Atomistry » Zinc » PDB 2w14-2wey » 2w9m
Atomistry »
  Zinc »
    PDB 2w14-2wey »
      2w9m »

Zinc in PDB 2w9m: Structure of Family X Dna Polymerase From Deinococcus Radiodurans

Protein crystallography data

The structure of Structure of Family X Dna Polymerase From Deinococcus Radiodurans, PDB code: 2w9m was solved by N.Leulliot, L.Cladiere, F.Lecointe, D.Durand, U.Hubscher, H.Van Tilbeurgh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.32 / 2.46
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.930, 138.250, 67.750, 90.00, 92.25, 90.00
R / Rfree (%) 20.3 / 24.9

Other elements in 2w9m:

The structure of Structure of Family X Dna Polymerase From Deinococcus Radiodurans also contains other interesting chemical elements:

Mercury (Hg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Family X Dna Polymerase From Deinococcus Radiodurans (pdb code 2w9m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Structure of Family X Dna Polymerase From Deinococcus Radiodurans, PDB code: 2w9m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 2w9m

Go back to Zinc Binding Sites List in 2w9m
Zinc binding site 1 out of 7 in the Structure of Family X Dna Polymerase From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Family X Dna Polymerase From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1565

b:34.7
occ:1.00
NE2 A:HIS364 2.1 32.6 1.0
NE2 A:HIS518 2.1 30.7 1.0
OD2 A:ASP339 2.3 32.2 1.0
OD1 A:ASP339 2.6 33.6 1.0
CG A:ASP339 2.8 32.1 1.0
CE1 A:HIS364 2.8 28.4 1.0
CD2 A:HIS518 3.0 21.6 1.0
CE1 A:HIS518 3.1 28.1 1.0
CD2 A:HIS364 3.2 29.1 1.0
CE1 A:HIS334 3.8 32.4 1.0
ND1 A:HIS334 3.8 29.1 1.0
CG A:PRO93 3.9 33.2 1.0
ND1 A:HIS364 4.0 30.2 1.0
NE2 A:HIS334 4.1 27.4 1.0
O A:HOH2029 4.1 34.2 1.0
CG A:HIS518 4.2 23.2 1.0
ND1 A:HIS518 4.2 30.0 1.0
O A:GLN91 4.2 43.1 1.0
CG A:HIS334 4.2 26.6 1.0
CG A:HIS364 4.2 28.2 1.0
CB A:ASP339 4.3 23.9 1.0
CD2 A:HIS334 4.4 24.2 1.0
CD A:PRO93 4.4 29.0 1.0
N A:PRO93 4.7 29.5 1.0
ZN A:ZN1566 4.8 24.9 1.0
CB A:PRO93 4.8 21.9 1.0
CB A:ALA371 4.8 28.3 1.0
CB A:HIS334 5.0 23.2 1.0

Zinc binding site 2 out of 7 in 2w9m

Go back to Zinc Binding Sites List in 2w9m
Zinc binding site 2 out of 7 in the Structure of Family X Dna Polymerase From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Family X Dna Polymerase From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1566

b:24.9
occ:1.00
OE1 A:GLU401 2.2 22.4 1.0
NE2 A:HIS332 2.3 28.8 1.0
NE2 A:HIS334 2.3 27.4 1.0
OD1 A:ASP516 2.4 29.0 1.0
ZN A:ZN1567 3.0 27.7 1.0
CG A:ASP516 3.0 25.6 1.0
OD2 A:ASP516 3.0 33.4 1.0
CD A:GLU401 3.1 31.5 1.0
CE1 A:HIS332 3.1 27.6 1.0
CE1 A:HIS334 3.2 32.4 1.0
CD2 A:HIS332 3.3 28.3 1.0
CD2 A:HIS334 3.3 24.2 1.0
OE2 A:GLU401 3.4 31.2 1.0
CE1 A:HIS364 4.2 28.4 1.0
ND1 A:HIS332 4.2 25.4 1.0
ND1 A:HIS334 4.3 29.1 1.0
O A:HOH2029 4.3 34.2 1.0
CG A:HIS332 4.3 25.3 1.0
CG A:GLU401 4.4 19.2 1.0
CE1 A:HIS518 4.4 28.1 1.0
CB A:ASP516 4.4 27.1 1.0
CG A:HIS334 4.4 26.6 1.0
NE2 A:HIS364 4.6 32.6 1.0
CB A:GLU401 4.7 21.1 1.0
ZN A:ZN1565 4.8 34.7 1.0
NE2 A:HIS518 4.8 30.7 1.0
NE2 A:HIS428 4.9 30.8 1.0
NE2 A:HIS456 4.9 21.4 1.0
O A:ALA362 4.9 31.9 1.0
CA A:ASP516 4.9 19.3 1.0
ND1 A:HIS364 4.9 30.2 1.0

Zinc binding site 3 out of 7 in 2w9m

Go back to Zinc Binding Sites List in 2w9m
Zinc binding site 3 out of 7 in the Structure of Family X Dna Polymerase From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Family X Dna Polymerase From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1567

b:27.7
occ:1.00
OE2 A:GLU401 2.1 31.2 1.0
NE2 A:HIS456 2.4 21.4 1.0
NE2 A:HIS428 2.4 30.8 1.0
CE1 A:HIS428 2.6 32.3 1.0
CD A:GLU401 2.9 31.5 1.0
ZN A:ZN1566 3.0 24.9 1.0
OE1 A:GLU401 3.1 22.4 1.0
CD2 A:HIS456 3.4 27.4 1.0
CE1 A:HIS456 3.4 27.5 1.0
O A:HOH2029 3.8 34.2 1.0
CD2 A:HIS428 3.8 38.8 1.0
OD2 A:ASP516 3.9 33.4 1.0
ND1 A:HIS428 3.9 41.9 1.0
NE2 A:HIS332 4.2 28.8 1.0
CE1 A:HIS364 4.3 28.4 1.0
CE1 A:HIS332 4.4 27.6 1.0
CG A:GLU401 4.4 19.2 1.0
OG A:SER426 4.4 33.7 1.0
CB A:SER426 4.4 17.1 1.0
CG A:HIS428 4.5 35.3 1.0
ND1 A:HIS456 4.5 27.4 1.0
NH2 A:ARG494 4.5 38.9 1.0
CG A:HIS456 4.5 21.4 1.0
CG A:ASP516 4.7 25.6 1.0
OD1 A:ASP516 4.8 29.0 1.0
ND1 A:HIS364 4.8 30.2 1.0
CZ A:ARG494 4.9 27.8 1.0
NE2 A:HIS334 5.0 27.4 1.0

Zinc binding site 4 out of 7 in 2w9m

Go back to Zinc Binding Sites List in 2w9m
Zinc binding site 4 out of 7 in the Structure of Family X Dna Polymerase From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Family X Dna Polymerase From Deinococcus Radiodurans within 5.0Å range:

Zinc binding site 5 out of 7 in 2w9m

Go back to Zinc Binding Sites List in 2w9m
Zinc binding site 5 out of 7 in the Structure of Family X Dna Polymerase From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Family X Dna Polymerase From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1565

b:28.8
occ:1.00
NE2 B:HIS364 2.1 28.6 1.0
NE2 B:HIS518 2.1 28.4 1.0
OD2 B:ASP339 2.3 32.8 1.0
OD1 B:ASP339 2.6 26.7 1.0
CG B:ASP339 2.8 25.9 1.0
CE1 B:HIS364 2.9 23.7 1.0
CD2 B:HIS518 3.0 22.8 1.0
CE1 B:HIS518 3.1 23.4 1.0
CD2 B:HIS364 3.2 25.1 1.0
CE1 B:HIS334 3.8 28.3 1.0
ND1 B:HIS334 3.9 25.0 1.0
CG B:PRO93 3.9 29.9 1.0
ND1 B:HIS364 4.1 28.0 1.0
NE2 B:HIS334 4.1 20.6 1.0
O B:HOH2037 4.1 32.3 1.0
CG B:HIS518 4.2 27.8 1.0
ND1 B:HIS518 4.2 26.1 1.0
CG B:HIS334 4.2 23.7 1.0
CG B:HIS364 4.3 28.5 1.0
CB B:ASP339 4.3 22.7 1.0
CD2 B:HIS334 4.4 22.5 1.0
CD B:PRO93 4.4 30.0 1.0
O B:GLN91 4.4 46.9 1.0
ZN B:ZN1566 4.7 25.1 1.0
CB B:PRO93 4.7 18.2 1.0
N B:PRO93 4.8 24.6 1.0
CB B:ALA371 4.8 26.9 1.0

Zinc binding site 6 out of 7 in 2w9m

Go back to Zinc Binding Sites List in 2w9m
Zinc binding site 6 out of 7 in the Structure of Family X Dna Polymerase From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Family X Dna Polymerase From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1566

b:25.1
occ:1.00
NE2 B:HIS334 2.2 20.6 1.0
OE1 B:GLU401 2.2 25.9 1.0
NE2 B:HIS332 2.3 28.9 1.0
OD1 B:ASP516 2.4 30.7 1.0
CE1 B:HIS334 3.0 28.3 1.0
CG B:ASP516 3.1 26.5 1.0
OD2 B:ASP516 3.1 31.4 1.0
CD B:GLU401 3.1 27.1 1.0
CE1 B:HIS332 3.2 23.3 1.0
ZN B:ZN1567 3.2 32.9 1.0
CD2 B:HIS334 3.2 22.5 1.0
CD2 B:HIS332 3.3 25.3 1.0
OE2 B:GLU401 3.5 24.3 1.0
CE1 B:HIS364 4.1 23.7 1.0
ND1 B:HIS334 4.2 25.0 1.0
ND1 B:HIS332 4.3 28.9 1.0
CG B:HIS334 4.3 23.7 1.0
CE1 B:HIS518 4.3 23.4 1.0
CG B:HIS332 4.3 25.1 1.0
O B:HOH2037 4.4 32.3 1.0
CG B:GLU401 4.4 18.1 1.0
CB B:ASP516 4.4 26.8 1.0
NE2 B:HIS364 4.6 28.6 1.0
NE2 B:HIS518 4.7 28.4 1.0
ZN B:ZN1565 4.7 28.8 1.0
CB B:GLU401 4.7 19.1 1.0
O B:ALA362 4.8 31.8 1.0
ND1 B:HIS364 4.9 28.0 1.0
NE2 B:HIS428 4.9 31.9 1.0
CA B:ASP516 4.9 20.9 1.0
NE2 B:HIS456 5.0 20.2 1.0

Zinc binding site 7 out of 7 in 2w9m

Go back to Zinc Binding Sites List in 2w9m
Zinc binding site 7 out of 7 in the Structure of Family X Dna Polymerase From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Family X Dna Polymerase From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1567

b:32.9
occ:1.00
OE2 B:GLU401 2.1 24.3 1.0
NE2 B:HIS456 2.4 20.2 1.0
NE2 B:HIS428 2.4 31.9 1.0
CE1 B:HIS428 2.6 31.4 1.0
CD B:GLU401 3.0 27.1 1.0
OE1 B:GLU401 3.1 25.9 1.0
ZN B:ZN1566 3.2 25.1 1.0
CD2 B:HIS456 3.3 26.3 1.0
CE1 B:HIS456 3.3 24.9 1.0
CD2 B:HIS428 3.7 38.6 1.0
ND1 B:HIS428 3.9 38.9 1.0
OD2 B:ASP516 3.9 31.4 1.0
O B:HOH2037 4.1 32.3 1.0
NE2 B:HIS332 4.3 28.9 1.0
CE1 B:HIS364 4.3 23.7 1.0
OG B:SER426 4.3 31.0 1.0
CB B:SER426 4.4 18.4 1.0
CG B:GLU401 4.4 18.1 1.0
CE1 B:HIS332 4.4 23.3 1.0
ND1 B:HIS456 4.5 24.3 1.0
CG B:HIS428 4.5 36.2 1.0
CG B:HIS456 4.5 22.8 1.0
NH2 B:ARG494 4.5 38.7 1.0
CG B:ASP516 4.8 26.5 1.0
CZ B:ARG494 4.8 29.1 1.0
OD1 B:ASP516 4.9 30.7 1.0
ND1 B:HIS364 4.9 28.0 1.0

Reference:

N.Leulliot, L.Cladiere, F.Lecointe, D.Durand, U.Hubscher, H.Van Tilbeurgh. The Family X Dna Polymerase From Deinococcus Radioduran Adopts A Non-Standard Extended Conformation. J.Biol.Chem. V. 284 11992 2009.
ISSN: ISSN 0021-9258
PubMed: 19251692
DOI: 10.1074/JBC.M809342200
Page generated: Wed Dec 16 03:57:07 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy