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Platinum in PDB 1ckt: Crystal Structure of HMG1 Domain A Bound to A Cisplatin-Modified Dna Duplex

Protein crystallography data

The structure of Crystal Structure of HMG1 Domain A Bound to A Cisplatin-Modified Dna Duplex, PDB code: 1ckt was solved by U.-M.Ohndorf, M.A.Rould, C.O.Pabo, S.J.Lippard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.210, 50.410, 53.130, 90.00, 99.82, 90.00
R / Rfree (%) 23.8 / 23.9

Other elements in 1ckt:

The structure of Crystal Structure of HMG1 Domain A Bound to A Cisplatin-Modified Dna Duplex also contains other interesting chemical elements:

Iodine (I) 1 atom

Platinum Binding Sites:

The binding sites of Platinum atom in the Crystal Structure of HMG1 Domain A Bound to A Cisplatin-Modified Dna Duplex (pdb code 1ckt). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total only one binding site of Platinum was determined in the Crystal Structure of HMG1 Domain A Bound to A Cisplatin-Modified Dna Duplex, PDB code: 1ckt:

Platinum binding site 1 out of 1 in 1ckt

Go back to Platinum Binding Sites List in 1ckt
Platinum binding site 1 out of 1 in the Crystal Structure of HMG1 Domain A Bound to A Cisplatin-Modified Dna Duplex


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Crystal Structure of HMG1 Domain A Bound to A Cisplatin-Modified Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt99

b:29.9
occ:1.00
PT1 B:CPT99 0.0 29.9 1.0
N7 B:DG109 1.9 30.2 1.0
N7 B:DG108 1.9 20.9 1.0
N1 B:CPT99 2.0 2.0 1.0
N2 B:CPT99 2.0 4.3 1.0
C8 B:DG108 2.6 24.8 1.0
C8 B:DG109 2.7 32.0 1.0
C5 B:DG109 3.1 32.7 1.0
C5 B:DG108 3.2 25.9 1.0
O6 B:DG109 3.7 35.9 1.0
C6 B:DG109 3.8 32.2 1.0
N9 B:DG108 3.9 26.4 1.0
C6 B:DG108 3.9 26.0 1.0
O6 B:DG108 4.0 26.4 1.0
O B:HOH374 4.0 30.8 1.0
N9 B:DG109 4.0 30.8 1.0
C4 B:DG109 4.2 31.7 1.0
C4 B:DG108 4.2 26.4 1.0
OP2 B:DG108 4.4 28.8 1.0
O C:HOH311 4.5 26.6 1.0
O B:HOH334 4.5 37.5 1.0
O B:HOH305 4.6 31.4 1.0

Reference:

U.M.Ohndorf, M.A.Rould, Q.He, C.O.Pabo, S.J.Lippard. Basis For Recognition of Cisplatin-Modified Dna By High-Mobility-Group Proteins. Nature V. 399 708 1999.
ISSN: ISSN 0028-0836
PubMed: 10385126
DOI: 10.1038/21460
Page generated: Wed Dec 16 02:03:34 2020

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