Magnesium in PDB 6doa: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 480 S at 21 C

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 480 S at 21 C, PDB code: 6doa 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)	31.14 / 1.47
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.731, 37.890, 62.695, 90.00, 96.66, 90.00
R / Rfree (%)	16 / 18.6

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

Potassium	(K)	3 atoms
Iodine	(I)	4 atoms

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 480 S at 21 C (pdb code 6doa). 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 480 S at 21 C, PDB code: 6doa:
Jump to Magnesium binding site number: 1; 2;

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 480 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 480 S at 21 C within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:16.9 occ:1.00 OD2 A:ASP71 2.0 14.8 1.0 OP3 b:C5 2.0 22.3 0.7 O A:HOH301 2.0 21.6 0.3 OD1 A:ASP192 2.0 19.4 1.0 O A:HOH307 2.1 20.2 1.0 O A:HOH320 2.1 17.8 1.0 OP1 b:C5 2.3 24.5 0.3 OP1 b:C5 2.4 20.1 0.7 P b:C5 2.7 18.3 0.7 CG A:ASP71 3.0 13.0 1.0 HA A:ASP192 3.1 22.0 1.0 CG A:ASP192 3.2 18.6 1.0 OD1 A:ASP71 3.4 13.7 1.0 P b:C5 3.5 15.0 0.3 HB2 A:ASP192 3.6 22.2 1.0 H A:TYR193 3.6 22.3 1.0 CB A:ASP192 3.7 18.5 1.0 OP2 b:C5 3.8 15.7 0.7 MG A:MG202 3.8 14.9 1.0 CA A:ASP192 3.9 18.3 1.0 O5' b:C5 3.9 16.9 0.7 NZ A:LYS196 3.9 24.7 0.7 OP2 b:C5 3.9 19.0 0.3 K A:K203 3.9 24.5 0.1 O b:HOH101 3.9 26.1 0.9 OP2 b:G6 4.0 21.4 1.0 OD2 A:ASP132 4.0 30.2 1.0 O A:VAL72 4.0 16.4 1.0 OE2 A:GLU188 4.1 44.5 1.0 HG22 A:ILE189 4.2 17.3 1.0 OD2 A:ASP192 4.2 21.6 1.0 O5' b:C5 4.2 17.5 0.3 C5' b:C5 4.3 17.4 1.0 N A:TYR193 4.3 18.6 1.0 CB A:ASP71 4.4 13.7 1.0 O A:HOH308 4.4 15.9 0.3 HB3 A:ASP71 4.4 16.4 1.0 HD1 A:TYR193 4.6 22.6 1.0 HB3 A:ASP192 4.7 22.2 1.0 C A:ASP192 4.7 20.4 1.0 HB2 A:ASP71 4.7 16.4 1.0 O3' B:U4 4.7 18.1 0.3 HG21 A:ILE189 4.7 17.3 1.0 CG2 A:ILE189 4.8 14.4 1.0 HG23 A:ILE189 4.9 17.3 1.0 HB2 A:TYR193 4.9 28.9 1.0 K A:K216 4.9 18.5 0.3 N A:ASP192 5.0 17.4 1.0

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 480 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 480 S at 21 C within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:14.9 occ:1.00 OD1 A:ASP71 2.0 13.7 1.0 OD1 A:ASP132 2.0 18.0 1.0 OE1 A:GLU109 2.0 14.0 1.0 OP1 b:C5 2.1 20.1 0.7 OP1 b:C5 2.2 24.5 0.3 O3' B:U4 2.6 18.1 0.3 CG A:ASP132 2.6 18.4 1.0 OD2 A:ASP132 2.6 30.2 1.0 P b:C5 2.9 15.0 0.3 CD A:GLU109 3.0 13.7 1.0 CG A:ASP71 3.1 13.0 1.0 O A:HOH342 3.2 15.6 1.0 OE2 A:GLU109 3.3 14.8 1.0 P b:C5 3.4 18.3 0.7 OD2 A:ASP71 3.5 14.8 1.0 C3' B:U4 3.6 21.3 0.7 HG12 A:VAL72 3.6 19.6 1.0 O3' B:U4 3.6 20.1 0.7 H A:VAL72 3.7 16.1 1.0 MG A:MG201 3.8 16.9 1.0 O A:HOH320 3.8 17.8 1.0 OP2 b:C5 3.9 15.7 0.7 C3' B:U4 3.9 31.5 0.3 HA A:ASP71 4.0 14.0 1.0 O5' b:C5 4.0 17.5 0.3 C5' b:C5 4.1 17.4 1.0 OP2 b:C5 4.1 19.0 0.3 CB A:ASP132 4.2 15.1 1.0 O5' b:C5 4.2 16.9 0.7 H A:ASP132 4.2 14.2 1.0 HB2 A:SER133 4.2 17.3 1.0 CB A:ASP71 4.3 13.7 1.0 OP3 b:C5 4.4 22.3 0.7 CG A:GLU109 4.4 11.4 1.0 C4' B:U4 4.4 24.9 0.3 O2' B:U4 4.4 16.9 0.3 HG21 A:ILE189 4.5 17.3 1.0 HG3 A:GLU109 4.5 13.7 1.0 C4' B:U4 4.5 23.0 0.7 N A:VAL72 4.5 13.4 1.0 CG1 A:VAL72 4.5 16.3 1.0 HB2 A:ASP71 4.6 16.4 1.0 CA A:ASP71 4.6 11.7 1.0 HB3 A:ASP132 4.6 18.1 1.0 HB2 A:ASP132 4.6 18.1 1.0 C5' B:U4 4.7 15.4 0.7 HG2 A:GLU109 4.7 13.7 1.0 C5' B:U4 4.7 30.2 0.3 C2' B:U4 4.7 20.0 0.7 C2' B:U4 4.8 23.3 0.3 O A:HOH307 4.8 20.2 1.0 CA A:ASP132 4.8 12.3 1.0 C A:ASP132 4.8 13.3 1.0 N A:ASP132 4.8 11.8 1.0 HG13 A:VAL72 4.9 19.6 1.0 K A:K216 4.9 18.5 0.3 O A:HOH301 4.9 21.6 0.3 O A:VAL72 4.9 16.4 1.0 HG22 A:ILE189 4.9 17.3 1.0 HG11 A:VAL72 4.9 19.6 1.0 O2' B:U4 5.0 23.3 0.7 N A:SER133 5.0 13.3 1.0

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