Chlorine in PDB 6dp8: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Li+ For 240 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 Li+ For 240 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 Li+ For 240 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 Li+ For 240 S at 21 C, PDB code: 6dp8 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) 23.46 / 1.32
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.426, 37.747, 61.811, 90.00, 95.45, 90.00
R / Rfree (%) 14.7 / 17

Other elements in 6dp8:

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 Li+ For 240 S at 21 C also contains other interesting chemical elements:

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 Li+ For 240 S at 21 C (pdb code 6dp8). 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 Li+ For 240 S at 21 C, PDB code: 6dp8:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6dp8

Go back to Chlorine Binding Sites List in 6dp8
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 Li+ For 240 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 Li+ For 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:49.7
occ:0.85
O3 A:GOL212 2.1 72.9 1.0
HH A:TYR83 2.2 31.2 1.0
C3 A:GOL212 2.9 48.7 1.0
OH A:TYR83 3.0 26.0 1.0
HB3 A:LEU111 3.1 15.5 1.0
HD13 A:LEU111 3.1 18.1 1.0
HE2 A:TYR83 3.2 22.5 1.0
HD22 A:LEU161 3.2 28.6 1.0
HD22 A:LEU111 3.2 16.6 1.0
HD13 A:LEU161 3.3 26.9 1.0
C2 A:GOL212 3.4 41.9 1.0
HB3 A:LEU161 3.4 18.9 1.0
HD3 A:ARG97 3.5 25.3 1.0
O A:HOH304 3.5 37.2 1.0
O2 A:GOL212 3.8 84.8 1.0
CE2 A:TYR83 3.8 18.8 1.0
CZ A:TYR83 3.8 21.0 1.0
HH11 A:ARG97 4.0 33.9 1.0
O A:HOH306 4.0 20.5 1.0
CB A:LEU111 4.0 12.9 1.0
CD1 A:LEU111 4.0 15.0 1.0
CD2 A:LEU111 4.1 13.8 1.0
CD2 A:LEU161 4.1 23.8 1.0
CD1 A:LEU161 4.2 22.4 1.0
CG A:LEU111 4.2 13.5 1.0
CB A:LEU161 4.3 15.8 1.0
CG A:LEU161 4.4 19.6 1.0
HG2 A:ARG97 4.5 21.9 1.0
HB2 A:HIS115 4.5 15.7 1.0
CD A:ARG97 4.5 21.1 1.0
NH1 A:ARG97 4.5 28.3 1.0
HB2 A:LEU111 4.5 15.5 1.0
HD11 A:LEU111 4.6 18.1 1.0
HD21 A:LEU161 4.6 28.6 1.0
HD12 A:LEU111 4.6 18.1 1.0
HD11 A:LEU161 4.6 26.9 1.0
HD21 A:LEU111 4.6 16.6 1.0
HD23 A:LEU111 4.7 16.6 1.0
HD11 A:ILE100 4.7 23.2 1.0
HD23 A:LEU161 4.7 28.6 1.0
HD12 A:LEU161 4.8 26.9 1.0
C1 A:GOL212 4.8 31.2 1.0
HB2 A:LEU161 4.8 18.9 1.0
HA A:LEU111 4.9 15.6 1.0
HH12 A:ARG97 4.9 33.9 1.0
O A:LEU111 4.9 13.5 1.0
O A:HOH367 4.9 20.6 1.0
HB2 A:ARG97 5.0 20.2 1.0
CA A:LEU111 5.0 13.0 1.0
CG A:ARG97 5.0 18.3 1.0

Chlorine binding site 2 out of 3 in 6dp8

Go back to Chlorine Binding Sites List in 6dp8
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 Li+ For 240 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 Li+ For 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:32.3
occ:0.60
O A:HOH365 3.0 20.3 1.0
HA A:GLN134 3.0 20.1 1.0
HD3 A:LYS180 3.1 21.1 1.0
O A:HOH462 3.1 47.2 1.0
HB2 A:LYS180 3.2 22.1 1.0
HG3 A:GLN134 3.2 23.9 1.0
O A:HOH346 3.3 25.3 1.0
HD12 A:ILE137 3.4 19.9 1.0
HD13 A:ILE137 3.7 19.9 1.0
HG2 A:LYS180 3.8 21.7 1.0
HG21 A:ILE137 3.8 20.9 1.0
HB A:ILE137 3.9 17.4 1.0
CD A:LYS180 3.9 17.6 1.0
CA A:GLN134 3.9 16.8 1.0
CB A:LYS180 4.0 18.4 1.0
CD1 A:ILE137 4.0 16.5 1.0
CG A:LYS180 4.1 18.1 1.0
CG A:GLN134 4.1 19.9 1.0
HB2 A:GLN134 4.1 20.0 1.0
CB A:GLN134 4.3 16.7 1.0
HE21 A:GLN134 4.3 23.8 1.0
HB3 A:LYS180 4.4 22.1 1.0
HE3 A:LYS180 4.4 22.2 1.0
CG2 A:ILE137 4.4 17.4 1.0
HG22 A:ILE137 4.5 20.9 1.0
CB A:ILE137 4.5 14.5 1.0
HG2 A:GLN134 4.6 23.9 1.0
O A:GLN134 4.6 16.8 1.0
HD2 A:LYS180 4.6 21.1 1.0
O A:HOH463 4.6 53.8 1.0
O A:HOH454 4.6 27.8 1.0
CE A:LYS180 4.7 18.5 1.0
HD11 A:ILE137 4.7 19.9 1.0
C A:GLN134 4.8 15.5 1.0
N A:GLN134 4.8 15.8 1.0
HE2 A:LYS180 4.9 22.2 1.0
CG1 A:ILE137 4.9 14.1 1.0
O A:HOH433 5.0 25.7 1.0
NE2 A:GLN134 5.0 19.8 1.0

Chlorine binding site 3 out of 3 in 6dp8

Go back to Chlorine Binding Sites List in 6dp8
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 Li+ For 240 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 Li+ For 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:50.2
occ:0.85
O A:HOH464 2.5 43.6 1.0
HG2 A:PRO177 2.9 20.6 1.0
HD11 A:LEU179 3.0 25.3 1.0
HD13 A:ILE64 3.0 40.7 1.0
HG3 A:PRO128 3.1 24.0 1.0
HB3 A:PRO128 3.4 21.7 1.0
HB2 A:PRO177 3.4 21.1 1.0
HD21 A:LEU179 3.6 26.3 1.0
CD1 A:ILE64 3.6 33.9 1.0
HD12 A:ILE64 3.7 40.7 1.0
HD11 A:ILE64 3.7 40.7 1.0
CG A:PRO177 3.7 17.2 1.0
CB A:PRO177 3.8 17.5 1.0
HB3 A:PRO177 3.8 21.1 1.0
CD1 A:LEU179 3.9 21.1 1.0
CG A:PRO128 4.0 20.0 1.0
CB A:PRO128 4.1 18.1 1.0
HG3 A:PRO177 4.2 20.6 1.0
HD13 A:LEU179 4.3 25.3 1.0
HG21 A:ILE64 4.3 26.8 1.0
HB2 A:PRO128 4.4 21.7 1.0
CD2 A:LEU179 4.4 21.9 1.0
HD3 A:PRO128 4.5 20.0 1.0
HD12 A:LEU179 4.5 25.3 1.0
HG2 A:PRO128 4.6 24.0 1.0
CG A:LEU179 4.6 19.0 1.0
HG A:LEU179 4.7 22.8 1.0
HD2 A:PRO177 4.7 18.9 1.0
HD22 A:LEU179 4.7 26.3 1.0
CD A:PRO128 4.8 16.6 1.0
CD A:PRO177 4.8 15.7 1.0
O A:HOH436 5.0 48.6 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

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