Cobalt in PDB 3khc: Crystal Structure of Escherichia Coli Alkb in Complex with Ssdna Containing A 1-Methylguanine Lesion

The structure of Crystal Structure of Escherichia Coli Alkb in Complex with Ssdna Containing A 1-Methylguanine Lesion, PDB code: 3khc was solved by T.Hollis, P.J.Holland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.74 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	147.809, 41.441, 85.622, 90.00, 120.98, 90.00
R / Rfree (%)	21.1 / 27.3

The binding sites of Cobalt atom in the Crystal Structure of Escherichia Coli Alkb in Complex with Ssdna Containing A 1-Methylguanine Lesion (pdb code 3khc). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of Escherichia Coli Alkb in Complex with Ssdna Containing A 1-Methylguanine Lesion, PDB code: 3khc:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of Escherichia Coli Alkb in Complex with Ssdna Containing A 1-Methylguanine Lesion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Escherichia Coli Alkb in Complex with Ssdna Containing A 1-Methylguanine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Co217 b:25.3 occ:1.00 O A:HOH245 2.0 3.2 1.0 NE2 A:HIS187 2.1 12.0 1.0 O2 A:AKG400 2.1 25.1 1.0 NE2 A:HIS131 2.2 9.0 1.0 OD1 A:ASP133 2.4 14.1 1.0 O5 A:AKG400 2.4 25.0 1.0 C1 A:AKG400 2.9 26.6 1.0 CE1 A:HIS187 3.0 10.4 1.0 C2 A:AKG400 3.0 25.5 1.0 CE1 A:HIS131 3.0 10.4 1.0 CG A:ASP133 3.1 13.6 1.0 CD2 A:HIS187 3.2 10.2 1.0 OD2 A:ASP133 3.2 10.1 1.0 CD2 A:HIS131 3.4 9.6 1.0 O1 A:AKG400 4.1 28.3 1.0 ND1 A:HIS187 4.1 9.4 1.0 ND1 A:HIS131 4.2 10.4 1.0 O A:HOH279 4.2 17.1 1.0 CG A:HIS187 4.2 10.2 1.0 CG A:HIS131 4.4 11.0 1.0 C3 A:AKG400 4.4 24.2 1.0 NH1 A:ARG210 4.4 15.1 1.0 CB A:ASP133 4.5 14.1 1.0 CZ2 A:TRP178 4.6 7.6 1.0 O A:HOH220 4.7 19.4 1.0 CD2 A:LEU128 4.9 13.2 1.0 N A:ASP133 4.9 13.8 1.0 C4 A:AKG400 5.0 23.2 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of Escherichia Coli Alkb in Complex with Ssdna Containing A 1-Methylguanine Lesion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Escherichia Coli Alkb in Complex with Ssdna Containing A 1-Methylguanine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ B:Co217 b:29.8 occ:1.00 O B:HOH260 1.9 10.0 1.0 O2 B:AKG401 2.1 24.3 1.0 NE2 B:HIS131 2.1 7.5 1.0 NE2 B:HIS187 2.1 13.5 1.0 OD1 B:ASP133 2.3 13.3 1.0 O5 B:AKG401 2.5 25.9 1.0 C1 B:AKG401 2.9 26.2 1.0 CE1 B:HIS131 3.0 7.1 1.0 C2 B:AKG401 3.1 26.8 1.0 CD2 B:HIS187 3.1 11.8 1.0 CE1 B:HIS187 3.1 12.8 1.0 CD2 B:HIS131 3.2 9.0 1.0 CG B:ASP133 3.2 12.6 1.0 OD2 B:ASP133 3.4 10.4 1.0 O1 B:AKG401 4.1 27.3 1.0 ND1 B:HIS131 4.1 7.3 1.0 ND1 B:HIS187 4.2 12.5 1.0 CG B:HIS187 4.2 13.1 1.0 NH2 B:ARG210 4.2 17.5 1.0 CG B:HIS131 4.2 10.0 1.0 O B:HOH224 4.5 21.1 1.0 C3 B:AKG401 4.5 27.7 1.0 N1 C:MG14 4.6 41.0 1.0 CM1 C:MG14 4.6 40.5 1.0 CB B:ASP133 4.6 13.1 1.0 C2 C:MG14 4.6 40.4 1.0 N2 C:MG14 4.7 40.2 1.0 CZ2 B:TRP178 4.7 5.0 1.0 N B:ASP133 4.8 13.2 1.0 CD2 B:LEU128 5.0 14.8 1.0

P.J.Holland, T.Hollis. Structural and Mutational Analysis of Escherichia Coli Alkb Provides Insight Into Substrate Specificity and Dna Damage Searching. Plos One V. 5 E8680 2010.
ISSN: ESSN 1932-6203
PubMed: 20084272
DOI: 10.1371/JOURNAL.PONE.0008680