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Magnesium in PDB 6dov: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 80 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 80 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 80 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 80 S at 21 C, PDB code: 6dov 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) 20.06 / 1.52
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.656, 37.396, 61.670, 90.00, 96.51, 90.00
R / Rfree (%) 15.3 / 19

Other elements in 6dov:

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 80 S at 21 C also contains other interesting chemical elements:

Rubidium (Rb) 5 atoms
Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 80 S at 21 C (pdb code 6dov). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium 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 80 S at 21 C, PDB code: 6dov:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6dov

Go back to Magnesium Binding Sites List in 6dov
Magnesium binding site 1 out of 2 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 80 S at 21 C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 80 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:23.8
occ:1.00
OD1 A:ASP192 2.0 35.4 1.0
O b:HOH101 2.0 27.9 1.0
O b:HOH103 2.0 28.1 1.0
O A:HOH314 2.1 30.0 0.8
OD2 A:ASP71 2.1 23.9 1.0
OP3 b:C5 2.1 58.5 0.2
OP1 b:C5 2.2 29.4 0.8
OP1 b:C5 2.2 34.3 0.2
P b:C5 2.7 41.0 0.2
CG A:ASP71 3.1 20.7 1.0
CG A:ASP192 3.2 28.2 1.0
HA A:ASP192 3.2 29.1 1.0
P b:C5 3.3 21.8 0.8
OD1 A:ASP71 3.5 22.6 1.0
H A:TYR193 3.6 38.5 1.0
OP2 b:C5 3.6 36.3 0.2
RB A:RB205 3.7 36.5 0.1
OP2 b:C5 3.7 27.9 0.8
HB2 A:ASP192 3.8 35.2 1.0
RB A:RB203 3.8 37.6 0.1
O A:HOH346 3.8 19.1 0.2
CB A:ASP192 3.9 29.3 1.0
MG A:MG202 3.9 19.8 1.0
OP2 b:G6 3.9 29.5 1.0
O5' b:C5 4.0 27.5 0.2
CA A:ASP192 4.0 24.2 1.0
HG22 A:ILE189 4.1 31.8 1.0
OD2 A:ASP192 4.1 35.7 1.0
O5' b:C5 4.1 22.5 0.8
O A:VAL72 4.1 21.7 1.0
OE1 A:GLU188 4.3 54.2 1.0
N A:TYR193 4.3 32.1 1.0
OD2 A:ASP132 4.3 30.9 1.0
C5' b:C5 4.4 21.3 1.0
CB A:ASP71 4.5 20.7 1.0
O3' B:U4 4.5 21.2 0.8
HB3 A:ASP71 4.5 24.9 1.0
O A:HOH337 4.6 32.6 0.8
HD1 A:TYR193 4.6 33.6 1.0
O A:HOH315 4.7 42.5 1.0
C A:ASP192 4.7 28.1 1.0
HG21 A:ILE189 4.8 31.8 1.0
HB2 A:ASP71 4.8 24.9 1.0
HB3 A:ASP192 4.8 35.2 1.0
CG2 A:ILE189 4.8 26.5 1.0
HB2 A:TYR193 4.8 39.6 1.0
HG23 A:ILE189 5.0 31.8 1.0

Magnesium binding site 2 out of 2 in 6dov

Go back to Magnesium Binding Sites List in 6dov
Magnesium binding site 2 out of 2 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 80 S at 21 C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 80 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:19.8
occ:1.00
OD1 A:ASP71 2.1 22.6 1.0
OE1 A:GLU109 2.2 26.2 1.0
OD1 A:ASP132 2.3 24.3 1.0
OP1 b:C5 2.3 34.3 0.2
OP1 b:C5 2.4 29.4 0.8
OD2 A:ASP132 2.7 30.9 1.0
O3' B:U4 2.7 21.2 0.8
CG A:ASP132 2.8 25.5 1.0
CD A:GLU109 3.1 23.7 1.0
O A:HOH372 3.1 22.4 1.0
CG A:ASP71 3.1 20.7 1.0
P b:C5 3.2 21.8 0.8
OE2 A:GLU109 3.2 23.9 1.0
C3' B:U4 3.5 26.7 0.2
HG12 A:VAL72 3.5 26.4 1.0
OD2 A:ASP71 3.6 23.9 1.0
O3' B:U4 3.6 25.5 0.2
P b:C5 3.7 41.0 0.2
H A:VAL72 3.7 23.5 1.0
O b:HOH103 3.8 28.1 1.0
MG A:MG201 3.9 23.8 1.0
HA A:ASP71 4.0 22.4 1.0
C3' B:U4 4.0 22.9 0.8
C5' b:C5 4.1 21.3 1.0
O5' b:C5 4.1 22.5 0.8
O2' B:U4 4.2 20.9 0.8
H A:ASP132 4.2 23.4 1.0
OP2 b:C5 4.3 36.3 0.2
O5' b:C5 4.3 27.5 0.2
CB A:ASP132 4.3 24.4 1.0
HG21 A:ILE189 4.4 31.8 1.0
OP2 b:C5 4.4 27.9 0.8
CB A:ASP71 4.4 20.7 1.0
C4' B:U4 4.4 21.5 0.8
HB2 A:SER133 4.4 27.2 1.0
C4' B:U4 4.4 23.5 0.2
CG1 A:VAL72 4.5 22.0 1.0
CG A:GLU109 4.5 21.3 1.0
N A:VAL72 4.5 19.6 1.0
C5' B:U4 4.6 27.6 0.2
CA A:ASP71 4.6 18.6 1.0
C2' B:U4 4.6 20.5 0.2
HB2 A:ASP71 4.6 24.9 1.0
HB3 A:ASP132 4.7 29.3 1.0
OP3 b:C5 4.7 58.5 0.2
HG3 A:GLU109 4.7 25.6 1.0
C2' B:U4 4.7 18.7 0.8
HG13 A:VAL72 4.7 26.4 1.0
HG2 A:GLU109 4.8 25.6 1.0
HB2 A:ASP132 4.8 29.3 1.0
O b:HOH101 4.8 27.9 1.0
HG22 A:ILE189 4.8 31.8 1.0
RB A:RB204 4.9 37.0 0.1
HG11 A:VAL72 4.9 26.4 1.0
N A:ASP132 4.9 19.5 1.0
O2' B:U4 4.9 27.1 0.2
C5' B:U4 4.9 21.4 0.8
CA A:ASP132 5.0 21.7 1.0
O A:VAL72 5.0 21.7 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: Mon Sep 30 23:22:38 2024

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