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Iodine in PDB 6uke: Hhai Endonuclease in Complex with Iodine-Labelled Dna

Protein crystallography data

The structure of Hhai Endonuclease in Complex with Iodine-Labelled Dna, PDB code: 6uke was solved by J.R.Horton, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.65 / 1.62
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.890, 37.193, 68.744, 90.00, 109.80, 90.00
R / Rfree (%) 17.1 / 20.3

Other elements in 6uke:

The structure of Hhai Endonuclease in Complex with Iodine-Labelled Dna also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Hhai Endonuclease in Complex with Iodine-Labelled Dna (pdb code 6uke). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Hhai Endonuclease in Complex with Iodine-Labelled Dna, PDB code: 6uke:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 6uke

Go back to Iodine Binding Sites List in 6uke
Iodine binding site 1 out of 2 in the Hhai Endonuclease in Complex with Iodine-Labelled Dna


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Hhai Endonuclease in Complex with Iodine-Labelled Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I3

b:36.9
occ:1.00
I5 B:5IU3 0.0 36.9 1.0
C5 B:5IU3 2.1 23.4 1.0
C6 B:5IU3 2.9 23.4 1.0
C4 B:5IU3 3.0 21.4 1.0
O4 B:5IU3 3.0 22.0 1.0
C2 X:EDO615 3.6 44.3 1.0
O X:HOH754 3.7 22.1 1.0
C8 B:DG2 3.7 33.8 1.0
C2' B:DG2 3.8 32.7 1.0
O X:HOH775 3.9 27.2 1.0
O2 X:EDO615 4.0 45.4 1.0
N9 B:DG2 4.0 31.3 1.0
N7 B:DG2 4.1 29.4 1.0
N3 B:5IU3 4.3 20.1 1.0
N1 B:5IU3 4.4 22.0 1.0
C1' B:DG2 4.5 32.2 1.0
C4 B:DG2 4.6 29.4 1.0
C5 B:DG2 4.6 26.5 1.0
O4 B:DT4 4.8 18.7 1.0
C2 B:5IU3 4.9 20.6 1.0
C7 B:DT4 4.9 20.4 1.0
C1 X:EDO615 4.9 43.4 1.0

Iodine binding site 2 out of 2 in 6uke

Go back to Iodine Binding Sites List in 6uke
Iodine binding site 2 out of 2 in the Hhai Endonuclease in Complex with Iodine-Labelled Dna


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Hhai Endonuclease in Complex with Iodine-Labelled Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I10

b:46.0
occ:1.00
I5 B:5IU10 0.0 46.0 1.0
C5 B:5IU10 2.1 39.4 1.0
C6 B:5IU10 2.9 37.0 1.0
C4 B:5IU10 3.1 36.2 1.0
O4 B:5IU10 3.1 33.4 1.0
C6 B:DT9 3.8 28.0 1.0
O A:HOH825 3.9 47.9 1.0
C5 B:DT9 3.9 27.1 1.0
OP2 B:5IU10 4.1 45.4 1.0
C2' B:DT9 4.2 39.7 1.0
C7 B:DT9 4.2 27.4 1.0
N1 B:DT9 4.3 28.2 1.0
N3 B:5IU10 4.4 33.6 1.0
N1 B:5IU10 4.4 37.8 1.0
O B:HOH501 4.5 31.7 1.0
C4 B:DT9 4.5 26.2 1.0
C3' B:DT9 4.7 39.6 1.0
C2 B:DT9 4.8 27.4 1.0
C1' B:DT9 4.9 32.7 1.0
N3 B:DT9 4.9 26.4 1.0
C2 B:5IU10 4.9 36.1 1.0
O6 B:DG11 4.9 44.3 1.0

Reference:

J.R.Horton, J.Yang, X.Zhang, T.Petronzio, A.Fomenkov, G.G.Wilson, R.J.Roberts, X.Cheng. Structure of Hhai Endonuclease with Cognate Dna at An Atomic Resolution of 1.0 Angstrom Nucleic Acids Res. 2019.
ISSN: ESSN 1362-4962
Page generated: Mon Aug 12 00:23:13 2024

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