Atomistry » Iodine » PDB 1lkr-1pvh » 1omk
Atomistry »
  Iodine »
    PDB 1lkr-1pvh »
      1omk »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy