Calcium in PDB 1yqr: Catalytically Inactive Human 8-Oxoguanine Glycosylase Crosslinked to Oxog Containing Dna

The structure of Catalytically Inactive Human 8-Oxoguanine Glycosylase Crosslinked to Oxog Containing Dna, PDB code: 1yqr was solved by A.Banerjee, W.Yang, M.Karplus, G.L.Verdine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.31 / 2.43
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.106, 92.106, 211.060, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 25.1

The binding sites of Calcium atom in the Catalytically Inactive Human 8-Oxoguanine Glycosylase Crosslinked to Oxog Containing Dna (pdb code 1yqr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Catalytically Inactive Human 8-Oxoguanine Glycosylase Crosslinked to Oxog Containing Dna, PDB code: 1yqr:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Catalytically Inactive Human 8-Oxoguanine Glycosylase Crosslinked to Oxog Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Catalytically Inactive Human 8-Oxoguanine Glycosylase Crosslinked to Oxog Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:74.2 occ:1.00 OP1 C:DG24 3.1 33.8 1.0 O C:HOH130 3.4 41.2 1.0 OP2 C:DG24 3.7 31.1 1.0 P C:DG24 3.8 29.1 1.0 C8 C:DA22 4.0 39.1 1.0 CG2 A:VAL269 4.1 24.0 1.0 O5' C:DG24 4.3 32.1 1.0 N7 C:DA22 4.4 39.1 1.0 CA A:CYS149 4.5 31.7 1.0 N7 C:DG24 4.6 33.7 1.0 C8 C:DG24 4.7 32.9 1.0 O A:HOH447 4.7 27.9 1.0 C2' C:DA22 4.8 39.3 1.0 O A:HOH448 4.9 35.3 1.0 SG A:CYS149 4.9 39.4 1.0 CB A:CYS149 5.0 32.6 1.0

Calcium binding site 2 out of 2 in the Catalytically Inactive Human 8-Oxoguanine Glycosylase Crosslinked to Oxog Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Catalytically Inactive Human 8-Oxoguanine Glycosylase Crosslinked to Oxog Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca328 b:69.5 occ:1.00 O A:CYS241 2.2 35.9 1.0 OP1 C:DC26 2.4 38.0 1.0 O A:VAL246 2.8 32.8 1.0 O A:LEU243 2.8 34.8 1.0 OP2 C:DC26 3.3 39.9 1.0 P C:DC26 3.3 38.7 1.0 C A:CYS241 3.3 35.9 1.0 O A:ILE242 3.7 37.2 1.0 C A:VAL246 3.7 33.1 1.0 C A:LEU243 3.8 33.6 1.0 C A:ILE242 3.9 37.5 1.0 N A:VAL246 4.1 30.4 1.0 CA A:CYS241 4.1 35.3 1.0 N A:ILE242 4.2 36.8 1.0 CA A:ILE242 4.3 38.5 1.0 CA A:VAL246 4.3 31.6 1.0 N A:LEU243 4.3 36.3 1.0 O3' C:DT25 4.3 39.4 1.0 O5' C:DC26 4.5 40.8 1.0 N A:GLY245 4.6 32.4 1.0 CB A:VAL246 4.6 30.2 1.0 N A:PRO244 4.7 32.7 1.0 CA A:PRO244 4.7 32.1 1.0 CA A:LEU243 4.7 35.0 1.0 N A:GLY247 4.7 34.4 1.0 CB A:CYS241 4.8 36.7 1.0 C A:PRO244 4.9 33.1 1.0 O A:LEU240 5.0 35.7 1.0

A.Banerjee, W.Yang, M.Karplus, G.L.Verdine. Structure of A Repair Enzyme Interrogating Undamaged Dna Elucidates Recognition of Damaged Dna. Nature V. 434 612 2005.
ISSN: ISSN 0028-0836
PubMed: 15800616
DOI: 10.1038/NATURE03458