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

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

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

Mercury

(Hg)

2 atoms

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 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 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 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 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 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 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 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

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