Zinc in PDB 2r6f: Crystal Structure of Bacillus Stearothermophilus Uvra

The structure of Crystal Structure of Bacillus Stearothermophilus Uvra, PDB code: 2r6f was solved by Y.Inuzuka, D.Pakotiprapha, B.R.Bowman, D.Jeruzalmi, G.L.Verdine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	102.713, 94.720, 130.481, 90.00, 108.80, 90.00
R / Rfree (%)	25.3 / 29.2

The binding sites of Zinc atom in the Crystal Structure of Bacillus Stearothermophilus Uvra (pdb code 2r6f). 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 Bacillus Stearothermophilus Uvra, PDB code: 2r6f:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Bacillus Stearothermophilus Uvra


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 Bacillus Stearothermophilus Uvra within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:96.3 occ:1.00 SG A:CYS250 2.1 0.5 1.0 ND1 A:HIS123 2.3 0.3 1.0 SG A:CYS120 2.4 0.8 1.0 SG A:CYS253 2.6 0.8 1.0 CB A:CYS250 3.0 0.5 1.0 CE1 A:HIS123 3.2 0.0 1.0 CG A:HIS123 3.2 0.6 1.0 CB A:CYS120 3.4 0.2 1.0 CB A:HIS123 3.5 0.7 1.0 CB A:CYS253 3.7 0.1 1.0 N A:CYS253 3.9 0.3 1.0 N A:HIS123 4.2 0.7 1.0 NE2 A:HIS123 4.2 0.5 1.0 CD2 A:HIS123 4.3 0.7 1.0 CA A:CYS253 4.4 0.3 1.0 C A:TYR252 4.4 0.3 1.0 CA A:CYS250 4.4 0.1 1.0 CA A:HIS123 4.5 0.0 1.0 CB A:THR122 4.6 0.3 1.0 CB A:TYR252 4.6 0.0 1.0 N A:TYR252 4.7 0.3 1.0 CA A:TYR252 4.7 0.9 1.0 C A:CYS250 4.8 0.9 1.0 CA A:CYS120 4.8 0.8 1.0 CG2 A:THR122 4.9 0.6 1.0 CB A:PHE255 5.0 0.3 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Bacillus Stearothermophilus Uvra


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 Bacillus Stearothermophilus Uvra within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:92.2 occ:1.00 SG A:CYS404 2.3 95.2 1.0 SG A:CYS407 2.3 89.5 1.0 SG A:CYS277 2.4 94.0 1.0 SG A:CYS274 2.4 97.3 1.0 CB A:CYS404 3.1 92.2 1.0 CB A:CYS274 3.2 95.0 1.0 CB A:CYS407 3.3 91.4 1.0 CB A:CYS277 3.3 95.4 1.0 N A:CYS407 3.8 94.8 1.0 N A:CYS277 4.0 99.4 1.0 CA A:CYS407 4.2 93.0 1.0 CA A:CYS277 4.3 97.2 1.0 CB A:THR406 4.3 100.0 1.0 C A:ASP276 4.6 0.5 1.0 CA A:CYS404 4.6 92.7 1.0 CA A:CYS274 4.7 96.3 1.0 C A:THR406 4.7 97.6 1.0 O A:CYS404 4.8 93.5 1.0 CA A:GLY281 4.8 87.8 1.0 C A:CYS404 4.9 94.2 1.0 CB A:ASP276 4.9 0.9 1.0 OG1 A:THR406 4.9 0.6 1.0 CA A:THR406 4.9 99.5 1.0 N A:GLY281 4.9 87.9 1.0 N A:THR406 5.0 98.6 1.0 CA A:ARG411 5.0 82.5 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Bacillus Stearothermophilus Uvra


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 Bacillus Stearothermophilus Uvra within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1006 b:89.7 occ:1.00 SG A:CYS739 2.3 0.6 1.0 SG A:CYS736 2.4 0.9 1.0 SG A:CYS759 2.4 0.7 1.0 SG A:CYS762 2.4 0.9 1.0 CB A:CYS759 3.1 1.0 1.0 CB A:CYS736 3.1 0.8 1.0 CB A:CYS762 3.3 0.6 1.0 CB A:CYS739 3.3 0.0 1.0 N A:CYS739 3.7 0.1 1.0 N A:CYS762 3.9 0.7 1.0 CA A:CYS739 4.2 0.2 1.0 CA A:CYS762 4.2 0.8 1.0 CB A:ALA738 4.2 0.4 1.0 CA A:GLY743 4.5 97.7 1.0 CA A:CYS736 4.5 0.1 1.0 CA A:CYS759 4.6 0.0 1.0 O A:CYS736 4.6 0.3 1.0 O A:GLY743 4.6 97.5 1.0 C A:ALA738 4.6 0.3 1.0 C A:CYS736 4.7 0.6 1.0 N A:GLY743 4.7 97.8 1.0 CA A:ALA738 4.8 0.5 1.0 C A:GLY743 4.8 96.8 1.0 CB A:VAL761 4.9 1.0 1.0 C A:VAL761 4.9 0.8 1.0 N A:ALA738 4.9 0.7 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Bacillus Stearothermophilus Uvra


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 Bacillus Stearothermophilus Uvra within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1007 b:94.5 occ:1.00 ND1 B:HIS123 2.2 0.6 1.0 SG B:CYS120 2.2 0.0 1.0 SG B:CYS250 2.3 84.1 1.0 SG B:CYS253 2.4 85.3 1.0 CE1 B:HIS123 3.1 0.1 1.0 CG B:HIS123 3.3 0.3 1.0 CB B:CYS250 3.3 84.0 1.0 CB B:CYS120 3.5 0.2 1.0 CB B:CYS253 3.6 85.2 1.0 CB B:HIS123 3.6 0.8 1.0 N B:CYS253 4.1 85.0 1.0 NE2 B:HIS123 4.2 0.4 1.0 N B:HIS123 4.3 0.5 1.0 CD2 B:HIS123 4.3 0.7 1.0 CA B:CYS253 4.4 85.1 1.0 CB B:THR122 4.4 0.6 1.0 C B:TYR252 4.6 84.9 1.0 CA B:HIS123 4.6 0.2 1.0 CA B:CYS250 4.7 84.0 1.0 CB B:PHE255 4.7 85.2 1.0 CA B:CYS120 4.8 0.2 1.0 CB B:TYR252 4.9 84.7 1.0 N B:TYR252 5.0 84.5 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Bacillus Stearothermophilus Uvra


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 Bacillus Stearothermophilus Uvra within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1008 b:0.1 occ:1.00 SG B:CYS277 2.1 98.9 1.0 SG B:CYS407 2.3 95.3 1.0 SG B:CYS274 2.4 0.5 1.0 SG B:CYS404 2.7 0.5 1.0 CB B:CYS407 3.2 96.0 1.0 CB B:CYS277 3.2 0.2 1.0 CB B:CYS274 3.3 98.4 1.0 CB B:CYS404 3.5 0.0 1.0 N B:CYS407 3.8 99.9 1.0 CA B:CYS407 4.1 97.4 1.0 N B:CYS277 4.2 0.1 1.0 C B:ASP276 4.3 0.8 1.0 CA B:CYS277 4.3 0.2 1.0 O B:ASP276 4.4 0.9 1.0 CA B:CYS274 4.6 99.7 1.0 O B:GLY281 4.7 95.6 1.0 CA B:GLY281 4.7 92.9 1.0 CB B:THR406 4.8 1.0 1.0 N B:GLY281 4.8 93.1 1.0 N B:ASP276 4.9 0.1 1.0 C B:CYS274 4.9 0.8 1.0 CA B:ASP276 4.9 1.0 1.0 CA B:CYS404 4.9 0.9 1.0 CA B:ARG411 5.0 87.2 1.0 CB B:ASP276 5.0 0.1 1.0 C B:THR406 5.0 0.2 1.0 O B:CYS274 5.0 0.4 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Bacillus Stearothermophilus Uvra


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 Bacillus Stearothermophilus Uvra within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1009 b:99.4 occ:1.00 SG B:CYS736 2.1 0.1 1.0 SG B:CYS762 2.4 0.2 1.0 SG B:CYS739 2.5 0.8 1.0 SG B:CYS759 2.7 0.1 1.0 CB B:CYS736 2.7 0.2 1.0 CB B:CYS759 3.4 0.8 1.0 CB B:CYS739 3.4 0.9 1.0 CB B:CYS762 3.5 0.5 1.0 N B:CYS739 3.9 1.0 1.0 CA B:CYS736 4.1 0.7 1.0 N B:CYS762 4.2 0.6 1.0 CA B:GLY743 4.2 0.2 1.0 O B:CYS736 4.3 0.1 1.0 CA B:CYS739 4.3 0.4 1.0 CA B:CYS762 4.5 0.5 1.0 C B:CYS736 4.5 0.9 1.0 N B:GLY743 4.6 0.6 1.0 CB B:ALA738 4.7 0.4 1.0 CA B:CYS759 4.8 0.3 1.0 O B:CYS759 4.9 0.6 1.0 C B:ALA738 4.9 0.8 1.0 O B:GLY743 4.9 0.7 1.0 C B:GLY743 4.9 0.6 1.0

D.Pakotiprapha, Y.Inuzuka, B.R.Bowman, G.F.Moolenaar, N.Goosen, D.Jeruzalmi, G.L.Verdine. Crystal Structure of Bacillus Stearothermophilus Uvra Provides Insight Into Atp-Modulated Dimerization, Uvrb Interaction, and Dna Binding. Mol.Cell V. 29 122 2008.
ISSN: ISSN 1097-2765
PubMed: 18158267
DOI: 10.1016/J.MOLCEL.2007.10.026