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Magnesium in PDB 6dob: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 200 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 200 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 200 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 200 S at 21 C, PDB code: 6dob 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) 32.29 / 1.34
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.376, 38.094, 62.117, 90.00, 96.16, 90.00
R / Rfree (%) 16.9 / 19.6

Other elements in 6dob:

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 200 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 200 S at 21 C (pdb code 6dob). 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 200 S at 21 C, PDB code: 6dob:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6dob

Go back to Magnesium Binding Sites List in 6dob
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 200 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 200 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:18.4
occ:1.00
OD1 A:ASP192 2.0 23.5 1.0
OD2 A:ASP71 2.0 16.2 1.0
O A:HOH302 2.0 25.6 0.5
OP3 b:C5 2.0 24.9 0.6
O A:HOH318 2.0 19.9 1.0
O A:HOH306 2.0 22.4 1.0
OP1 b:C5 2.3 24.7 0.5
OP1 b:C5 2.4 21.0 0.6
P b:C5 2.7 19.4 0.6
CG A:ASP71 3.0 16.4 1.0
CG A:ASP192 3.2 23.3 1.0
HA A:ASP192 3.2 22.6 1.0
OD1 A:ASP71 3.4 14.9 1.0
P b:C5 3.4 21.0 0.5
HB2 A:ASP192 3.6 25.8 1.0
H A:TYR193 3.6 26.8 1.0
CB A:ASP192 3.8 21.5 1.0
MG A:MG202 3.8 18.4 1.0
OP2 b:C5 3.8 18.8 0.6
NZ A:LYS196 3.8 22.9 0.6
OP2 b:C5 3.8 20.8 0.5
K A:K203 3.9 26.3 0.1
O5' b:C5 3.9 17.8 0.6
CA A:ASP192 3.9 18.8 1.0
OP2 b:G6 4.0 21.4 1.0
O A:VAL72 4.0 17.8 1.0
O b:HOH101 4.0 29.2 0.9
OD2 A:ASP132 4.1 30.6 1.0
OE2 A:GLU188 4.1 45.2 1.0
HG22 A:ILE189 4.2 20.5 1.0
OD2 A:ASP192 4.2 24.2 1.0
O5' b:C5 4.2 26.8 0.5
C5' b:C5 4.3 22.1 1.0
O A:HOH310 4.3 28.5 0.5
N A:TYR193 4.4 22.3 1.0
CB A:ASP71 4.4 13.4 1.0
HB3 A:ASP71 4.5 16.1 1.0
HD1 A:TYR193 4.6 22.8 1.0
O3' B:U4 4.6 22.9 0.5
HG21 A:ILE189 4.7 20.5 1.0
HB3 A:ASP192 4.7 25.8 1.0
HB2 A:ASP71 4.7 16.1 1.0
C A:ASP192 4.7 24.2 1.0
CG2 A:ILE189 4.8 17.1 1.0
K A:K217 4.9 23.7 0.3
HB2 A:TYR193 4.9 33.5 1.0
HG23 A:ILE189 4.9 20.5 1.0
CE A:LYS196 4.9 25.3 0.6

Magnesium binding site 2 out of 2 in 6dob

Go back to Magnesium Binding Sites List in 6dob
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 200 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 200 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:18.4
occ:1.00
OD1 A:ASP71 2.0 14.9 1.0
OE1 A:GLU109 2.0 16.9 1.0
OP1 b:C5 2.1 21.0 0.6
OD1 A:ASP132 2.1 19.3 1.0
OP1 b:C5 2.1 24.7 0.5
O3' B:U4 2.6 22.9 0.5
OD2 A:ASP132 2.7 30.6 1.0
CG A:ASP132 2.7 19.5 1.0
P b:C5 2.9 21.0 0.5
CD A:GLU109 3.0 15.4 1.0
CG A:ASP71 3.1 16.4 1.0
O A:HOH336 3.2 16.9 1.0
OE2 A:GLU109 3.3 16.1 1.0
P b:C5 3.4 19.4 0.6
HG12 A:VAL72 3.5 20.8 1.0
OD2 A:ASP71 3.5 16.2 1.0
C3' B:U4 3.6 21.6 0.6
O3' B:U4 3.6 17.7 0.6
H A:VAL72 3.7 19.5 1.0
MG A:MG201 3.8 18.4 1.0
O A:HOH318 3.8 19.9 1.0
HA A:ASP71 3.9 15.5 1.0
O5' b:C5 3.9 26.8 0.5
C3' B:U4 4.0 30.9 0.5
OP2 b:C5 4.0 18.8 0.6
C5' b:C5 4.1 22.1 1.0
OP2 b:C5 4.1 20.8 0.5
H A:ASP132 4.2 14.6 1.0
O5' b:C5 4.2 17.8 0.6
CB A:ASP132 4.2 14.8 1.0
HB2 A:SER133 4.3 15.1 1.0
CB A:ASP71 4.3 13.4 1.0
CG A:GLU109 4.4 12.2 1.0
OP3 b:C5 4.4 24.9 0.6
HG21 A:ILE189 4.4 20.5 1.0
O2' B:U4 4.4 21.4 0.5
CG1 A:VAL72 4.4 17.4 1.0
C4' B:U4 4.4 27.4 0.5
N A:VAL72 4.5 16.3 1.0
HG3 A:GLU109 4.5 14.6 1.0
C4' B:U4 4.5 27.7 0.6
HB2 A:ASP71 4.6 16.1 1.0
CA A:ASP71 4.6 12.9 1.0
HB3 A:ASP132 4.7 17.7 1.0
HG2 A:GLU109 4.7 14.6 1.0
HB2 A:ASP132 4.7 17.7 1.0
C5' B:U4 4.7 17.4 0.6
C2' B:U4 4.7 22.3 0.6
HG13 A:VAL72 4.7 20.8 1.0
C2' B:U4 4.8 22.2 0.5
C5' B:U4 4.8 29.4 0.5
O A:HOH306 4.8 22.4 1.0
HG11 A:VAL72 4.8 20.8 1.0
K A:K217 4.9 23.7 0.3
N A:ASP132 4.9 12.2 1.0
O A:HOH302 4.9 25.6 0.5
O A:VAL72 4.9 17.8 1.0
CA A:ASP132 4.9 13.8 1.0
HG22 A:ILE189 4.9 20.5 1.0
C A:ASP132 4.9 15.0 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 23:17:07 2024

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