Chlorine in PDB 6dox: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 360 S at 21 C

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 360 S at 21 C

All present enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 360 S at 21 C:
3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 360 S at 21 C, PDB code: 6dox was solved by N.L.Samara, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.89 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.324, 37.894, 62.145, 90.00, 96.71, 90.00
R / Rfree (%) 15.4 / 17.5

Other elements in 6dox:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 360 S at 21 C also contains other interesting chemical elements:

Rubidium (Rb) 5 atoms
Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 360 S at 21 C (pdb code 6dox). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 360 S at 21 C, PDB code: 6dox:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6dox

Go back to Chlorine Binding Sites List in 6dox
Chlorine binding site 1 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 360 S at 21 C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 360 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:28.9
occ:0.65
 HH A:TYR83 2.3 26.5 1.0
HD22 A:LEU111 2.9 20.7 1.0
HB3 A:LEU111 3.0 17.9 1.0
OH A:TYR83 3.1 22.1 1.0
HD13 A:LEU111 3.1 19.6 1.0
O A:HOH383 3.2 30.1 1.0
HE2 A:TYR83 3.2 23.4 1.0
HD22 A:LEU161 3.3 29.2 1.0
HB3 A:LEU161 3.3 21.6 1.0
O A:HOH329 3.3 40.0 1.0
HD13 A:LEU161 3.3 26.8 1.0
C3 A:GOL212 3.5 44.5 1.0
O A:HOH369 3.6 20.3 1.0
CD2 A:LEU111 3.8 17.2 1.0
CE2 A:TYR83 3.9 19.5 1.0
CZ A:TYR83 3.9 17.8 1.0
CB A:LEU111 3.9 14.9 1.0
HD3 A:ARG97 3.9 26.4 1.0
CD1 A:LEU111 4.0 16.3 1.0
CG A:LEU111 4.1 15.8 1.0
CD2 A:LEU161 4.2 24.3 1.0
CB A:LEU161 4.2 18.0 1.0
CD1 A:LEU161 4.2 22.3 1.0
HH11 A:ARG97 4.4 44.0 1.0
O3 A:GOL212 4.4 34.4 1.0
HD23 A:LEU111 4.4 20.7 1.0
HD21 A:LEU111 4.4 20.7 1.0
CG A:LEU161 4.4 20.5 1.0
HB2 A:LEU111 4.5 17.9 1.0
HD11 A:LEU111 4.5 19.6 1.0
HB2 A:HIS115 4.5 19.1 1.0
C2 A:GOL212 4.6 64.6 1.0
HD12 A:LEU111 4.6 19.6 1.0
O A:HOH398 4.6 23.1 1.0
HB2 A:LEU161 4.7 21.6 1.0
HG2 A:ARG97 4.7 24.1 1.0
HA A:LEU111 4.7 16.9 1.0
O A:HOH422 4.7 35.2 1.0
HD21 A:LEU161 4.7 29.2 1.0
HD23 A:LEU161 4.7 29.2 1.0
HD11 A:LEU161 4.7 26.8 1.0
HD12 A:LEU161 4.8 26.8 1.0
O A:LEU111 4.8 14.4 1.0
CA A:LEU111 4.8 14.1 1.0
NH1 A:ARG97 4.8 36.7 1.0
CD A:ARG97 4.9 22.0 1.0
O2 A:GOL212 4.9 73.1 1.0
HD11 A:ILE100 4.9 27.0 1.0
HB2 A:ALA165 5.0 20.0 1.0

Chlorine binding site 2 out of 3 in 6dox

Go back to Chlorine Binding Sites List in 6dox
Chlorine binding site 2 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 360 S at 21 C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 360 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:37.6
occ:0.50
 O A:HOH443 2.7 37.3 1.0
O A:HOH354 2.8 23.7 1.0
HD12 A:ILE137 3.1 22.5 1.0
HA A:GLN134 3.1 22.7 1.0
HB2 A:LYS180 3.2 23.2 1.0
HD3 A:LYS180 3.3 28.0 1.0
HG3 A:GLN134 3.4 32.5 1.0
HG21 A:ILE137 3.4 26.7 1.0
HD13 A:ILE137 3.5 22.5 1.0
HB A:ILE137 3.5 22.2 1.0
CD1 A:ILE137 3.8 18.8 1.0
CA A:GLN134 4.1 18.9 1.0
CB A:LYS180 4.1 19.3 1.0
CG2 A:ILE137 4.1 22.3 1.0
CD A:LYS180 4.2 23.3 1.0
CB A:ILE137 4.2 18.5 1.0
HG22 A:ILE137 4.2 26.7 1.0
O A:HOH366 4.2 34.8 1.0
CG A:GLN134 4.3 27.1 1.0
HG2 A:LYS180 4.3 27.2 1.0
O A:HOH440 4.4 54.0 1.0
CG A:LYS180 4.4 22.6 1.0
HB2 A:GLN134 4.5 27.6 1.0
O A:GLN134 4.5 20.9 1.0
CB A:GLN134 4.5 23.0 1.0
HD11 A:ILE137 4.5 22.5 1.0
HB3 A:LYS180 4.6 23.2 1.0
O A:HOH436 4.6 40.7 1.0
CG1 A:ILE137 4.6 17.8 1.0
HG2 A:GLN134 4.6 32.5 1.0
O A:HOH420 4.6 30.4 1.0
HD2 A:LYS180 4.8 28.0 1.0
C A:GLN134 4.8 21.9 1.0
HA A:LYS180 4.9 21.1 1.0
HE3 A:LYS180 5.0 31.9 1.0
HE2 A:LYS180 5.0 31.9 1.0
HG23 A:ILE137 5.0 26.7 1.0
N A:GLN134 5.0 18.1 1.0

Chlorine binding site 3 out of 3 in 6dox

Go back to Chlorine Binding Sites List in 6dox
Chlorine binding site 3 out of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 360 S at 21 C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 360 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:37.2
occ:0.75
 O A:HOH450 2.7 33.3 1.0
HD11 A:LEU179 3.2 25.7 1.0
HG3 A:PRO128 3.2 28.0 1.0
HB3 A:PRO128 3.2 22.2 1.0
CG A:PRO177 3.6 20.2 1.0
HD21 A:LEU179 3.7 25.4 1.0
CB A:PRO177 3.7 18.2 1.0
CD1 A:ILE64 3.8 36.2 1.0
CG A:PRO128 3.9 23.3 1.0
CB A:PRO128 4.0 18.5 1.0
CD1 A:LEU179 4.1 21.4 1.0
HD3 A:PRO128 4.2 22.6 1.0
O A:HOH448 4.3 49.5 0.8
HB2 A:PRO128 4.3 22.2 1.0
HD13 A:LEU179 4.5 25.7 1.0
CD2 A:LEU179 4.5 21.2 1.0
HD12 A:LEU179 4.6 25.7 1.0
CD A:PRO128 4.7 18.9 1.0
HG2 A:PRO128 4.7 28.0 1.0
CD A:PRO177 4.7 18.8 1.0
HG A:LEU179 4.7 23.2 1.0
CG A:LEU179 4.7 19.4 1.0
HD22 A:LEU179 4.9 25.4 1.0

Reference:

N.L.Samara, W.Yang. Cation Trafficking Propels Rna Hydrolysis. Nat. Struct. Mol. Biol. V. 25 715 2018.
ISSN: ESSN 1545-9985
PubMed: 30076410
DOI: 10.1038/S41594-018-0099-4
Page generated: Sat Dec 12 12:53:34 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy