Zinc in PDB 1no5: Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase.
Protein crystallography data
The structure of Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase., PDB code: 1no5
was solved by
C.Lehmann,
S.Pullalarevu,
A.Galkin,
W.Krajewski,
M.A.Willis,
A.Howard,
O.Herzberg,
Structure 2 Function Project (S2F),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.79 /
1.80
|
Space group
|
P 63
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.560,
89.560,
61.480,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
20 /
28.2
|
Other elements in 1no5:
The structure of Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase. also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase.
(pdb code 1no5). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase., PDB code: 1no5:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 1no5
Go back to
Zinc Binding Sites List in 1no5
Zinc binding site 1 out
of 8 in the Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase.
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn501
b:23.5
occ:1.00
|
O
|
A:HOH1105
|
1.9
|
21.2
|
1.0
|
O
|
A:HOH1102
|
2.0
|
23.9
|
1.0
|
OD2
|
A:ASP48
|
2.1
|
20.3
|
1.0
|
OD1
|
A:ASP46
|
2.1
|
20.1
|
1.0
|
O
|
A:HOH1104
|
2.1
|
23.6
|
1.0
|
O
|
A:HOH1103
|
2.2
|
21.9
|
1.0
|
CG
|
A:ASP48
|
3.1
|
29.6
|
1.0
|
CG
|
A:ASP46
|
3.1
|
25.4
|
1.0
|
ZN
|
A:ZN511
|
3.4
|
22.8
|
1.0
|
OD1
|
A:ASP48
|
3.4
|
19.7
|
1.0
|
OD2
|
A:ASP46
|
3.5
|
19.5
|
1.0
|
ZN
|
A:ZN531
|
3.7
|
53.1
|
1.0
|
O
|
A:ASP46
|
4.1
|
22.1
|
1.0
|
OG
|
A:SER35
|
4.2
|
25.1
|
1.0
|
N
|
A:SER35
|
4.2
|
26.7
|
1.0
|
O
|
A:HOH1113
|
4.3
|
19.7
|
1.0
|
O
|
A:HOH1305
|
4.4
|
68.1
|
1.0
|
CB
|
A:ASP48
|
4.4
|
20.5
|
1.0
|
C
|
A:ASP46
|
4.5
|
20.3
|
1.0
|
CB
|
A:ASP46
|
4.5
|
22.4
|
1.0
|
N
|
A:ASP46
|
4.5
|
19.3
|
1.0
|
N
|
A:ASP48
|
4.7
|
18.6
|
1.0
|
CA
|
A:GLY34
|
4.7
|
29.6
|
1.0
|
CA
|
A:ASP46
|
4.7
|
20.4
|
1.0
|
C
|
A:GLY34
|
5.0
|
35.2
|
1.0
|
CB
|
A:SER35
|
5.0
|
28.4
|
1.0
|
|
Zinc binding site 2 out
of 8 in 1no5
Go back to
Zinc Binding Sites List in 1no5
Zinc binding site 2 out
of 8 in the Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase.
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn511
b:22.8
occ:1.00
|
OD2
|
A:ASP79
|
2.0
|
21.8
|
1.0
|
OD2
|
A:ASP46
|
2.1
|
19.5
|
1.0
|
O
|
A:HOH1105
|
2.1
|
21.2
|
1.0
|
OD1
|
A:ASP48
|
2.1
|
19.7
|
1.0
|
CG
|
A:ASP46
|
3.1
|
25.4
|
1.0
|
ZN
|
A:ZN531
|
3.1
|
53.1
|
1.0
|
CG
|
A:ASP79
|
3.1
|
16.0
|
1.0
|
CG
|
A:ASP48
|
3.1
|
29.6
|
1.0
|
OD1
|
A:ASP46
|
3.3
|
20.1
|
1.0
|
O
|
A:HOH1245
|
3.3
|
21.8
|
1.0
|
OD2
|
A:ASP48
|
3.4
|
20.3
|
1.0
|
ZN
|
A:ZN501
|
3.4
|
23.5
|
1.0
|
CB
|
A:ASP79
|
3.5
|
19.1
|
1.0
|
O
|
A:HOH1134
|
3.7
|
24.4
|
1.0
|
O
|
A:HOH1226
|
4.0
|
35.4
|
1.0
|
OD1
|
A:ASP79
|
4.3
|
23.8
|
1.0
|
CB
|
A:ASP46
|
4.4
|
22.4
|
1.0
|
CB
|
A:ASP48
|
4.5
|
20.5
|
1.0
|
O
|
A:HOH1102
|
4.5
|
23.9
|
1.0
|
O
|
A:HOH1129
|
4.7
|
21.2
|
1.0
|
ZN
|
A:ZN521
|
4.8
|
29.2
|
1.0
|
O
|
A:HOH1104
|
4.9
|
23.6
|
1.0
|
|
Zinc binding site 3 out
of 8 in 1no5
Go back to
Zinc Binding Sites List in 1no5
Zinc binding site 3 out
of 8 in the Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase.
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn521
b:29.2
occ:1.00
|
OD1
|
A:ASP79
|
2.1
|
23.8
|
1.0
|
O
|
A:HOH1269
|
2.6
|
36.5
|
1.0
|
CG
|
A:ASP79
|
2.8
|
16.0
|
1.0
|
OD2
|
A:ASP79
|
3.0
|
21.8
|
1.0
|
O
|
A:HOH1245
|
3.3
|
21.8
|
1.0
|
O
|
A:HOH1226
|
3.7
|
35.4
|
1.0
|
O
|
A:LEU80
|
4.1
|
24.2
|
1.0
|
CB
|
A:ASP79
|
4.2
|
19.1
|
1.0
|
O
|
A:HOH1315
|
4.4
|
58.0
|
1.0
|
NH2
|
A:ARG77
|
4.6
|
26.9
|
0.7
|
C
|
A:ASP79
|
4.7
|
20.4
|
1.0
|
CA
|
A:ASP79
|
4.7
|
20.3
|
1.0
|
ZN
|
A:ZN511
|
4.8
|
22.8
|
1.0
|
C
|
A:LEU80
|
4.9
|
30.6
|
1.0
|
N
|
A:LEU80
|
4.9
|
21.0
|
1.0
|
|
Zinc binding site 4 out
of 8 in 1no5
Go back to
Zinc Binding Sites List in 1no5
Zinc binding site 4 out
of 8 in the Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase.
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn531
b:53.1
occ:1.00
|
O
|
A:HOH1105
|
2.3
|
21.2
|
1.0
|
ZN
|
A:ZN511
|
3.1
|
22.8
|
1.0
|
O
|
A:HOH1245
|
3.4
|
21.8
|
1.0
|
O
|
A:HOH1104
|
3.7
|
23.6
|
1.0
|
OD1
|
A:ASP48
|
3.7
|
19.7
|
1.0
|
ZN
|
A:ZN501
|
3.7
|
23.5
|
1.0
|
OD2
|
A:ASP48
|
3.8
|
20.3
|
1.0
|
CG
|
A:ASP48
|
4.0
|
29.6
|
1.0
|
OD2
|
A:ASP79
|
4.6
|
21.8
|
1.0
|
O
|
A:HOH1102
|
4.6
|
23.9
|
1.0
|
OD2
|
A:ASP46
|
4.8
|
19.5
|
1.0
|
O
|
A:HOH1252
|
4.9
|
59.1
|
1.0
|
O
|
A:HOH1305
|
4.9
|
68.1
|
1.0
|
O
|
A:HOH1302
|
5.0
|
60.9
|
1.0
|
|
Zinc binding site 5 out
of 8 in 1no5
Go back to
Zinc Binding Sites List in 1no5
Zinc binding site 5 out
of 8 in the Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase.
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn561
b:33.3
occ:1.00
|
OE2
|
A:GLU92
|
1.5
|
25.0
|
1.0
|
OE2
|
A:GLU88
|
1.8
|
31.8
|
1.0
|
OD1
|
B:ASP8
|
2.0
|
33.7
|
1.0
|
O
|
A:HOH1110
|
2.3
|
29.8
|
1.0
|
CD
|
A:GLU92
|
2.6
|
38.8
|
1.0
|
CD
|
A:GLU88
|
2.8
|
28.7
|
1.0
|
CG
|
B:ASP8
|
2.9
|
35.5
|
1.0
|
CG
|
A:GLU88
|
3.2
|
33.0
|
1.0
|
OD2
|
B:ASP8
|
3.3
|
33.2
|
1.0
|
CG
|
A:GLU92
|
3.4
|
41.9
|
1.0
|
OE1
|
A:GLU92
|
3.5
|
72.6
|
1.0
|
O
|
B:HOH1222
|
3.8
|
56.5
|
1.0
|
NH2
|
A:ARG95
|
3.8
|
32.6
|
1.0
|
OE1
|
A:GLU88
|
4.0
|
30.3
|
1.0
|
CB
|
B:ASP8
|
4.3
|
21.3
|
1.0
|
C
|
B:ASP8
|
4.4
|
30.2
|
1.0
|
CA
|
B:ASP8
|
4.5
|
24.6
|
1.0
|
O
|
B:ASP8
|
4.6
|
28.3
|
1.0
|
O
|
B:HOH1330
|
4.6
|
62.5
|
1.0
|
N
|
B:ILE9
|
4.7
|
25.2
|
1.0
|
CB
|
A:GLU88
|
4.7
|
35.5
|
1.0
|
NZ
|
B:LYS43
|
4.7
|
57.3
|
1.0
|
O
|
A:GLU88
|
4.8
|
35.5
|
1.0
|
CB
|
A:GLU92
|
4.8
|
33.4
|
1.0
|
CZ
|
A:ARG95
|
5.0
|
16.6
|
1.0
|
|
Zinc binding site 6 out
of 8 in 1no5
Go back to
Zinc Binding Sites List in 1no5
Zinc binding site 6 out
of 8 in the Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase.
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn541
b:26.1
occ:1.00
|
OD2
|
B:ASP46
|
2.0
|
20.8
|
1.0
|
O
|
B:HOH1107
|
2.2
|
22.1
|
1.0
|
OD1
|
B:ASP48
|
2.2
|
24.5
|
1.0
|
O
|
B:HOH1106
|
2.2
|
21.2
|
1.0
|
CG
|
B:ASP46
|
3.1
|
24.9
|
1.0
|
CG
|
B:ASP48
|
3.2
|
21.7
|
1.0
|
ZN
|
B:ZN551
|
3.5
|
24.3
|
1.0
|
OD1
|
B:ASP46
|
3.5
|
21.1
|
1.0
|
OD2
|
B:ASP48
|
3.6
|
24.9
|
1.0
|
O
|
B:HOH1162
|
3.8
|
37.1
|
1.0
|
OG
|
B:SER35
|
4.1
|
29.4
|
1.0
|
O
|
B:ASP46
|
4.2
|
21.0
|
1.0
|
O
|
B:HOH1111
|
4.3
|
23.7
|
1.0
|
N
|
B:SER35
|
4.3
|
20.2
|
1.0
|
CB
|
B:ASP46
|
4.4
|
21.7
|
1.0
|
CB
|
B:ASP48
|
4.5
|
20.4
|
1.0
|
C
|
B:ASP46
|
4.5
|
16.6
|
1.0
|
N
|
B:ASP46
|
4.6
|
23.3
|
1.0
|
O
|
B:HOH1108
|
4.7
|
27.4
|
1.0
|
CA
|
B:ASP46
|
4.8
|
18.6
|
1.0
|
CB
|
B:SER35
|
4.8
|
24.2
|
1.0
|
N
|
B:ASP48
|
4.9
|
16.6
|
1.0
|
CA
|
B:GLY34
|
5.0
|
23.7
|
1.0
|
|
Zinc binding site 7 out
of 8 in 1no5
Go back to
Zinc Binding Sites List in 1no5
Zinc binding site 7 out
of 8 in the Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase.
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn551
b:24.3
occ:1.00
|
OD2
|
B:ASP79
|
1.9
|
20.8
|
1.0
|
OD2
|
B:ASP48
|
2.0
|
24.9
|
1.0
|
OD1
|
B:ASP46
|
2.1
|
21.1
|
1.0
|
O
|
B:HOH1108
|
2.3
|
27.4
|
1.0
|
CG
|
B:ASP79
|
2.9
|
24.4
|
1.0
|
CG
|
B:ASP48
|
3.0
|
21.7
|
1.0
|
CG
|
B:ASP46
|
3.1
|
24.9
|
1.0
|
CB
|
B:ASP79
|
3.3
|
19.8
|
1.0
|
OD2
|
B:ASP46
|
3.3
|
20.8
|
1.0
|
OD1
|
B:ASP48
|
3.3
|
24.5
|
1.0
|
ZN
|
B:ZN541
|
3.5
|
26.1
|
1.0
|
O
|
B:HOH1137
|
4.0
|
23.9
|
1.0
|
NH2
|
B:ARG77
|
4.0
|
28.8
|
1.0
|
OD1
|
B:ASP79
|
4.0
|
24.5
|
1.0
|
O
|
B:HOH1162
|
4.3
|
37.1
|
1.0
|
CB
|
B:ASP48
|
4.3
|
20.4
|
1.0
|
CB
|
B:ASP46
|
4.4
|
21.7
|
1.0
|
O
|
B:HOH1107
|
4.7
|
22.1
|
1.0
|
CA
|
B:ASP79
|
4.8
|
20.6
|
1.0
|
O
|
B:HOH1124
|
4.8
|
32.3
|
1.0
|
CZ
|
B:ARG77
|
4.9
|
55.1
|
1.0
|
CA
|
B:ASP48
|
4.9
|
18.5
|
1.0
|
|
Zinc binding site 8 out
of 8 in 1no5
Go back to
Zinc Binding Sites List in 1no5
Zinc binding site 8 out
of 8 in the Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase.
 Mono view
 Stereo pair view
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A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Structure of HI0073 From Haemophilus Influenzae, the Nucleotide Binding Domain of the HI0073/HI0074 Two Protein Nucleotidyl Transferase. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn571
b:30.1
occ:1.00
|
OE2
|
B:GLU67
|
1.7
|
24.1
|
1.0
|
O3
|
B:SO4602
|
1.9
|
36.4
|
1.0
|
OE2
|
B:GLU71
|
2.0
|
26.1
|
1.0
|
O3
|
B:SO4601
|
2.1
|
43.9
|
1.0
|
CD
|
B:GLU67
|
2.6
|
27.3
|
1.0
|
CD
|
B:GLU71
|
2.7
|
19.9
|
1.0
|
OE1
|
B:GLU71
|
2.9
|
20.9
|
1.0
|
S
|
B:SO4602
|
3.0
|
47.7
|
1.0
|
CG
|
B:GLU67
|
3.1
|
23.5
|
1.0
|
S
|
B:SO4601
|
3.2
|
33.3
|
1.0
|
O1
|
B:SO4602
|
3.4
|
60.5
|
1.0
|
O1
|
B:SO4601
|
3.5
|
74.7
|
1.0
|
O4
|
B:SO4601
|
3.5
|
70.5
|
1.0
|
O2
|
B:SO4602
|
3.7
|
70.5
|
1.0
|
OE1
|
B:GLU67
|
3.8
|
26.9
|
1.0
|
CG
|
B:GLU71
|
4.1
|
19.8
|
1.0
|
O4
|
B:SO4602
|
4.2
|
0.2
|
1.0
|
NA
|
B:NA701
|
4.2
|
20.1
|
1.0
|
O2
|
B:SO4601
|
4.4
|
47.9
|
1.0
|
CB
|
B:GLU67
|
4.6
|
22.9
|
1.0
|
|
Reference:
C.Lehmann,
S.Pullalarevu,
W.Krajewski,
M.A.Willis,
A.Galkin,
A.Howard,
O.Herzberg.
Structure of HI0073 From Haemophilus Influenzae, the Nucleotide-Binding Domain of A Two-Protein Nucleotidyl Transferase Proteins V. 60 807 2005.
ISSN: ISSN 0887-3585
PubMed: 16028221
DOI: 10.1002/PROT.20586
Page generated: Wed Oct 16 17:20:03 2024
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