Bromine in PDB 1k3x: Crystal Structure of A Trapped Reaction Intermediate of the Dna Repair Enzyme Endonuclease VIII with Brominated-Dna

The structure of Crystal Structure of A Trapped Reaction Intermediate of the Dna Repair Enzyme Endonuclease VIII with Brominated-Dna, PDB code: 1k3x was solved by G.Golan, D.O.Zharkov, R.Gilboa, A.S.Fernandes, J.H.Kycia, S.E.Gerchman, R.A.Rieger, A.P.Grollman, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.25
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	76.495, 76.495, 164.310, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 18.1

The structure of Crystal Structure of A Trapped Reaction Intermediate of the Dna Repair Enzyme Endonuclease VIII with Brominated-Dna also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Bromine atom in the Crystal Structure of A Trapped Reaction Intermediate of the Dna Repair Enzyme Endonuclease VIII with Brominated-Dna (pdb code 1k3x). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of A Trapped Reaction Intermediate of the Dna Repair Enzyme Endonuclease VIII with Brominated-Dna, PDB code: 1k3x:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of A Trapped Reaction Intermediate of the Dna Repair Enzyme Endonuclease VIII with Brominated-Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of A Trapped Reaction Intermediate of the Dna Repair Enzyme Endonuclease VIII with Brominated-Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Br404 b:50.0 occ:1.00 BR B:BRU404 0.0 50.0 1.0 C5 B:BRU404 1.9 50.2 1.0 O4 B:BRU404 2.6 56.8 1.0 C4 B:BRU404 2.6 48.4 1.0 C6 B:BRU404 3.0 47.5 1.0 OG A:SER251 3.4 32.2 1.0 C2' B:DC403 3.5 53.7 1.0 C6 B:DC403 3.6 38.5 1.0 CB A:SER251 3.6 30.5 1.0 O B:HOH903 3.8 37.9 1.0 N1 B:DC403 3.8 43.5 1.0 N3 B:BRU404 3.9 42.2 1.0 O A:HOH993 4.0 53.0 1.0 C5 B:DC403 4.0 34.1 1.0 C1' B:DC403 4.1 48.9 1.0 N1 B:BRU404 4.2 41.7 1.0 O B:HOH765 4.2 28.1 1.0 O4 B:BRU405 4.4 27.0 1.0 C2 B:DC403 4.4 39.8 1.0 C2 B:BRU404 4.7 38.9 1.0 C4 B:DC403 4.7 33.5 1.0 N3 B:DC403 4.8 36.9 1.0 O A:HOH1009 4.8 42.0 1.0 N6 C:DA430 4.8 47.5 1.0 C3' B:DC403 4.9 56.0 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of A Trapped Reaction Intermediate of the Dna Repair Enzyme Endonuclease VIII with Brominated-Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of A Trapped Reaction Intermediate of the Dna Repair Enzyme Endonuclease VIII with Brominated-Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Br405 b:65.4 occ:1.00 BR B:BRU405 0.0 65.4 1.0 C5 B:BRU405 1.9 23.4 1.0 C6 B:BRU405 2.8 23.2 1.0 C4 B:BRU405 2.8 21.3 1.0 O4 B:BRU405 3.1 27.0 1.0 O B:HOH921 3.2 43.0 1.0 C2' B:BRU404 3.4 48.2 1.0 O B:HOH765 3.6 28.1 1.0 C6 B:BRU404 3.7 47.5 1.0 N1 B:BRU404 3.8 41.7 1.0 N1 B:BRU405 4.0 23.4 1.0 C5 B:BRU404 4.1 50.2 1.0 N3 B:BRU405 4.1 23.1 1.0 C1' B:BRU404 4.2 42.6 1.0 C2 B:BRU404 4.2 38.9 1.0 N3 B:BRU404 4.5 42.2 1.0 C4 B:BRU404 4.5 48.4 1.0 C2 B:BRU405 4.6 19.7 1.0 C3' B:BRU404 4.6 57.0 1.0 N4 B:DC406 4.7 23.5 1.0 O2 B:BRU404 4.8 36.7 1.0

Bromine binding site 3 out of 4 in the Crystal Structure of A Trapped Reaction Intermediate of the Dna Repair Enzyme Endonuclease VIII with Brominated-Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of A Trapped Reaction Intermediate of the Dna Repair Enzyme Endonuclease VIII with Brominated-Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Br408 b:33.4 occ:1.00 BR B:BRU408 0.0 33.4 1.0 C5 B:BRU408 1.8 16.6 1.0 C6 B:BRU408 2.8 17.5 1.0 C4 B:BRU408 2.9 18.4 1.0 O B:HOH1010 2.9 48.5 1.0 O4 B:BRU408 3.2 20.4 1.0 C8 B:DA407 3.3 25.2 1.0 N7 B:DA407 3.4 25.9 1.0 O B:HOH1021 3.6 42.7 1.0 O B:HOH874 3.8 44.1 1.0 O B:HOH782 3.9 33.8 1.0 N9 B:DA407 4.0 20.4 1.0 N1 B:BRU408 4.1 15.5 1.0 N3 B:BRU408 4.1 16.1 1.0 N4 B:DC409 4.2 29.1 1.0 C5 B:DA407 4.2 25.2 1.0 O B:HOH971 4.2 44.0 1.0 C2' B:DA407 4.4 19.6 1.0 C4 B:DA407 4.4 20.1 1.0 C2 B:BRU408 4.6 15.5 1.0 C1' B:DA407 4.8 17.7 1.0 C4 B:DC409 4.9 26.1 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of A Trapped Reaction Intermediate of the Dna Repair Enzyme Endonuclease VIII with Brominated-Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of A Trapped Reaction Intermediate of the Dna Repair Enzyme Endonuclease VIII with Brominated-Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Br411 b:0.2 occ:1.00 BR B:BRU411 0.0 0.2 1.0 C5 B:BRU411 1.9 57.1 1.0 C6 B:BRU411 2.8 59.8 1.0 C4 B:BRU411 2.9 54.1 1.0 C2' B:DC410 3.1 52.5 1.0 OP2 B:BRU411 3.1 0.8 1.0 O4 B:BRU411 3.2 60.0 1.0 C1' B:DC410 3.7 49.2 1.0 N1 B:DC410 3.7 47.5 1.0 C6 B:DC410 3.9 43.5 1.0 N1 B:BRU411 4.1 57.0 1.0 O6 B:DG412 4.2 64.0 1.0 N3 B:BRU411 4.2 54.0 1.0 N4 C:DC422 4.3 47.1 1.0 C2 B:DC410 4.3 46.1 1.0 P B:BRU411 4.3 88.4 1.0 C3' B:DC410 4.4 59.9 1.0 O5' B:BRU411 4.4 82.1 1.0 C5 B:DC410 4.6 42.6 1.0 O2 B:DC410 4.7 43.5 1.0 C2 B:BRU411 4.7 52.5 1.0 O3' B:DC410 4.7 69.6 1.0 N3 B:DC410 4.9 40.1 1.0

D.O.Zharkov, G.Golan, R.Gilboa, A.S.Fernandes, S.E.Gerchman, J.H.Kycia, R.A.Rieger, A.P.Grollman, G.Shoham. Structural Analysis of An Escherichia Coli Endonuclease VIII Covalent Reaction Intermediate. Embo J. V. 21 789 2002.
ISSN: ISSN 0261-4189
PubMed: 11847126
DOI: 10.1093/EMBOJ/21.4.789