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Iodine 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:

Platinum (Pt) 1 atom

Iodine Binding Sites:

The binding sites of Iodine 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 Iodine atom.
In total only one binding site of Iodine was determined in the Crystal Structure of HMG1 Domain A Bound to A Cisplatin-Modified Dna Duplex, PDB code: 1ckt:

Iodine binding site 1 out of 1 in 1ckt

Go back to Iodine Binding Sites List in 1ckt
Iodine 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 Iodine with other atoms in the I 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:I103

b:64.8
occ:1.00
I5 B:5IU103 0.0 64.8 1.0
C5 B:5IU103 2.2 54.9 1.0
C6 B:5IU103 3.0 54.5 1.0
C4 B:5IU103 3.0 54.3 1.0
O4 B:5IU103 3.3 54.1 1.0
C2' B:DC102 3.7 51.2 1.0
OP2 B:5IU103 3.9 57.0 1.0
C6 B:DC102 4.0 42.2 1.0
N1 B:DC102 4.1 42.8 1.0
C5 B:DC102 4.2 41.0 1.0
N3 B:5IU103 4.3 51.6 1.0
N1 B:5IU103 4.3 54.9 1.0
C2 B:DC102 4.3 41.7 1.0
C3' B:DC102 4.5 52.4 1.0
C4 B:DC102 4.5 40.2 1.0
N3 B:DC102 4.5 40.7 1.0
C1' B:DC102 4.5 47.9 1.0
C2 B:5IU103 4.9 53.9 1.0
O2 B:DC102 4.9 41.2 1.0
O5' B:5IU103 5.0 57.2 1.0
P B:5IU103 5.0 56.7 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: Sun Dec 13 19:19:15 2020

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