
|
|
HB2
|
D:CYS64
|
3.9
|
116.4
|
1.0
|
|
N
|
D:GLY74
|
3.9
|
132.8
|
1.0
|
|
N
|
D:CYS73
|
3.9
|
138.5
|
1.0
|
|
H
|
D:VAL75
|
4.0
|
143.8
|
1.0
|
|
HB3
|
D:CYS73
|
4.0
|
138.8
|
1.0
|
|
N
|
D:CYS76
|
4.0
|
145.5
|
1.0
|
|
HB3
|
D:CYS79
|
4.1
|
131.9
|
1.0
|
|
CA
|
D:CYS64
|
4.1
|
116.1
|
1.0
|
|
HB2
|
D:CYS76
|
4.1
|
145.2
|
1.0
|
|
N
|
D:GLU65
|
4.2
|
121.4
|
1.0
|
|
CA
|
D:CYS76
|
4.2
|
144.9
|
1.0
|
|
CA
|
D:CYS73
|
4.3
|
139.2
|
1.0
|
|
N
|
D:CYS79
|
4.3
|
125.8
|
1.0
|
|
CA
|
D:CYS79
|
4.4
|
129.3
|
1.0
|
|
HB3
|
D:CYS64
|
4.5
|
116.0
|
1.0
|
|
H
|
D:THR66
|
4.5
|
122.1
|
1.0
|
|
HB2
|
D:GLU65
|
4.5
|
126.1
|
1.0
|
|
HB2
|
D:CYS73
|
4.5
|
139.1
|
1.0
|
|
HB3
|
D:PRO72
|
4.6
|
111.9
|
1.0
|
|
C
|
D:CYS73
|
4.6
|
137.8
|
1.0
|
|
N
|
D:VAL75
|
4.6
|
144.2
|
1.0
|
|
HB2
|
D:ASN78
|
4.7
|
126.8
|
1.0
|
|
HA
|
D:PRO72
|
4.7
|
111.5
|
1.0
|
|
C
|
D:CYS64
|
4.7
|
114.5
|
1.0
|
|
HA
|
D:CYS79
|
4.7
|
131.0
|
1.0
|
|
HA2
|
D:GLY74
|
4.7
|
132.3
|
1.0
|
|
HG2
|
D:GLU65
|
4.8
|
125.7
|
1.0
|
|
CA
|
D:GLY74
|
4.8
|
131.8
|
1.0
|
|
C
|
D:CYS76
|
4.8
|
144.2
|
1.0
|
|
O
|
D:CYS76
|
4.9
|
143.1
|
1.0
|
|
C
|
D:PRO72
|
4.9
|
116.0
|
1.0
|
|
HG12
|
D:VAL75
|
5.0
|
144.0
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8gj3
Go back to
Zinc Binding Sites List in 8gj3
Zinc binding site 4 out
of 4 in the E. Coli Clamp Loader on Primed Template Dna
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of E. Coli Clamp Loader on Primed Template Dna within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn2001
b:234.9
occ:1.00
|
SG
|
E:CYS59
|
2.3
|
159.8
|
1.0
|
|
SG
|
E:CYS62
|
2.3
|
165.8
|
1.0
|
|
SG
|
E:CYS65
|
2.3
|
146.1
|
1.0
|
|
SG
|
E:CYS50
|
2.3
|
153.5
|
1.0
|
|
H
|
E:GLY60
|
3.0
|
147.2
|
1.0
|
|
H
|
E:CYS62
|
3.0
|
160.3
|
1.0
|
|
HB3
|
E:CYS62
|
3.3
|
159.9
|
1.0
|
|
H
|
E:CYS59
|
3.3
|
155.7
|
1.0
|
|
HB2
|
E:CYS65
|
3.4
|
141.2
|
1.0
|
|
CB
|
E:CYS62
|
3.4
|
161.8
|
1.0
|
|
HA
|
E:CYS50
|
3.4
|
142.0
|
1.0
|
|
H
|
E:CYS65
|
3.5
|
140.0
|
1.0
|
|
CB
|
E:CYS50
|
3.5
|
143.6
|
1.0
|
|
CB
|
E:CYS65
|
3.5
|
141.1
|
1.0
|
|
H
|
E:GLN51
|
3.6
|
135.4
|
1.0
|
|
HB2
|
E:CYS50
|
3.6
|
141.7
|
1.0
|
|
H
|
E:GLN52
|
3.7
|
154.8
|
1.0
|
|
CB
|
E:CYS59
|
3.7
|
157.3
|
1.0
|
|
N
|
E:GLY60
|
3.7
|
148.7
|
1.0
|
|
H
|
E:HIS61
|
3.7
|
153.8
|
1.0
|
|
HB3
|
E:CYS59
|
3.8
|
155.9
|
1.0
|
|
N
|
E:CYS62
|
3.8
|
162.8
|
1.0
|
|
N
|
E:CYS59
|
3.9
|
157.5
|
1.0
|
|
HB2
|
E:SER58
|
3.9
|
140.4
|
1.0
|
|
CA
|
E:CYS50
|
4.0
|
142.4
|
1.0
|
|
N
|
E:CYS65
|
4.2
|
137.1
|
1.0
|
|
CA
|
E:CYS62
|
4.2
|
161.7
|
1.0
|
|
N
|
E:GLN51
|
4.2
|
136.2
|
1.0
|
|
HB2
|
E:CYS62
|
4.2
|
159.8
|
1.0
|
|
CA
|
E:CYS59
|
4.2
|
158.0
|
1.0
|
|
HB3
|
E:CYS65
|
4.2
|
140.2
|
1.0
|
|
HB3
|
E:CYS50
|
4.3
|
141.0
|
1.0
|
|
N
|
E:HIS61
|
4.4
|
152.8
|
1.0
|
|
C
|
E:CYS59
|
4.4
|
156.4
|
1.0
|
|
CA
|
E:CYS65
|
4.4
|
137.5
|
1.0
|
|
HB2
|
E:CYS59
|
4.5
|
156.2
|
1.0
|
|
HA2
|
E:GLY60
|
4.5
|
146.8
|
1.0
|
|
N
|
E:GLN52
|
4.5
|
154.7
|
1.0
|
|
C
|
E:CYS50
|
4.5
|
139.9
|
1.0
|
|
CA
|
E:GLY60
|
4.6
|
146.2
|
1.0
|
|
O
|
E:GLN52
|
4.6
|
154.6
|
1.0
|
|
HA
|
E:CYS65
|
4.7
|
139.9
|
1.0
|
|
HB3
|
E:GLN52
|
4.8
|
155.4
|
1.0
|
|
C
|
E:CYS62
|
4.8
|
159.3
|
1.0
|
|
CB
|
E:SER58
|
4.8
|
138.8
|
1.0
|
|
O
|
E:CYS62
|
4.9
|
160.7
|
1.0
|
|
C
|
E:GLY60
|
4.9
|
144.4
|
1.0
|
|
C
|
E:SER58
|
4.9
|
144.4
|
1.0
|
|
C
|
E:HIS61
|
5.0
|
152.3
|
1.0
|
|
HA
|
E:SER58
|
5.0
|
140.5
|
1.0
|
|
C
|
E:GLN52
|
5.0
|
153.5
|
1.0
|
|
Reference:
Z.-Q.Xu,
A.J.Oakley,
N.E.Dixon.
Structural Characterisation of the Complete Cycle of Sliding Clamp Loading in E. Coli To Be Published.
Page generated: Wed Oct 30 20:56:24 2024
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