Platinum in PDB 5a39: Structure of RAD14 in Complex with Cisplatin Containing Dna

The structure of Structure of RAD14 in Complex with Cisplatin Containing Dna, PDB code: 5a39 was solved by S.C.Koch, J.Kuper, K.L.Gasteiger, N.Wichlein, R.Strasser, D.Eisen, S.Geiger, S.Schneider, C.Kisker, T.Carell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.42 / 2.80
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	54.421, 54.421, 130.773, 90.00, 90.00, 90.00
R / Rfree (%)	21.255 / 25.554

The structure of Structure of RAD14 in Complex with Cisplatin Containing Dna also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Platinum atom in the Structure of RAD14 in Complex with Cisplatin Containing Dna (pdb code 5a39). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 4 binding sites of Platinum where determined in the Structure of RAD14 in Complex with Cisplatin Containing Dna, PDB code: 5a39:
Jump to Platinum binding site number: 1; 2; 3; 4;

Platinum binding site 1 out of 4 in the Structure of RAD14 in Complex with Cisplatin Containing Dna


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Structure of RAD14 in Complex with Cisplatin Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Pt1015 b:44.4 occ:0.30 PT1 C:CPT1015 0.0 44.4 0.3 C7 C:DT10 1.0 59.2 0.2 C5 F:DC8 1.1 51.0 0.2 C4 F:DC9 1.8 48.5 0.2 N4 F:DC9 1.8 47.4 0.2 C4 F:DC8 1.9 49.0 0.2 C6 F:DC8 1.9 53.1 0.2 N7 C:DG9 2.0 75.0 0.3 N1 C:CPT1015 2.0 42.0 0.3 N7 C:DG8 2.0 76.5 0.3 N2 C:CPT1015 2.0 43.3 0.3 C5 C:DT10 2.2 58.0 0.2 C5 F:DC9 2.2 50.7 0.2 C5 H:DC6 2.3 43.9 0.3 N7 H:DG7 2.3 43.8 0.3 O6 H:DG7 2.3 40.2 0.3 C4 H:DC6 2.4 42.3 0.3 N7 C:DG9 2.5 84.4 0.2 N4 F:DC8 2.6 47.1 0.2 C6 H:DC6 2.6 45.4 0.3 N3 F:DC9 2.6 47.9 0.2 C8 C:DG9 2.7 83.6 0.2 C5 C:DG9 2.7 80.6 0.2 C5 H:DG7 2.8 42.5 0.3 C6 H:DG7 2.8 40.8 0.3 N3 H:DC6 2.8 42.3 0.3 N1 F:DC8 2.8 53.6 0.2 N3 F:DC8 2.8 49.5 0.2 N9 C:DG9 2.9 80.6 0.2 C4 C:DG9 2.9 80.1 0.2 C4 C:DT10 2.9 56.3 0.2 O4 C:DT10 2.9 55.5 0.2 N1 H:DC6 3.0 45.5 0.3 C5 C:DG9 3.0 72.1 0.3 C8 C:DG8 3.0 75.8 0.3 C8 C:DG9 3.0 73.8 0.3 N4 H:DC6 3.1 40.9 0.3 C5 C:DG8 3.1 73.5 0.3 C2 H:DC6 3.1 43.9 0.3 N1 C:CPT1016 3.1 50.1 0.2 C6 F:DC9 3.2 52.0 0.2 C2 F:DC8 3.2 51.9 0.2 C6 C:DT10 3.3 59.1 0.2 O6 C:DG9 3.4 69.9 0.3 C2 F:DC9 3.5 49.4 0.2 C8 H:DG7 3.5 45.1 0.3 O6 C:DG8 3.6 69.0 0.3 C6 C:DG9 3.6 77.5 0.2 C6 C:DG9 3.7 70.7 0.3 PT1 C:CPT1016 3.7 54.3 0.2 N1 F:DC9 3.7 51.4 0.2 N3 C:DG9 3.8 78.9 0.2 C6 C:DG8 3.8 71.0 0.3 C1' C:DG9 3.9 79.3 0.2 C2' C:DG9 3.9 78.6 0.2 C4 H:DG7 4.1 43.2 0.3 O2 H:DC6 4.1 44.4 0.3 C1' F:DC8 4.1 56.6 0.2 N4 C:DC11 4.1 58.0 0.2 N1 H:DG7 4.1 40.1 0.3 C1' H:DC6 4.1 47.4 0.3 O6 C:DG9 4.1 77.0 0.2 N9 C:DG9 4.2 70.9 0.3 N9 C:DG8 4.2 73.4 0.3 N3 C:DT10 4.2 55.9 0.2 C4 C:DG9 4.2 71.4 0.3 C2' H:DC6 4.2 48.2 0.3 O4 C:DT10 4.2 50.8 0.3 N1 C:DG9 4.3 76.5 0.2 C4 C:DG8 4.3 73.7 0.3 C2 C:DG9 4.3 77.2 0.2 C2' F:DC8 4.4 57.9 0.2 O6 F:DG10 4.4 46.8 0.2 O2 F:DC8 4.4 53.1 0.2 N9 H:DG7 4.4 44.9 0.3 C5 C:DC7 4.5 51.5 0.3 N1 C:DT10 4.5 58.7 0.2 O2 F:DC9 4.6 49.5 0.2 C7 C:DT10 4.6 53.4 0.3 N6 E:DA7 4.7 56.9 0.2 OP2 C:DG8 4.7 58.9 0.3 O6 E:DG6 4.8 56.6 0.2 O4 H:DT8 4.8 43.2 0.3 C4 C:DT10 4.8 51.6 0.3 C6 C:DC7 4.9 52.9 0.3 C4 C:DC11 4.9 58.0 0.2 N6 G:DA4 4.9 49.0 0.3 C2 C:DT10 4.9 57.0 0.2 N7 C:DG8 5.0 87.6 0.2 N1 C:DG9 5.0 70.7 0.3

Platinum binding site 2 out of 4 in the Structure of RAD14 in Complex with Cisplatin Containing Dna


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Structure of RAD14 in Complex with Cisplatin Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Pt1016 b:54.3 occ:0.20 PT1 C:CPT1016 0.0 54.3 0.2 N4 H:DC6 1.2 40.9 0.3 C5 C:DC7 1.2 51.5 0.3 C5 H:DC5 1.6 43.1 0.3 N4 F:DC8 1.7 47.1 0.2 C4 H:DC6 1.7 42.3 0.3 N7 C:DG8 2.0 87.6 0.2 N7 C:DG9 2.0 84.4 0.2 N2 C:CPT1016 2.0 50.3 0.2 N1 C:CPT1016 2.0 50.1 0.2 C4 F:DC8 2.1 49.0 0.2 C4 C:DC7 2.1 51.0 0.3 C5 H:DC6 2.2 43.9 0.3 N7 F:DA7 2.3 50.1 0.2 C4 H:DC5 2.3 42.1 0.3 N2 C:CPT1015 2.3 43.3 0.3 C6 C:DC7 2.4 52.9 0.3 N4 C:DC7 2.4 49.6 0.3 C6 H:DC5 2.6 45.0 0.3 N4 H:DC5 2.6 40.4 0.3 N3 F:DC8 2.6 49.5 0.2 C8 F:DA7 2.7 53.0 0.2 N3 H:DC6 2.9 42.3 0.3 C5 F:DC8 3.0 51.0 0.2 C5 C:DG9 3.0 80.6 0.2 C8 C:DG8 3.0 86.9 0.2 C5 C:DG8 3.0 84.3 0.2 C8 C:DG9 3.0 83.6 0.2 C5 F:DA7 3.1 50.3 0.2 O6 C:DG9 3.3 77.0 0.2 N3 C:DC7 3.4 51.9 0.3 O6 C:DG8 3.4 80.5 0.2 N3 H:DC5 3.4 43.3 0.3 O6 C:DG8 3.4 69.0 0.3 C6 H:DC6 3.4 45.4 0.3 N1 C:DC7 3.5 54.0 0.3 C6 C:DG9 3.6 77.5 0.2 N1 H:DC5 3.6 46.1 0.3 C6 C:DG8 3.6 81.3 0.2 N9 F:DA7 3.7 55.0 0.2 PT1 C:CPT1015 3.7 44.4 0.3 C6 C:DG8 3.7 71.0 0.3 C2 F:DC8 3.7 51.9 0.2 N7 C:DG8 3.7 76.5 0.3 C5 C:DG8 3.7 73.5 0.3 C4 F:DA7 3.8 53.4 0.2 C6 F:DA7 3.8 48.5 0.2 C2 H:DC6 3.9 43.9 0.3 C2 C:DC7 3.9 53.5 0.3 C6 F:DC8 3.9 53.1 0.2 C2 H:DC5 4.0 45.4 0.3 N6 F:DA7 4.0 45.8 0.2 N1 H:DC6 4.1 45.5 0.3 N9 C:DG8 4.2 83.9 0.2 N9 C:DG9 4.2 80.6 0.2 C4 C:DG9 4.2 80.1 0.2 C4 C:DG8 4.2 84.1 0.2 N4 F:DC9 4.2 47.4 0.2 N1 F:DC8 4.3 53.6 0.2 O6 H:DG7 4.4 40.2 0.3 OP2 H:DC5 4.5 46.1 0.3 N1 C:DG8 4.6 71.4 0.3 C2' F:DG6 4.6 54.8 0.2 C2' H:DA4 4.6 45.3 0.3 C8 F:DG6 4.6 48.5 0.2 O2 F:DC8 4.6 53.1 0.2 C8 C:DG8 4.7 75.8 0.3 N1 C:CPT1015 4.7 42.0 0.3 OP2 C:DG8 4.7 70.5 0.2 C7 C:DT10 4.7 59.2 0.2 C4 C:DG8 4.8 73.7 0.3 C8 H:DA4 4.8 41.7 0.3 C1' F:DA7 4.8 58.8 0.2 C1' C:DC7 4.8 55.9 0.3 C1' H:DC5 4.9 48.6 0.3 O6 D:DG9 4.9 77.5 0.2 N1 C:DG9 4.9 76.5 0.2 O5' H:DC5 4.9 48.4 0.3 N7 F:DG6 4.9 46.6 0.2 C2' F:DA7 4.9 59.8 0.2 N1 F:DA7 5.0 50.1 0.2 N1 C:DG8 5.0 80.9 0.2 OP2 C:DG8 5.0 58.9 0.3 O2 H:DC6 5.0 44.4 0.3 C2' C:DC7 5.0 64.3 0.2 N3 F:DA7 5.0 55.1 0.2

Platinum binding site 3 out of 4 in the Structure of RAD14 in Complex with Cisplatin Containing Dna


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Structure of RAD14 in Complex with Cisplatin Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Pt1015 b:44.1 occ:0.30 PT1 D:CPT1015 0.0 44.1 0.3 C5 E:DC8 0.9 59.8 0.2 C7 D:DT10 1.1 64.5 0.2 C5 G:DC6 1.4 46.2 0.3 C4 E:DC8 1.8 58.8 0.2 C5 E:DC9 1.9 60.1 0.2 C6 E:DC8 1.9 60.9 0.2 C5 D:DT10 1.9 63.9 0.2 N7 G:DG7 2.0 46.0 0.3 N7 D:DG8 2.0 88.7 0.3 N7 D:DG9 2.0 91.3 0.3 N2 D:CPT1015 2.0 41.8 0.3 N1 D:CPT1015 2.0 40.9 0.3 C4 E:DC9 2.0 59.0 0.2 C6 G:DC6 2.1 46.1 0.3 O4 D:DT10 2.2 61.6 0.2 N4 E:DC9 2.2 58.3 0.2 C4 D:DT10 2.3 62.3 0.2 N4 E:DC8 2.4 57.8 0.2 N7 D:DG9 2.4 83.2 0.2 C4 G:DC6 2.5 46.0 0.3 C8 D:DG9 2.5 82.8 0.2 O6 G:DG7 2.7 45.5 0.3 C5 G:DG7 2.7 45.8 0.3 C5 D:DG9 2.8 81.1 0.2 C6 E:DC9 2.9 60.9 0.2 N3 E:DC8 2.9 58.9 0.2 N9 D:DG9 2.9 81.1 0.2 C8 D:DG9 3.0 90.6 0.3 C6 G:DG7 3.0 45.6 0.3 N1 E:DC8 3.0 61.1 0.2 N4 G:DC6 3.0 46.1 0.3 C8 D:DG8 3.0 88.2 0.3 C5 D:DG8 3.0 85.5 0.3 N1 D:CPT1016 3.1 44.0 0.2 C4 D:DG9 3.1 81.2 0.2 C5 D:DG9 3.1 89.3 0.3 N3 E:DC9 3.1 58.7 0.2 C8 G:DG7 3.1 46.2 0.3 C6 D:DT10 3.2 65.1 0.2 N1 G:DC6 3.3 46.0 0.3 C2 E:DC8 3.4 60.1 0.2 O6 D:DG8 3.4 79.5 0.3 PT1 D:CPT1016 3.5 46.3 0.2 N3 G:DC6 3.5 46.1 0.3 O6 D:DG9 3.6 88.2 0.3 N3 D:DT10 3.7 62.0 0.2 C6 D:DG8 3.7 82.4 0.3 N1 E:DC9 3.7 60.6 0.2 C6 D:DG9 3.7 78.8 0.2 C2 E:DC9 3.8 59.5 0.2 N4 D:DC11 3.8 59.4 0.2 C6 D:DG9 3.8 88.1 0.3 C2 G:DC6 3.9 46.2 0.3 C1' D:DG9 3.9 80.4 0.2 C4 G:DG7 4.0 46.0 0.3 N3 D:DG9 4.0 81.8 0.2 N9 D:DG9 4.1 88.8 0.3 N9 G:DG7 4.2 46.2 0.3 N9 D:DG8 4.2 85.8 0.3 C2' D:DG9 4.2 80.0 0.2 O6 D:DG9 4.2 77.5 0.2 C4 D:DG9 4.2 89.4 0.3 C4 D:DG8 4.3 85.8 0.3 C1' E:DC8 4.3 62.6 0.2 N1 D:DT10 4.3 65.0 0.2 N1 G:DG7 4.4 45.8 0.3 C1' G:DC6 4.5 46.1 0.3 O4 D:DT10 4.5 70.4 0.3 OP2 G:DC6 4.5 48.7 0.3 N1 D:DG9 4.5 79.0 0.2 C2' E:DC8 4.6 63.3 0.2 C2 D:DT10 4.6 63.4 0.2 C2' G:DC6 4.6 46.0 0.3 O2 E:DC8 4.6 60.6 0.2 N6 F:DA7 4.6 45.8 0.2 C2 D:DG9 4.7 81.1 0.2 C4 D:DC11 4.7 60.2 0.2 C7 D:DT10 4.7 73.6 0.3 N7 D:DG8 4.8 80.8 0.2 O6 E:DG10 4.8 58.8 0.2 O2 E:DC9 4.9 59.6 0.2 O4 G:DT8 5.0 48.1 0.3 C5 D:DC11 5.0 61.9 0.2 O6 C:DG8 5.0 80.5 0.2 C4 D:DT10 5.0 71.9 0.3

Platinum binding site 4 out of 4 in the Structure of RAD14 in Complex with Cisplatin Containing Dna


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Structure of RAD14 in Complex with Cisplatin Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Pt1016 b:46.3 occ:0.20 PT1 D:CPT1016 0.0 46.3 0.2 N4 G:DC6 0.9 46.1 0.3 C4 G:DC6 1.8 46.0 0.3 C5 D:DC7 1.8 62.3 0.3 N7 D:DG8 2.0 80.8 0.2 C5 G:DC5 2.0 47.8 0.3 N7 D:DG9 2.0 83.2 0.2 N2 D:CPT1016 2.0 44.9 0.2 N2 D:CPT1015 2.0 41.8 0.3 N1 D:CPT1016 2.0 44.0 0.2 N4 E:DC8 2.1 57.8 0.2 C4 E:DC8 2.3 58.8 0.2 N7 E:DA7 2.4 59.3 0.2 C4 D:DC7 2.5 61.6 0.3 N3 G:DC6 2.6 46.1 0.3 N4 D:DC7 2.7 60.1 0.3 C5 G:DC6 2.7 46.2 0.3 C4 G:DC5 2.7 47.5 0.3 C6 G:DC5 2.7 48.4 0.3 C6 D:DC7 2.8 64.0 0.3 C8 E:DA7 2.8 60.8 0.2 C5 D:DG9 2.9 81.1 0.2 N3 E:DC8 2.9 58.9 0.2 C5 E:DC8 3.0 59.8 0.2 C8 D:DG8 3.0 80.3 0.2 C5 D:DG8 3.0 78.2 0.2 N4 G:DC5 3.1 47.0 0.3 O6 D:DG9 3.1 77.5 0.2 C8 D:DG9 3.1 82.8 0.2 O6 D:DG8 3.3 79.5 0.3 O6 D:DG8 3.3 74.6 0.2 C5 E:DA7 3.4 59.3 0.2 C6 D:DG9 3.4 78.8 0.2 PT1 D:CPT1015 3.5 44.1 0.3 C6 D:DG8 3.6 75.7 0.2 N3 D:DC7 3.6 62.8 0.3 C6 D:DG8 3.7 82.4 0.3 N3 G:DC5 3.8 48.0 0.3 N1 G:DC5 3.8 48.8 0.3 C2 G:DC6 3.8 46.2 0.3 N7 D:DG8 3.9 88.7 0.3 C6 G:DC6 3.9 46.1 0.3 N1 D:DC7 3.9 65.4 0.3 C2 E:DC8 3.9 60.1 0.2 C6 E:DC8 3.9 60.9 0.2 C5 D:DG8 3.9 85.5 0.3 N9 E:DA7 3.9 61.7 0.2 N9 D:DG8 4.1 78.0 0.2 C6 E:DA7 4.2 58.2 0.2 C4 D:DG9 4.2 81.2 0.2 C4 E:DA7 4.2 60.8 0.2 N1 D:CPT1015 4.2 40.9 0.3 C4 D:DG8 4.2 78.3 0.2 C2 G:DC5 4.2 48.7 0.3 C2 D:DC7 4.2 64.7 0.3 N9 D:DG9 4.2 81.1 0.2 N6 E:DA7 4.2 56.9 0.2 N1 E:DC8 4.3 61.1 0.2 O6 G:DG7 4.3 45.5 0.3 C7 D:DT10 4.3 64.5 0.2 N1 G:DC6 4.3 46.0 0.3 N4 E:DC9 4.4 58.3 0.2 O4 D:DT10 4.4 61.6 0.2 C2' E:DG6 4.5 61.5 0.2 C2' G:DA4 4.6 50.9 0.3 OP2 G:DC6 4.6 48.7 0.3 O6 C:DG9 4.7 77.0 0.2 N1 D:DG8 4.7 82.6 0.3 C8 E:DG6 4.7 58.3 0.2 OP2 D:DC7 4.7 61.4 0.3 N1 D:DG9 4.8 79.0 0.2 O2 E:DC8 4.8 60.6 0.2 O2 G:DC6 4.8 46.5 0.3 C8 D:DG8 4.9 88.2 0.3 C8 G:DA4 4.9 49.1 0.3 OP2 D:DG8 4.9 62.4 0.2 N1 D:DG8 4.9 75.7 0.2 C1' G:DC5 4.9 49.6 0.3 OP2 G:DC5 4.9 51.7 0.3 C2' G:DC5 4.9 49.0 0.3

S.C.Koch, J.Kuper, K.L.Gasteiger, N.Simon, R.Strasser, D.Eisen, S.Geiger, S.Schneider, C.Kisker, T.Carell. Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesion By RAD14 (Xpa). Proc.Natl.Acad.Sci.Usa V. 112 8272 2015.
ISSN: ISSN 0027-8424
PubMed: 26100901
DOI: 10.1073/PNAS.1508509112