Magnesium in PDB 6dou: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 120 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 120 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 120 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 120 S at 21 C, PDB code: 6dou 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) 19.94 / 1.49
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.541, 37.383, 62.437, 90.00, 96.57, 90.00
R / Rfree (%) 15.5 / 18.8

Other elements in 6dou:

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 120 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 120 S at 21 C (pdb code 6dou). 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 120 S at 21 C, PDB code: 6dou:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6dou

Go back to Magnesium Binding Sites List in 6dou
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 120 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 120 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:25.3
occ:1.00
OD2 A:ASP71 2.0 24.8 1.0
OD1 A:ASP192 2.0 36.9 1.0
O A:HOH316 2.1 28.7 1.0
O A:HOH324 2.1 30.4 1.0
OP3 b:C5 2.1 61.4 0.5
OP1 b:C5 2.2 38.7 0.5
O b:HOH101 2.2 27.5 0.5
OP1 b:C5 2.2 34.5 0.5
P b:C5 2.7 34.7 0.5
CG A:ASP71 3.0 21.9 1.0
HA A:ASP192 3.2 32.5 1.0
CG A:ASP192 3.2 29.4 1.0
P b:C5 3.3 27.8 0.5
OD1 A:ASP71 3.4 25.2 1.0
H A:TYR193 3.6 37.0 1.0
OP2 b:C5 3.6 41.9 0.5
HB2 A:ASP192 3.7 37.5 1.0
OP2 b:C5 3.8 28.8 0.5
MG A:MG202 3.8 25.7 1.0
CB A:ASP192 3.8 31.3 1.0
O5' b:C5 3.8 36.9 0.5
RB A:RB203 3.9 32.4 0.1
O b:HOH102 3.9 24.3 0.5
CA A:ASP192 3.9 27.1 1.0
RB A:RB205 3.9 40.2 0.1
OP2 b:G6 4.0 34.0 1.0
O A:VAL72 4.0 24.1 1.0
O5' b:C5 4.1 26.8 0.5
OD2 A:ASP132 4.1 34.7 1.0
HG22 A:ILE189 4.2 31.4 1.0
OD2 A:ASP192 4.2 32.0 1.0
C5' b:C5 4.2 34.0 1.0
O A:HOH308 4.3 30.6 0.5
N A:TYR193 4.3 30.8 1.0
OE1 A:GLU188 4.4 65.2 1.0
CB A:ASP71 4.4 20.6 1.0
HB3 A:ASP71 4.4 24.8 1.0
O3' B:U4 4.5 26.7 0.5
HD1 A:TYR193 4.5 32.2 1.0
HB2 A:ASP71 4.7 24.8 1.0
HG21 A:ILE189 4.7 31.4 1.0
C A:ASP192 4.7 28.9 1.0
HB3 A:ASP192 4.8 37.5 1.0
CG2 A:ILE189 4.8 26.1 1.0
HB2 A:TYR193 4.9 41.0 1.0
HG23 A:ILE189 4.9 31.4 1.0
H A:VAL72 5.0 26.5 1.0

Magnesium binding site 2 out of 2 in 6dou

Go back to Magnesium Binding Sites List in 6dou
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 120 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 120 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:25.7
occ:1.00
OD1 A:ASP71 2.1 25.2 1.0
OE1 A:GLU109 2.1 24.4 1.0
OD1 A:ASP132 2.1 25.5 1.0
OP1 b:C5 2.2 38.7 0.5
OP1 b:C5 2.3 34.5 0.5
O3' B:U4 2.6 26.7 0.5
OD2 A:ASP132 2.7 34.7 1.0
CG A:ASP132 2.7 27.9 1.0
P b:C5 3.0 27.8 0.5
CD A:GLU109 3.0 24.8 1.0
CG A:ASP71 3.1 21.9 1.0
O A:HOH347 3.2 23.5 1.0
OE2 A:GLU109 3.4 25.3 1.0
C3' B:U4 3.5 33.0 0.5
O3' B:U4 3.5 32.1 0.5
HG12 A:VAL72 3.6 29.6 1.0
OD2 A:ASP71 3.6 24.8 1.0
P b:C5 3.6 34.7 0.5
O A:HOH324 3.7 30.4 1.0
H A:VAL72 3.7 26.5 1.0
MG A:MG201 3.8 25.3 1.0
C3' B:U4 3.9 33.5 0.5
HA A:ASP71 4.0 20.0 1.0
O5' b:C5 4.0 26.8 0.5
OP2 b:C5 4.1 41.9 0.5
OP2 b:C5 4.1 28.8 0.5
C5' b:C5 4.1 34.0 1.0
H A:ASP132 4.2 23.6 1.0
CB A:ASP132 4.2 22.0 1.0
HB2 A:SER133 4.3 24.4 1.0
C4' B:U4 4.3 27.9 0.5
O2' B:U4 4.3 28.0 0.5
O5' b:C5 4.3 36.9 0.5
CB A:ASP71 4.4 20.6 1.0
HG21 A:ILE189 4.4 31.4 1.0
CG A:GLU109 4.4 23.1 1.0
C4' B:U4 4.5 28.4 0.5
CG1 A:VAL72 4.5 24.6 1.0
N A:VAL72 4.5 22.1 1.0
HG3 A:GLU109 4.6 27.7 1.0
C2' B:U4 4.6 25.4 0.5
OP3 b:C5 4.6 61.4 0.5
HB2 A:ASP71 4.6 24.8 1.0
CA A:ASP71 4.6 16.6 1.0
C5' B:U4 4.7 32.9 0.5
HB3 A:ASP132 4.7 26.4 1.0
HB2 A:ASP132 4.7 26.4 1.0
C2' B:U4 4.7 28.5 0.5
HG2 A:GLU109 4.7 27.7 1.0
C5' B:U4 4.7 32.6 0.5
HG13 A:VAL72 4.8 29.6 1.0
HG11 A:VAL72 4.9 29.6 1.0
CA A:ASP132 4.9 21.5 1.0
N A:ASP132 4.9 19.7 1.0
O A:HOH316 4.9 28.7 1.0
O A:VAL72 4.9 24.1 1.0
O2' B:U4 4.9 29.8 0.5
C A:ASP132 4.9 22.3 1.0
HG22 A:ILE189 4.9 31.4 1.0
RB A:RB204 4.9 32.3 0.2
O b:HOH101 5.0 27.5 0.5

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 Dec 14 22:36:11 2020

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