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Magnesium in PDB 6dod: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ 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 2 Mm MG2+ and 200 Mm K+ 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 2 Mm MG2+ and 200 Mm K+ 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 2 Mm MG2+ and 200 Mm K+ For 360 S at 21 C, PDB code: 6dod 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) 31.09 / 1.54
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.726, 37.835, 62.619, 90.00, 96.77, 90.00
R / Rfree (%) 16 / 19.5

Other elements in 6dod:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 360 S at 21 C also contains other interesting chemical elements:

Potassium (K) 3 atoms
Iodine (I) 4 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 2 Mm MG2+ and 200 Mm K+ For 360 S at 21 C (pdb code 6dod). 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 2 Mm MG2+ and 200 Mm K+ For 360 S at 21 C, PDB code: 6dod:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6dod

Go back to Magnesium Binding Sites List in 6dod
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 2 Mm MG2+ and 200 Mm K+ For 360 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 2 Mm MG2+ and 200 Mm K+ For 360 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:19.0
occ:1.00
OD2 A:ASP71 2.0 16.4 1.0
OP3 b:C5 2.0 25.0 0.7
O A:HOH301 2.0 23.0 0.3
OD1 A:ASP192 2.1 19.6 1.0
O A:HOH326 2.1 18.8 1.0
O A:HOH319 2.1 22.0 1.0
OP1 b:C5 2.3 26.2 0.3
OP1 b:C5 2.4 19.4 0.7
P b:C5 2.7 20.9 0.7
CG A:ASP71 3.0 14.4 1.0
CG A:ASP192 3.2 22.0 1.0
HA A:ASP192 3.2 24.3 1.0
OD1 A:ASP71 3.4 16.3 1.0
P b:C5 3.4 19.4 0.3
HB2 A:ASP192 3.6 24.1 1.0
H A:TYR193 3.6 24.3 1.0
CB A:ASP192 3.7 20.1 1.0
MG A:MG202 3.8 17.7 1.0
OP2 b:C5 3.8 21.3 0.7
OP2 b:C5 3.9 20.4 0.3
NZ A:LYS196 3.9 30.1 0.7
O5' b:C5 3.9 16.9 0.7
CA A:ASP192 3.9 20.2 1.0
OP2 b:G6 4.0 23.9 1.0
K A:K203 4.0 27.9 0.1
O b:HOH101 4.0 28.0 0.9
OD2 A:ASP132 4.0 33.9 1.0
O A:VAL72 4.0 19.2 1.0
OE2 A:GLU188 4.1 42.7 1.0
HG22 A:ILE189 4.1 21.4 1.0
O5' b:C5 4.2 19.8 0.3
OD2 A:ASP192 4.2 22.4 1.0
C5' b:C5 4.3 20.8 1.0
N A:TYR193 4.4 20.3 1.0
CB A:ASP71 4.4 14.2 1.0
HB3 A:ASP71 4.4 17.0 1.0
O A:HOH308 4.5 16.1 0.3
HD1 A:TYR193 4.6 22.6 1.0
HB3 A:ASP192 4.7 24.1 1.0
O3' B:U4 4.7 23.1 0.3
HB2 A:ASP71 4.7 17.0 1.0
C A:ASP192 4.7 22.5 1.0
HG21 A:ILE189 4.7 21.4 1.0
CG2 A:ILE189 4.8 17.9 1.0
HB2 A:TYR193 4.9 27.8 1.0
HG23 A:ILE189 4.9 21.4 1.0
K A:K217 4.9 18.4 0.3
N A:ASP192 5.0 18.6 1.0

Magnesium binding site 2 out of 2 in 6dod

Go back to Magnesium Binding Sites List in 6dod
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 2 Mm MG2+ and 200 Mm K+ For 360 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 2 Mm MG2+ and 200 Mm K+ For 360 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:17.7
occ:1.00
OD1 A:ASP71 2.0 16.3 1.0
OD1 A:ASP132 2.0 20.1 1.0
OE1 A:GLU109 2.0 16.9 1.0
OP1 b:C5 2.1 19.4 0.7
OP1 b:C5 2.2 26.2 0.3
O3' B:U4 2.6 23.1 0.3
CG A:ASP132 2.6 18.6 1.0
OD2 A:ASP132 2.7 33.9 1.0
P b:C5 2.9 19.4 0.3
CD A:GLU109 3.0 16.5 1.0
CG A:ASP71 3.0 14.4 1.0
O A:HOH349 3.2 19.4 1.0
OE2 A:GLU109 3.3 17.2 1.0
P b:C5 3.5 20.9 0.7
OD2 A:ASP71 3.5 16.4 1.0
C3' B:U4 3.6 25.1 0.7
HG12 A:VAL72 3.6 20.8 1.0
O3' B:U4 3.7 22.0 0.7
H A:VAL72 3.7 17.5 1.0
MG A:MG201 3.8 19.0 1.0
O A:HOH326 3.9 18.8 1.0
HA A:ASP71 3.9 16.3 1.0
C3' B:U4 3.9 31.6 0.3
O5' b:C5 4.0 19.8 0.3
OP2 b:C5 4.0 21.3 0.7
OP2 b:C5 4.1 20.4 0.3
H A:ASP132 4.1 16.2 1.0
C5' b:C5 4.1 20.8 1.0
CB A:ASP132 4.1 18.2 1.0
HB2 A:SER133 4.2 21.2 1.0
O5' b:C5 4.2 16.9 0.7
CB A:ASP71 4.3 14.2 1.0
CG A:GLU109 4.3 13.6 1.0
C4' B:U4 4.4 26.5 0.3
OP3 b:C5 4.4 25.0 0.7
HG21 A:ILE189 4.4 21.4 1.0
HG3 A:GLU109 4.4 16.3 1.0
N A:VAL72 4.5 14.6 1.0
C4' B:U4 4.5 25.4 0.7
O2' B:U4 4.5 17.2 0.3
CG1 A:VAL72 4.5 17.3 1.0
CA A:ASP71 4.6 13.6 1.0
HB2 A:ASP71 4.6 17.0 1.0
HB2 A:ASP132 4.6 21.9 1.0
HB3 A:ASP132 4.6 21.9 1.0
C5' B:U4 4.6 29.6 0.3
C5' B:U4 4.6 17.6 0.7
HG2 A:GLU109 4.7 16.3 1.0
C2' B:U4 4.7 24.9 0.7
N A:ASP132 4.8 13.5 1.0
CA A:ASP132 4.8 14.0 1.0
C A:ASP132 4.8 16.1 1.0
C2' B:U4 4.8 26.8 0.3
HG13 A:VAL72 4.9 20.8 1.0
O A:HOH319 4.9 22.0 1.0
O A:VAL72 4.9 19.2 1.0
O A:HOH301 4.9 23.0 0.3
K A:K217 4.9 18.4 0.3
HG22 A:ILE189 4.9 21.4 1.0
HG11 A:VAL72 4.9 20.8 1.0
N A:SER133 4.9 14.0 1.0
O2' B:U4 5.0 26.7 0.7

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 23:17:38 2024

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