Calcium in PDB 1yql: Catalytically Inactive HOGG1 Crosslinked with 7-Deaza-8- Azaguanine Containing Dna

The structure of Catalytically Inactive HOGG1 Crosslinked with 7-Deaza-8- Azaguanine Containing Dna, PDB code: 1yql 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)	39.98 / 2.60
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.322, 92.322, 210.744, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 26

The binding sites of Calcium atom in the Catalytically Inactive HOGG1 Crosslinked with 7-Deaza-8- Azaguanine Containing Dna (pdb code 1yql). 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 HOGG1 Crosslinked with 7-Deaza-8- Azaguanine Containing Dna, PDB code: 1yql:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Catalytically Inactive HOGG1 Crosslinked with 7-Deaza-8- Azaguanine 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 HOGG1 Crosslinked with 7-Deaza-8- Azaguanine Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:70.5 occ:1.00 OP1 C:DG24 2.7 36.1 1.0 P C:DG24 3.4 34.9 1.0 OP2 C:DG24 3.4 34.8 1.0 C8 C:DA22 3.6 37.7 1.0 O5' C:DG24 4.0 34.0 1.0 N7 C:DA22 4.0 37.6 1.0 CA A:CYS149 4.2 25.4 1.0 C2' C:DA22 4.3 41.2 1.0 OP2 C:DA22 4.4 67.8 1.0 N9 C:DA22 4.6 39.2 1.0 SG A:CYS149 4.7 29.2 1.0 CG2 A:VAL269 4.8 21.1 1.0 CB A:CYS149 4.8 25.8 1.0 N7 C:DG24 4.8 35.5 1.0 O C:HOH205 4.8 25.4 1.0 C8 C:DG24 4.8 34.5 1.0 N A:CYS149 4.8 25.6 1.0 C5' C:DG24 4.8 33.2 1.0 O A:HOH432 4.9 26.0 1.0 O C:HOH202 4.9 33.6 1.0 O3' C:PPW23 4.9 33.3 1.0 O5' C:DA22 5.0 64.0 1.0 C A:CYS149 5.0 25.4 1.0

Calcium binding site 2 out of 2 in the Catalytically Inactive HOGG1 Crosslinked with 7-Deaza-8- Azaguanine 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 HOGG1 Crosslinked with 7-Deaza-8- Azaguanine Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca328 b:49.5 occ:1.00 OP1 C:DC26 2.4 33.4 1.0 O A:CYS241 2.4 30.8 1.0 O A:LEU243 2.7 30.7 1.0 O A:VAL246 2.9 29.9 1.0 P C:DC26 3.3 32.4 1.0 OP2 C:DC26 3.4 34.6 1.0 C A:CYS241 3.4 30.3 1.0 C A:LEU243 3.7 29.4 1.0 C A:VAL246 3.7 29.2 1.0 O A:ILE242 3.9 31.4 1.0 N A:VAL246 3.9 30.3 1.0 C A:ILE242 3.9 31.3 1.0 CA A:CYS241 4.2 28.9 1.0 CA A:VAL246 4.3 29.3 1.0 N A:LEU243 4.3 31.3 1.0 N A:ILE242 4.3 32.3 1.0 O3' C:DT25 4.4 32.6 1.0 N A:GLY245 4.4 31.4 1.0 CA A:ILE242 4.5 32.2 1.0 N A:PRO244 4.5 28.7 1.0 O5' C:DC26 4.5 34.2 1.0 CB A:VAL246 4.5 27.8 1.0 CA A:PRO244 4.6 29.0 1.0 CA A:LEU243 4.6 30.7 1.0 N A:GLY247 4.7 29.5 1.0 C A:PRO244 4.8 30.4 1.0 CB A:CYS241 4.8 28.9 1.0 C A:GLY245 5.0 31.4 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