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Iodine in PDB 1omk: The Crystal Structure of D(Cacg(5IU)G)

Protein crystallography data

The structure of The Crystal Structure of D(Cacg(5IU)G), PDB code: 1omk was solved by G.Schuerman, K.Van Hecke, L.Van Meervelt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 18.155, 30.034, 41.988, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1omk:

The structure of The Crystal Structure of D(Cacg(5IU)G) also contains other interesting chemical elements:

Cobalt (Co) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the The Crystal Structure of D(Cacg(5IU)G) (pdb code 1omk). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the The Crystal Structure of D(Cacg(5IU)G), PDB code: 1omk:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 1omk

Go back to Iodine Binding Sites List in 1omk
Iodine binding site 1 out of 2 in the The Crystal Structure of D(Cacg(5IU)G)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of The Crystal Structure of D(Cacg(5IU)G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I5

b:12.2
occ:1.00
I5 A:5IU5 0.0 12.2 1.0
C5 A:5IU5 2.1 11.2 1.0
C6 A:5IU5 3.0 9.2 1.0
C4 A:5IU5 3.0 10.0 1.0
O4 A:5IU5 3.3 12.5 1.0
N4 B:DC7 3.7 12.5 1.0
C4 A:DG4 3.8 8.0 1.0
N9 A:DG4 3.8 8.5 1.0
C5 A:DG4 3.8 10.9 1.0
C8 A:DG4 3.8 11.5 1.0
N4 A:NCO31 3.9 12.3 1.0
O A:HOH123 3.9 21.4 1.0
N7 A:DG4 3.9 10.6 1.0
C2' A:DG4 4.1 11.1 1.0
O6 A:DG6 4.1 12.3 1.0
O B:HOH118 4.2 21.4 1.0
N2 A:NCO31 4.2 15.4 1.0
N1 A:5IU5 4.3 10.3 1.0
N3 A:5IU5 4.3 10.3 1.0
N3 A:DG4 4.3 8.2 1.0
C1' A:DG4 4.4 8.9 1.0
C6 A:DG4 4.5 8.5 1.0
C4 B:DC7 4.5 12.4 1.0
C2 A:DG4 4.8 9.8 1.0
C2 A:5IU5 4.8 10.1 1.0
N1 A:DG4 4.9 9.0 1.0

Iodine binding site 2 out of 2 in 1omk

Go back to Iodine Binding Sites List in 1omk
Iodine binding site 2 out of 2 in the The Crystal Structure of D(Cacg(5IU)G)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of The Crystal Structure of D(Cacg(5IU)G) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I11

b:25.5
occ:1.00
I5 B:5IU11 0.0 25.5 1.0
C5 B:5IU11 2.1 12.8 1.0
C6 B:5IU11 3.0 13.1 1.0
C4 B:5IU11 3.0 13.0 1.0
O4 B:5IU11 3.2 20.2 1.0
O A:HOH103 3.6 19.1 1.0
C2' B:DG10 3.6 16.1 1.0
N4 A:DC1 3.7 14.6 1.0
N9 B:DG10 4.0 13.1 1.0
C8 B:DG10 4.0 13.3 1.0
C1' B:DG10 4.2 15.9 1.0
N1 B:5IU11 4.3 13.4 1.0
N3 B:5IU11 4.3 14.9 1.0
C4 B:DG10 4.4 10.6 1.0
N7 B:DG10 4.5 15.2 1.0
C4 A:DC1 4.5 13.1 1.0
C5 B:DG10 4.6 11.7 1.0
C2 B:5IU11 4.8 11.1 1.0
C5 A:DC1 4.9 13.3 1.0
N3 B:DG10 5.0 10.1 1.0
C3' B:DG10 5.0 16.3 1.0

Reference:

G.Schuerman, K.Van Hecke, L.Van Meervelt. Exploration of the Influence of 5-Iodo-2'-Deoxyuridine Incorporation on the Structure of D[Cacg(Idu)G]. Acta Crystallogr.,Sect.D V. 59 1525 2003.
ISSN: ISSN 0907-4449
PubMed: 12876373
DOI: 10.1107/S0907444903012381
Page generated: Sun Aug 11 12:33:01 2024

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