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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:

Sodium (Na) 1 atom

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

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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

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: Mon Jan 25 16:10:28 2021

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