Calcium in PDB 3m9n: Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion

All present enzymatic activity of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion:
2.7.7.7;

The structure of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion, PDB code: 3m9n was solved by J.H.Y.Wong, H.Ling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.60 / 1.93
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.227, 103.233, 52.259, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 26.1

The structure of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion also contains other interesting chemical elements:

Platinum

(Pt)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion (pdb code 3m9n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion, PDB code: 3m9n:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4001 b:23.5 occ:1.00 OP1 P:DC13 2.4 21.0 1.0 OE2 B:GLU106 2.5 22.6 1.0 OD2 B:ASP7 2.5 25.3 1.0 O B:HOH406 2.6 22.9 1.0 O B:HOH373 2.6 15.1 1.0 O B:HOH407 2.6 25.3 1.0 CD B:GLU106 3.3 23.6 1.0 CG B:ASP7 3.5 25.0 1.0 P P:DC13 3.7 23.8 1.0 CG B:GLU106 3.9 21.7 1.0 O5' P:DC13 4.0 22.7 1.0 NZ B:LYS159 4.0 26.9 1.0 OD1 B:ASP7 4.0 20.9 1.0 CE B:LYS152 4.1 29.4 1.0 O1A B:CTP2001 4.1 20.6 1.0 OE1 B:GLU106 4.1 24.2 1.0 C5' P:DC13 4.2 25.1 1.0 NZ B:LYS152 4.3 27.8 1.0 O P:HOH147 4.4 35.5 1.0 CZ B:PHE5 4.5 23.5 1.0 OP2 P:DC13 4.5 23.4 1.0 O B:HOH408 4.6 27.6 1.0 CB B:ASP7 4.7 21.7 1.0 O3' P:DG12 4.8 26.0 1.0 O B:HOH377 4.9 32.1 1.0 OD1 B:ASP105 4.9 19.5 1.0 CE2 B:PHE5 5.0 23.7 1.0 C3' P:DC13 5.0 26.2 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4002 b:33.1 occ:1.00 O B:ALA181 2.5 35.5 1.0 O B:ILE186 2.6 24.6 1.0 O P:HOH60 2.7 30.6 1.0 O B:HOH429 2.7 32.5 1.0 O B:HOH367 2.7 47.1 1.0 O P:HOH194 2.7 30.5 1.0 C B:ALA181 3.6 35.7 1.0 C B:ILE186 3.8 26.5 1.0 O B:HOH470 3.9 46.2 1.0 CA B:GLY187 4.3 26.7 1.0 CA B:ALA181 4.3 36.3 1.0 OP2 P:DG12 4.5 25.3 1.0 OP1 P:DG12 4.5 26.2 1.0 N B:GLY187 4.5 26.0 1.0 CB B:ALA181 4.5 37.6 1.0 N B:ASP182 4.6 34.4 1.0 C B:GLY187 4.6 28.7 1.0 CA B:ASP182 4.6 33.7 1.0 O B:GLY187 4.8 27.2 1.0 CA B:ILE186 4.8 25.9 1.0 CB B:ILE186 4.9 25.9 1.0 O B:VAL183 5.0 25.4 1.0 OD1 B:ASP182 5.0 38.8 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4003 b:21.6 occ:1.00 OD2 B:ASP105 2.4 20.9 1.0 O B:PHE8 2.4 18.3 1.0 OD1 B:ASP7 2.4 20.9 1.0 O2B B:CTP2001 2.5 23.5 1.0 O1A B:CTP2001 2.6 20.6 1.0 O1G B:CTP2001 2.7 38.3 1.0 PB B:CTP2001 3.5 25.7 1.0 CG B:ASP105 3.5 24.4 1.0 C B:PHE8 3.5 22.1 1.0 CG B:ASP7 3.6 25.0 1.0 O B:HOH373 3.6 15.1 1.0 PA B:CTP2001 3.7 22.2 1.0 PG B:CTP2001 3.8 42.0 1.0 O3B B:CTP2001 3.9 30.2 1.0 C5' B:CTP2001 4.0 23.6 1.0 O3A B:CTP2001 4.0 24.6 1.0 O B:HOH353 4.0 24.3 1.0 OD2 B:ASP7 4.1 25.3 1.0 N B:PHE8 4.1 20.4 1.0 OD1 B:ASP105 4.1 19.5 1.0 O5' B:CTP2001 4.2 21.8 1.0 CA B:PHE8 4.3 20.5 1.0 C B:ASP7 4.4 22.2 1.0 O B:HOH406 4.4 22.9 1.0 NZ B:LYS159 4.4 26.9 1.0 O3G B:CTP2001 4.4 35.2 1.0 N B:ASP9 4.5 21.6 1.0 N B:TYR10 4.6 20.4 1.0 CA B:ASP9 4.6 21.1 1.0 CB B:ASP105 4.6 21.0 1.0 N B:PHE11 4.7 21.2 1.0 O B:ASP7 4.7 22.2 1.0 C B:ASP9 4.7 21.1 1.0 CB B:ASP7 4.7 21.7 1.0 CB B:PHE11 4.8 20.0 1.0 CB B:PHE8 4.9 20.1 1.0 CA B:ASP7 4.9 21.8 1.0 O1B B:CTP2001 4.9 23.6 1.0

J.H.Wong, J.A.Brown, Z.Suo, P.Blum, T.Nohmi, H.Ling. Structural Insight Into Dynamic Bypass of the Major Cisplatin-Dna Adduct By Y-Family Polymerase DPO4. Embo J. V. 29 2059 2010.
ISSN: ISSN 0261-4189
PubMed: 20512114
DOI: 10.1038/EMBOJ.2010.101