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Mercury 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:

Zinc (Zn) 7 atoms

Mercury Binding Sites:

The binding sites of Mercury 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 Mercury atom.
In total 2 binding sites of Mercury where determined in the Structure of Family X Dna Polymerase From Deinococcus Radiodurans, PDB code: 2w9m:
Jump to Mercury binding site number: 1; 2;

Mercury binding site 1 out of 2 in 2w9m

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


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg 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:Hg1568

b:88.8
occ:0.54
SG A:CYS237 3.1 55.7 1.0
O A:GLY204 3.1 40.9 1.0
O A:CYS237 3.3 36.0 1.0
C A:CYS237 3.4 36.8 1.0
CD A:PRO206 3.4 35.8 1.0
CB A:CYS237 3.5 39.9 1.0
N A:ALA238 3.7 42.1 1.0
CA A:THR205 3.9 42.2 1.0
CA A:CYS237 3.9 32.0 1.0
CG A:PRO206 4.0 28.6 1.0
CA A:ALA238 4.1 33.2 1.0
N A:PRO206 4.1 44.4 1.0
C A:GLY204 4.2 38.8 1.0
C A:THR205 4.4 45.0 1.0
N A:CYS237 4.5 34.4 1.0
N A:THR205 4.5 40.2 1.0
C A:ALA238 4.8 41.1 1.0
CB A:THR205 4.9 51.9 1.0

Mercury binding site 2 out of 2 in 2w9m

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


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg 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
B:Hg1568

b:74.1
occ:0.53
O B:GLY204 3.0 35.2 1.0
O B:CYS237 3.2 29.6 1.0
C B:CYS237 3.2 29.9 1.0
SG B:CYS237 3.2 54.6 1.0
N B:ALA238 3.5 22.1 1.0
CB B:CYS237 3.5 37.3 1.0
CD B:PRO206 3.7 37.5 1.0
CA B:ALA238 3.8 28.3 1.0
CA B:CYS237 3.9 29.3 1.0
CA B:THR205 4.0 34.5 1.0
CA B:GLY222 4.1 46.1 1.0
C B:GLY204 4.1 35.2 1.0
CG B:PRO206 4.3 27.5 1.0
O B:GLY222 4.4 44.9 1.0
N B:PRO206 4.4 39.5 1.0
C B:ALA238 4.5 37.6 1.0
N B:CYS237 4.5 34.2 1.0
C B:THR205 4.6 39.6 1.0
N B:THR205 4.6 40.7 1.0
C B:GLY222 4.7 48.1 1.0
O B:HOH2011 4.9 47.0 1.0
CD B:PRO239 4.9 44.5 1.0
CB B:THR205 5.0 43.3 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 Oct 28 18:42:02 2020

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