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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5swm:

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
Bromine (Br) 3 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Bacillus Halodurans Rnase H Mutant D132N in Complex with 12-Mer Frna/Dna Hybrid, PDB code: 5swm:

Sodium binding site 1 out of 1 in 5swm

Go back to Sodium Binding Sites List in 5swm
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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
A:Na201

b:21.5
occ:1.00
 OG1 A:THR183 2.8 14.3 1.0
O A:HOH302 2.8 25.2 1.0
N A:ILE189 3.0 14.6 1.0
OD1 A:ASN132 3.0 15.1 1.0
OE1 A:GLU188 3.5 48.2 1.0
CG2 A:ILE189 3.5 13.4 1.0
CB A:ILE189 3.6 13.1 1.0
CG2 A:THR183 3.7 16.1 1.0
CA A:GLU188 3.7 17.8 1.0
CB A:ASN132 3.7 10.6 1.0
C A:GLU188 3.8 16.0 1.0
CB A:THR183 3.8 15.8 1.0
CG A:ASN132 3.8 11.0 1.0
CA A:ILE189 3.9 14.2 1.0
OP1 C:UFT11 4.0 11.6 0.4
CD1 A:TRP181 4.0 13.3 1.0
CD A:GLU188 4.0 34.8 1.0
CB A:GLU188 4.3 21.9 1.0
O A:GLY187 4.4 17.5 1.0
NE1 A:TRP181 4.5 14.9 1.0
O2P C:CFZ5 4.5 11.5 0.4
OE2 A:GLU188 4.5 49.4 1.0
OP1 C:AF24 4.6 9.7 0.2
C5' C:UFT11 4.8 12.1 0.4
CG A:GLU188 4.8 27.9 1.0
O2P C:CFZ5 4.8 11.2 0.2
N A:GLU188 4.8 18.4 1.0
CA A:THR183 4.8 16.9 1.0
O2P C:CFZ6 4.8 12.4 0.4
OD1 A:ASP192 4.9 34.2 1.0
O1P C:CFZ5 5.0 11.7 0.2
C A:GLY187 5.0 17.8 1.0

Reference:

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
Page generated: Mon Oct 7 23:55:36 2024

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