Atomistry » Zinc » PDB 1ndw-1nvb » 1no5
Atomistry »
  Zinc »
    PDB 1ndw-1nvb »
      1no5 »

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

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

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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy