Bromine in PDB 5swm: Bacillus Halodurans Rnase H Mutant D132N in Complex with 12-Mer Frna/Dna Hybrid

All present enzymatic activity of Bacillus Halodurans Rnase H Mutant D132N in Complex with 12-Mer Frna/Dna Hybrid:
3.1.26.4;

The structure of Bacillus Halodurans Rnase H Mutant D132N in Complex with 12-Mer Frna/Dna Hybrid, PDB code: 5swm was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.60 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	37.474, 44.500, 62.174, 84.42, 89.90, 65.10
R / Rfree (%)	16.1 / 18.5

The structure of Bacillus Halodurans Rnase H Mutant D132N in Complex with 12-Mer Frna/Dna Hybrid also contains other interesting chemical elements:

Fluorine	(F)	36 atoms
Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

The binding sites of Bromine atom in the Bacillus Halodurans Rnase H Mutant D132N in Complex with 12-Mer Frna/Dna Hybrid (pdb code 5swm). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the Bacillus Halodurans Rnase H Mutant D132N in Complex with 12-Mer Frna/Dna Hybrid, PDB code: 5swm:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in the Bacillus Halodurans Rnase H Mutant D132N in Complex with 12-Mer Frna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Bacillus Halodurans Rnase H Mutant D132N in Complex with 12-Mer Frna/Dna Hybrid within 5.0Å range: probe atom residue distance (Å) B Occ D:Br4 b:16.0 occ:0.40 BR D:BRU4 0.0 16.0 0.4 C5 D:BRU4 1.8 12.7 0.4 C5 D:DC5 2.2 10.8 0.2 C6 D:BRU4 2.8 12.4 0.4 C4 D:BRU4 2.8 12.9 0.4 C6 D:DC5 3.0 10.7 0.2 O4 D:BRU4 3.1 12.0 0.4 C4 D:DC5 3.2 10.8 0.2 C5 D:BRU4 3.3 17.9 0.2 N4 D:DC5 3.5 10.6 0.2 C6 D:BRU4 3.5 16.5 0.2 BR D:BRU4 3.6 28.4 0.2 N7 D:DA3 3.7 8.0 0.4 C8 D:DA3 3.8 8.1 0.4 O D:HOH230 3.9 25.3 1.0 C4 D:BRU4 3.9 17.2 0.2 N1 D:BRU4 4.0 11.7 0.4 N3 D:BRU4 4.0 12.1 0.4 N1 D:BRU4 4.1 14.3 0.2 N1 D:DC5 4.2 10.8 0.2 O4 D:BRU4 4.4 16.3 0.2 C5 D:DA3 4.4 8.0 0.4 N3 D:DC5 4.4 10.8 0.2 N9 D:DA3 4.5 8.2 0.4 N3 D:BRU4 4.5 15.9 0.2 C2 D:BRU4 4.5 12.1 0.4 C2 D:BRU4 4.6 14.9 0.2 C2' D:BRU4 4.8 12.4 0.2 C4 D:DA3 4.8 8.1 0.4 C2 D:DC5 4.8 10.7 0.2 C1' D:BRU4 5.0 13.2 0.2

Bromine binding site 2 out of 3 in the Bacillus Halodurans Rnase H Mutant D132N in Complex with 12-Mer Frna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Bacillus Halodurans Rnase H Mutant D132N in Complex with 12-Mer Frna/Dna Hybrid within 5.0Å range: probe atom residue distance (Å) B Occ D:Br4 b:20.6 occ:0.40 BR D:BRU4 0.0 20.6 0.4 C7 D:DT11 0.5 11.8 0.2 C5 D:BRU4 1.9 17.6 0.4 C5 D:DT11 1.9 11.7 0.2 N7 D:DG10 2.4 10.8 0.4 C6 D:DT11 2.8 11.6 0.2 C6 D:BRU4 2.8 17.2 0.4 C4 D:BRU4 2.9 18.6 0.4 C8 D:DG10 2.9 10.8 0.4 C4 D:DT11 3.0 11.7 0.2 O4 D:BRU4 3.2 17.3 0.4 O4 D:DT11 3.4 11.6 0.2 O D:HOH216 3.4 31.8 1.0 O D:HOH201 3.5 25.4 1.0 C8 D:DG10 3.5 11.1 0.2 N7 D:DG10 3.6 11.1 0.2 C7 D:DT9 3.7 9.8 0.4 C5 D:DT9 3.7 9.8 0.4 C5 D:DG10 3.7 10.6 0.4 O D:HOH229 3.9 26.2 1.0 C6 D:DT9 3.9 9.8 0.4 N7 D:DA3 3.9 14.3 0.4 N1 D:BRU4 4.0 15.8 0.4 N3 D:BRU4 4.1 17.5 0.4 N1 D:DT11 4.1 11.4 0.2 C8 D:DA3 4.2 14.0 0.4 N9 D:DG10 4.2 10.7 0.4 N3 D:DT11 4.2 11.5 0.2 C4 D:DT9 4.2 9.8 0.4 N9 D:DG10 4.3 11.1 0.2 C5 D:DG10 4.4 11.2 0.2 C5 D:DA3 4.5 14.5 0.4 O6 D:DG10 4.5 10.7 0.4 C6 D:DG10 4.5 10.6 0.4 C2 D:BRU4 4.5 16.6 0.4 C7 D:DT11 4.6 14.2 0.4 N1 D:DT9 4.6 9.8 0.4 C4 D:DG10 4.6 10.6 0.4 O4 D:DT9 4.7 9.8 0.4 N9 D:DA3 4.7 13.7 0.4 C2 D:DT11 4.7 11.4 0.2 C4 D:DG10 4.8 11.1 0.2 C2' D:DG10 4.8 11.2 0.2 O4 D:DT11 4.9 15.3 0.4 N3 D:DT9 4.9 9.7 0.4 C4 D:DA3 4.9 14.1 0.4 C2' D:DT9 5.0 10.1 0.4

Bromine binding site 3 out of 3 in the Bacillus Halodurans Rnase H Mutant D132N in Complex with 12-Mer Frna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Bacillus Halodurans Rnase H Mutant D132N in Complex with 12-Mer Frna/Dna Hybrid within 5.0Å range: probe atom residue distance (Å) B Occ D:Br4 b:28.4 occ:0.20 BR D:BRU4 0.0 28.4 0.2 C5 D:BRU4 1.9 17.9 0.2 N7 D:DA3 2.4 8.0 0.4 C6 D:BRU4 2.9 16.5 0.2 C4 D:BRU4 3.0 17.2 0.2 C8 D:DA3 3.1 8.1 0.4 O4 D:BRU4 3.2 16.3 0.2 O D:HOH220 3.5 30.5 1.0 N7 D:DA2 3.5 11.4 0.4 BR D:BRU4 3.6 16.0 0.4 C8 D:DA2 3.7 11.2 0.4 N7 D:DA3 3.7 11.3 0.2 C8 D:DA3 3.7 11.2 0.2 C5 D:DA2 3.7 11.0 0.4 C5 D:DA3 3.7 8.0 0.4 C5 D:DA3 3.8 11.1 0.2 N9 D:DA3 3.8 11.6 0.2 N9 D:DA2 3.9 12.1 0.4 C4 D:DA2 3.9 11.2 0.4 C4 D:DA3 4.0 11.2 0.2 O4 D:BRU4 4.1 12.0 0.4 C2' D:DA2 4.2 12.9 0.4 N1 D:BRU4 4.2 14.3 0.2 N3 D:BRU4 4.2 15.9 0.2 N4 D:DC5 4.2 10.6 0.2 C2' D:DA3 4.3 12.5 0.2 N6 D:DA3 4.3 8.1 0.4 C6 D:DA2 4.3 11.3 0.4 N9 D:DA3 4.4 8.2 0.4 C5 D:BRU4 4.5 12.7 0.4 C5 D:DC5 4.5 10.8 0.2 C6 D:DA3 4.5 11.2 0.2 C6 D:DA3 4.5 8.1 0.4 C4 D:BRU4 4.6 12.9 0.4 C1' D:DA3 4.6 12.1 0.2 C1' D:DA2 4.6 12.7 0.4 C4 D:DA3 4.7 8.1 0.4 N3 D:DA3 4.7 11.2 0.2 C2 D:BRU4 4.7 14.9 0.2 N3 D:DA2 4.8 11.2 0.4 C4 D:DC5 4.8 10.8 0.2 N6 D:DA2 4.8 11.6 0.4 N1 D:DA2 4.9 11.2 0.4

P.S.Pallan, T.P.Prakash, A.R.De Leon, M.Egli. Limits of Rna 2'-Oh Mimicry By Fluorine: Crystal Structure of Bacillus Halodurans Rnase H Bound to A 2'-Frna:Dna Hybrid. Biochemistry V. 55 5321 2016.
ISSN: ISSN 0006-2960
PubMed: 27611889
DOI: 10.1021/ACS.BIOCHEM.6B00849