Zinc in PDB 2vf7: Crystal Structure of UVRA2 From Deinococcus Radiodurans

The structure of Crystal Structure of UVRA2 From Deinococcus Radiodurans, PDB code: 2vf7 was solved by J.Timmins, E.Gordon, S.Caria, G.Leonard, M.S.Kuo, V.Monchois, S.Mcsweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	271.710, 111.670, 103.290, 90.00, 100.80, 90.00
R / Rfree (%)	21.9 / 29.5

The structure of Crystal Structure of UVRA2 From Deinococcus Radiodurans also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of UVRA2 From Deinococcus Radiodurans (pdb code 2vf7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of UVRA2 From Deinococcus Radiodurans, PDB code: 2vf7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of UVRA2 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 Crystal Structure of UVRA2 From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:59.2 occ:0.50 SG A:CYS290 2.0 66.5 1.0 SG A:CYS287 2.1 62.8 1.0 SG A:CYS154 2.3 66.4 1.0 SG A:CYS151 2.4 65.3 1.0 CB A:CYS151 3.2 65.9 1.0 CB A:CYS287 3.2 63.8 1.0 CB A:CYS154 3.4 66.5 1.0 CB A:CYS290 3.7 66.7 1.0 N A:CYS154 3.8 66.9 1.0 N A:CYS290 4.0 66.5 1.0 CB A:GLU153 4.2 67.2 1.0 CA A:CYS154 4.3 66.6 1.0 CA A:CYS290 4.3 66.8 1.0 O A:CYS290 4.4 67.5 1.0 CA A:CYS151 4.6 66.0 1.0 CA A:CYS287 4.6 63.8 1.0 CA A:GLY158 4.7 64.2 1.0 C A:GLU153 4.7 67.1 1.0 O A:LYS293 4.7 67.7 1.0 C A:LEU289 4.8 65.9 1.0 N A:GLY158 4.8 64.7 1.0 O A:ARG294 4.8 67.0 1.0 C A:CYS290 4.8 67.3 1.0 C A:ARG294 4.8 67.1 1.0 CB A:LEU289 4.8 65.6 1.0 O A:CYS151 4.9 66.3 1.0 CA A:GLU153 4.9 67.3 1.0 C A:CYS151 4.9 66.3 1.0 CA A:ARG294 4.9 67.0 1.0 N A:GLU153 4.9 67.2 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of UVRA2 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 Crystal Structure of UVRA2 From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn904 b:55.9 occ:1.00 SG A:CYS667 2.3 56.1 1.0 SG A:CYS644 2.3 58.6 1.0 SG A:CYS664 2.4 57.6 1.0 SG A:CYS641 2.5 54.0 1.0 CB A:CYS664 3.1 57.1 1.0 CB A:CYS641 3.2 54.1 1.0 CB A:CYS667 3.3 57.6 1.0 CB A:CYS644 3.4 55.6 1.0 N A:CYS667 3.6 57.6 1.0 N A:CYS644 4.0 56.0 1.0 CA A:CYS667 4.0 57.9 1.0 CA A:CYS644 4.4 56.3 1.0 CA A:CYS641 4.6 54.2 1.0 CA A:CYS664 4.6 57.3 1.0 C A:VAL666 4.7 57.1 1.0 CB A:VAL666 4.7 56.5 1.0 CB A:HIS643 4.7 55.5 1.0 CA A:GLY648 4.7 58.4 1.0 O A:CYS641 4.8 54.7 1.0 C A:CYS641 4.8 54.4 1.0 C A:CYS667 4.8 58.4 1.0 N A:HIS668 4.9 58.6 1.0 C A:HIS643 4.9 55.7 1.0 N A:GLY648 4.9 57.8 1.0 CA A:ARG671 5.0 57.2 1.0 N A:VAL666 5.0 57.1 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of UVRA2 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 Crystal Structure of UVRA2 From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn903 b:71.0 occ:1.00 SG B:CYS154 2.2 65.6 1.0 SG B:CYS290 2.4 65.0 1.0 SG B:CYS287 2.4 68.6 1.0 SG B:CYS151 2.5 64.7 1.0 CB B:CYS154 3.1 66.6 1.0 CB B:CYS287 3.3 67.3 1.0 CB B:CYS151 3.3 65.5 1.0 CB B:CYS290 3.6 66.4 1.0 N B:CYS154 3.7 67.2 1.0 CA B:CYS154 4.0 66.7 1.0 N B:CYS290 4.1 67.0 1.0 CA B:CYS290 4.4 66.4 1.0 CG B:GLU153 4.5 69.0 1.0 CA B:GLY158 4.6 64.1 1.0 O B:LYS293 4.6 64.1 1.0 CA B:CYS151 4.7 65.5 1.0 N B:GLY158 4.7 64.3 1.0 CA B:CYS287 4.7 67.5 1.0 O B:CYS151 4.7 66.1 1.0 C B:GLU153 4.8 67.9 1.0 O B:HOH1159 4.8 56.1 1.0 C B:CYS151 4.8 66.2 1.0 C B:CYS154 4.9 66.8 1.0 C B:GLY158 4.9 63.9 1.0 N B:GLU153 4.9 67.6 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of UVRA2 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 Crystal Structure of UVRA2 From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn904 b:59.8 occ:0.35 SG B:CYS641 2.0 54.6 1.0 SG B:CYS664 2.3 60.5 1.0 SG B:CYS644 2.3 57.4 1.0 SG B:CYS667 2.5 59.6 1.0 CB B:CYS641 3.0 55.3 1.0 CB B:CYS667 3.2 61.0 1.0 CB B:CYS664 3.3 60.9 1.0 CB B:CYS644 3.5 57.4 1.0 N B:CYS667 3.5 61.0 1.0 N B:CYS644 3.8 57.0 1.0 CA B:CYS667 3.9 61.1 1.0 CA B:CYS644 4.3 57.2 1.0 CA B:CYS641 4.4 55.4 1.0 CB B:HIS643 4.4 56.8 1.0 N B:HIS643 4.5 56.7 1.0 CB B:VAL666 4.6 60.6 1.0 C B:CYS641 4.6 55.7 1.0 C B:VAL666 4.6 60.8 1.0 C B:HIS643 4.7 56.9 1.0 CA B:GLY648 4.7 59.7 1.0 CA B:CYS664 4.8 60.9 1.0 CA B:HIS643 4.8 56.8 1.0 C B:CYS667 4.8 61.5 1.0 N B:VAL666 4.9 60.6 1.0 CA B:VAL666 4.9 60.6 1.0 N B:GLU642 4.9 56.1 1.0 N B:GLY648 5.0 59.6 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of UVRA2 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 Crystal Structure of UVRA2 From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn903 b:70.5 occ:0.40 SG C:CYS290 2.3 61.0 1.0 SG C:CYS151 2.3 65.3 1.0 SG C:CYS287 2.5 65.8 1.0 SG C:CYS154 2.6 65.7 1.0 CB C:CYS287 3.2 65.8 1.0 CB C:CYS290 3.3 60.5 1.0 CB C:CYS154 3.6 66.9 1.0 CB C:CYS151 3.9 65.8 1.0 N C:CYS154 4.1 67.1 1.0 N C:CYS290 4.1 61.0 1.0 CA C:CYS290 4.3 60.5 1.0 CA C:GLY158 4.4 64.5 1.0 CA C:CYS154 4.5 67.0 1.0 CB C:GLU153 4.6 67.4 1.0 N C:GLY158 4.6 64.7 1.0 C C:GLY158 4.6 64.3 1.0 CA C:CYS287 4.6 65.8 1.0 O C:GLY158 5.0 64.2 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of UVRA2 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 Crystal Structure of UVRA2 From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn904 b:66.2 occ:0.80 SG C:CYS667 2.3 55.9 1.0 SG C:CYS641 2.3 57.9 1.0 SG C:CYS644 2.6 60.4 1.0 SG C:CYS664 2.7 54.0 1.0 CB C:CYS641 3.2 57.5 1.0 CB C:CYS667 3.2 57.1 1.0 CB C:CYS664 3.3 55.3 1.0 CB C:CYS644 3.4 59.0 1.0 N C:CYS667 3.6 57.0 1.0 N C:CYS644 3.8 59.0 1.0 CA C:CYS667 4.0 57.3 1.0 CA C:CYS644 4.2 59.3 1.0 CA C:CYS641 4.5 57.6 1.0 O C:CYS641 4.6 58.3 1.0 CB C:VAL666 4.7 56.5 1.0 CB C:HIS643 4.7 58.6 1.0 C C:VAL666 4.7 56.6 1.0 C C:CYS641 4.8 58.0 1.0 CA C:GLY648 4.8 59.1 1.0 CA C:CYS664 4.8 55.2 1.0 CA C:ARG671 4.8 58.4 1.0 N C:ARG671 4.9 58.5 1.0 N C:HIS668 4.9 58.2 1.0 N C:GLY648 4.9 58.9 1.0 C C:HIS643 4.9 58.8 1.0 C C:CYS667 4.9 57.9 1.0 C C:CYS644 5.0 59.4 1.0 N C:HIS643 5.0 58.9 1.0 N C:GLN645 5.0 59.5 1.0 CA C:VAL666 5.0 56.5 1.0

J.Timmins, E.Gordon, S.Caria, G.Leonard, S.Acajjaoui, M.S.Kuo, V.Monchois, S.Mcsweeney. Structural and Mutational Analyses of Deinococcus Radiodurans UVRA2 Provide Insight Into Dna Binding and Damage Recognition By Uvras. Structure V. 17 547 2009.
ISSN: ISSN 0969-2126
PubMed: 19368888
DOI: 10.1016/J.STR.2009.02.008