Calcium in PDB 1yqm: Catalytically Inactive Human 8-Oxoguanine Glycosylase Crosslinked to 7-Deazaguanine Containing Dna

The structure of Catalytically Inactive Human 8-Oxoguanine Glycosylase Crosslinked to 7-Deazaguanine Containing Dna, PDB code: 1yqm 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)	37.29 / 2.50
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.508, 92.508, 210.649, 90.00, 90.00, 120.00
R / Rfree (%)	21.2 / 26.1

The binding sites of Calcium atom in the Catalytically Inactive Human 8-Oxoguanine Glycosylase Crosslinked to 7-Deazaguanine Containing Dna (pdb code 1yqm). 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 7-Deazaguanine Containing Dna, PDB code: 1yqm:
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 7-Deazaguanine 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 7-Deazaguanine Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:76.3 occ:1.00 OP1 C:DG24 2.7 44.3 1.0 OP2 C:DG24 2.9 40.6 1.0 P C:DG24 3.2 42.9 1.0 C8 C:DA22 3.6 46.4 1.0 C2' C:DA22 3.9 48.5 1.0 O5' C:DG24 3.9 41.4 1.0 N7 C:DA22 4.1 46.9 1.0 CA A:CYS149 4.1 32.1 1.0 OP2 C:DA22 4.3 68.6 1.0 N9 C:DA22 4.4 48.5 1.0 O3' C:7GU23 4.6 39.1 1.0 O C:HOH206 4.7 37.6 1.0 CG2 A:VAL269 4.7 31.1 1.0 C A:CYS149 4.7 30.2 1.0 O5' C:DA22 4.7 65.4 1.0 N A:ASN150 4.8 29.2 1.0 C1' C:DA22 4.8 48.2 1.0 N A:CYS149 4.8 33.5 1.0 SG A:CYS149 4.9 39.0 1.0 CB A:CYS149 4.9 32.7 1.0 C5' C:DG24 4.9 39.5 1.0

Calcium binding site 2 out of 2 in the Catalytically Inactive Human 8-Oxoguanine Glycosylase Crosslinked to 7-Deazaguanine 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 7-Deazaguanine Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca328 b:60.3 occ:1.00 O A:CYS241 2.3 35.8 1.0 OP1 C:DC26 2.5 41.9 1.0 O A:VAL246 2.7 30.3 1.0 O A:LEU243 2.8 36.2 1.0 OP2 C:DC26 3.2 43.0 1.0 P C:DC26 3.3 39.6 1.0 C A:CYS241 3.4 35.9 1.0 C A:VAL246 3.6 29.1 1.0 C A:LEU243 3.7 34.5 1.0 N A:VAL246 3.8 27.4 1.0 CA A:CYS241 4.1 35.5 1.0 CA A:VAL246 4.1 28.8 1.0 C A:ILE242 4.2 36.1 1.0 O A:ILE242 4.3 37.0 1.0 N A:LEU243 4.3 36.0 1.0 N A:ILE242 4.4 37.1 1.0 O3' C:DT25 4.4 41.1 1.0 CB A:VAL246 4.4 27.9 1.0 N A:GLY245 4.4 32.9 1.0 O5' C:DC26 4.4 41.8 1.0 N A:PRO244 4.5 33.2 1.0 CA A:PRO244 4.6 33.3 1.0 CA A:LEU243 4.6 34.7 1.0 CA A:ILE242 4.6 37.1 1.0 N A:GLY247 4.7 30.0 1.0 CB A:CYS241 4.7 36.0 1.0 C A:PRO244 4.8 34.0 1.0 C A:GLY245 4.9 29.7 1.0 CA A:GLY247 5.0 29.1 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