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Magnesium in PDB 6dot: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 40 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 40 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 40 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 40 S at 21 C, PDB code: 6dot 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) 23.35 / 1.42
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.557, 37.229, 62.052, 90.00, 96.61, 90.00
R / Rfree (%) 14.2 / 16.8

Other elements in 6dot:

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

Rubidium (Rb) 3 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 40 S at 21 C (pdb code 6dot). 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 40 S at 21 C, PDB code: 6dot:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6dot

Go back to Magnesium Binding Sites List in 6dot
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 40 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 40 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:20.1
occ:1.00
OD1 A:ASP192 2.0 31.1 1.0
O A:HOH322 2.0 24.0 1.0
O A:HOH349 2.1 29.5 1.0
OD2 A:ASP71 2.2 22.8 1.0
OP1 b:C5 2.2 23.4 1.0
O A:HOH329 2.3 43.7 1.0
CG A:ASP192 3.1 26.9 1.0
CG A:ASP71 3.2 17.5 1.0
HA A:ASP192 3.2 28.5 1.0
P b:C5 3.4 19.9 0.9
OD1 A:ASP71 3.5 22.7 1.0
H A:TYR193 3.6 31.5 1.0
HB2 A:ASP192 3.8 30.4 1.0
OP2 b:C5 3.9 23.2 1.0
CB A:ASP192 3.9 25.4 1.0
RB A:RB203 3.9 40.0 0.3
CA A:ASP192 4.0 23.7 1.0
OP2 b:G6 4.0 23.6 1.0
MG A:MG202 4.0 20.2 1.0
OD2 A:ASP192 4.1 34.8 1.0
OE1 A:GLU188 4.1 51.6 1.0
HG22 A:ILE189 4.1 27.0 1.0
O5' b:C5 4.2 19.0 1.0
O A:VAL72 4.2 19.4 1.0
O A:HOH335 4.3 45.6 1.0
N A:TYR193 4.3 26.2 1.0
OD2 A:ASP132 4.4 27.4 1.0
CB A:ASP71 4.5 19.1 1.0
C5' b:C5 4.6 19.2 1.0
O3' B:U4 4.6 19.6 1.0
HB3 A:ASP71 4.6 22.9 1.0
O b:HOH104 4.7 32.4 1.0
C A:ASP192 4.7 23.8 1.0
HD1 A:TYR193 4.7 30.0 1.0
HG21 A:ILE189 4.8 27.0 1.0
HB3 A:ASP192 4.8 30.4 1.0
HB2 A:TYR193 4.8 40.2 1.0
HB2 A:ASP71 4.8 22.9 1.0
CG2 A:ILE189 4.8 22.5 1.0
HG23 A:ILE189 5.0 27.0 1.0

Magnesium binding site 2 out of 2 in 6dot

Go back to Magnesium Binding Sites List in 6dot
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 40 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 40 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:20.2
occ:1.00
OD1 A:ASP71 2.1 22.7 1.0
OD1 A:ASP132 2.3 20.5 1.0
OE1 A:GLU109 2.3 22.6 1.0
OP1 b:C5 2.5 23.4 1.0
OD2 A:ASP132 2.7 27.4 1.0
O3' B:U4 2.8 19.6 1.0
CG A:ASP132 2.8 22.3 1.0
O A:HOH373 3.0 18.6 1.0
CD A:GLU109 3.1 19.9 1.0
CG A:ASP71 3.1 17.5 1.0
OE2 A:GLU109 3.1 22.0 1.0
P b:C5 3.3 19.9 0.9
OD2 A:ASP71 3.6 22.8 1.0
HG12 A:VAL72 3.6 20.8 1.0
H A:VAL72 3.7 20.2 1.0
O A:HOH349 3.8 29.5 1.0
HA A:ASP71 3.9 18.2 1.0
MG A:MG201 4.0 20.1 1.0
C3' B:U4 4.1 19.8 1.0
C5' b:C5 4.1 19.2 1.0
H A:ASP132 4.2 20.1 1.0
O2' B:U4 4.2 22.3 1.0
O5' b:C5 4.2 19.0 1.0
HG21 A:ILE189 4.3 27.0 1.0
CB A:ASP132 4.3 20.2 1.0
HB2 A:SER133 4.3 20.0 1.0
CB A:ASP71 4.3 19.1 1.0
C4' B:U4 4.4 20.7 1.0
OP2 b:C5 4.5 23.2 1.0
CG A:GLU109 4.5 20.6 1.0
N A:VAL72 4.6 16.8 1.0
CG1 A:VAL72 4.6 17.3 1.0
HB2 A:ASP71 4.6 22.9 1.0
CA A:ASP71 4.6 15.2 1.0
HB3 A:ASP132 4.7 24.3 1.0
C2' B:U4 4.8 19.0 1.0
O A:HOH322 4.8 24.0 1.0
HG3 A:GLU109 4.8 24.7 1.0
HG2 A:GLU109 4.8 24.7 1.0
HG22 A:ILE189 4.8 27.0 1.0
HB2 A:ASP132 4.8 24.3 1.0
N A:ASP132 4.9 16.8 1.0
HG13 A:VAL72 4.9 20.8 1.0
HG11 A:VAL72 4.9 20.8 1.0
CA A:ASP132 4.9 17.3 1.0
C A:ASP132 5.0 18.1 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 23:21:54 2024

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