Magnesium in PDB 6do8: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ 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 2 Mm MG2+ and 200 Mm K+ 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 2 Mm MG2+ and 200 Mm K+ 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 2 Mm MG2+ and 200 Mm K+ For 80 S at 21 C, PDB code: 6do8 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) 19.85 / 1.41
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.284, 37.778, 62.072, 90.00, 96.22, 90.00
R / Rfree (%) 15 / 16.8

Other elements in 6do8:

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

Potassium (K) 2 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 80 S at 21 C (pdb code 6do8). 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 80 S at 21 C, PDB code: 6do8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6do8

Go back to Magnesium Binding Sites List in 6do8
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 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 2 Mm MG2+ and 200 Mm K+ For 80 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:19.2
occ:1.00
OD2 A:ASP71 1.9 23.5 1.0
OD1 A:ASP192 2.0 32.1 1.0
O A:HOH318 2.0 23.3 1.0
OP1 b:C5 2.1 22.0 0.8
O A:HOH338 2.2 23.6 1.0
O A:HOH308 2.3 26.7 0.8
CG A:ASP71 3.0 17.7 1.0
CG A:ASP192 3.1 31.0 1.0
HA A:ASP192 3.2 27.7 1.0
P b:C5 3.4 17.4 0.8
OD1 A:ASP71 3.4 22.5 1.0
H A:TYR193 3.5 35.6 1.0
HB2 A:ASP192 3.8 36.5 1.0
MG A:MG202 3.8 19.6 1.0
K A:K203 3.8 26.3 0.3
CB A:ASP192 3.8 30.4 1.0
OP2 b:C5 3.9 20.5 0.8
CA A:ASP192 4.0 23.1 1.0
O A:VAL72 4.1 18.4 1.0
OD2 A:ASP192 4.1 32.2 1.0
OP2 b:G6 4.1 23.4 1.0
HG22 A:ILE189 4.2 26.3 1.0
N A:TYR193 4.2 29.6 1.0
O5' b:C5 4.3 18.1 1.0
OE2 A:GLU188 4.3 72.7 1.0
CB A:ASP71 4.3 18.4 1.0
HB3 A:ASP71 4.4 22.1 1.0
OD2 A:ASP132 4.4 23.6 1.0
O A:HOH317 4.5 38.8 0.6
O3' B:U4 4.5 16.9 0.8
C5' b:C5 4.6 18.1 1.0
HB2 A:ASP71 4.6 22.1 1.0
HD1 A:TYR193 4.6 28.4 1.0
O b:HOH103 4.6 40.0 1.0
HG21 A:ILE189 4.6 26.3 1.0
C A:ASP192 4.7 24.8 1.0
HB2 A:TYR193 4.7 45.0 1.0
CG2 A:ILE189 4.7 21.9 1.0
HB3 A:ASP192 4.8 36.5 1.0
H A:VAL72 4.8 20.8 1.0
HG23 A:ILE189 4.9 26.3 1.0
CD A:GLU188 5.0 78.4 1.0

Magnesium binding site 2 out of 2 in 6do8

Go back to Magnesium Binding Sites List in 6do8
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 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 2 Mm MG2+ and 200 Mm K+ For 80 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:19.6
occ:1.00
OD1 A:ASP71 2.0 22.5 1.0
OD1 A:ASP132 2.3 17.8 1.0
OE1 A:GLU109 2.4 23.3 1.0
OP1 b:C5 2.6 22.0 0.8
O3' B:U4 2.8 16.9 0.8
OD2 A:ASP132 2.9 23.6 1.0
CG A:ASP132 2.9 18.2 1.0
CG A:ASP71 3.0 17.7 1.0
O A:HOH344 3.1 17.1 1.0
CD A:GLU109 3.2 20.0 1.0
OE2 A:GLU109 3.2 17.3 1.0
P b:C5 3.3 17.4 0.8
OD2 A:ASP71 3.5 23.5 1.0
HG12 A:VAL72 3.6 22.5 1.0
O A:HOH338 3.6 23.6 1.0
H A:VAL72 3.7 20.8 1.0
MG A:MG201 3.8 19.2 1.0
HA A:ASP71 3.9 19.1 1.0
C3' B:U4 4.0 19.5 0.8
C5' b:C5 4.1 18.1 1.0
O2' B:U4 4.2 19.5 1.0
H A:ASP132 4.2 15.8 1.0
O5' b:C5 4.2 18.1 1.0
CB A:ASP71 4.3 18.4 1.0
HG21 A:ILE189 4.3 26.3 1.0
C4' B:U4 4.4 21.0 1.0
HB2 A:SER133 4.4 16.9 1.0
CB A:ASP132 4.4 16.3 1.0
OP2 b:C5 4.5 20.5 0.8
HB2 A:ASP71 4.5 22.1 1.0
N A:VAL72 4.5 17.4 1.0
CG1 A:VAL72 4.5 18.8 1.0
CA A:ASP71 4.6 15.9 1.0
CG A:GLU109 4.6 17.2 1.0
O A:HOH318 4.7 23.3 1.0
C2' B:U4 4.8 16.5 1.0
HB3 A:ASP132 4.8 19.6 1.0
HG13 A:VAL72 4.8 22.5 1.0
HG3 A:GLU109 4.8 20.6 1.0
HG22 A:ILE189 4.9 26.3 1.0
HG11 A:VAL72 4.9 22.5 1.0
HG2 A:GLU109 4.9 20.6 1.0
N A:ASP132 4.9 13.1 1.0
HB2 A:ASP132 4.9 19.6 1.0
C5' B:U4 5.0 19.7 1.0
O A:VAL72 5.0 18.4 1.0
CA A:ASP132 5.0 14.5 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 Dec 14 22:35:48 2020

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