Magnesium in PDB 7vsa: E. Coli Ribonuclease Hi in Complex with Two MG2+

All present enzymatic activity of E. Coli Ribonuclease Hi in Complex with Two MG2+:
3.1.26.4;

The structure of E. Coli Ribonuclease Hi in Complex with Two MG2+, PDB code: 7vsa was solved by Z.Liao, T.Oyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.89 / 1.76
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	61.639, 64.288, 80.288, 90, 90, 90
R / Rfree (%)	20.1 / 23.3

The binding sites of Magnesium atom in the E. Coli Ribonuclease Hi in Complex with Two MG2+ (pdb code 7vsa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the E. Coli Ribonuclease Hi in Complex with Two MG2+, PDB code: 7vsa:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the E. Coli Ribonuclease Hi in Complex with Two MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Ribonuclease Hi in Complex with Two MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:17.8 occ:0.55 OE2 A:GLU48 2.0 30.2 1.0 O A:HOH304 2.0 29.5 1.0 OD1 A:ASP10 2.1 26.4 1.0 O A:HOH338 2.1 32.7 1.0 O A:HOH336 2.1 24.7 1.0 O A:HOH305 2.2 31.7 1.0 CD A:GLU48 3.0 26.4 1.0 CG A:ASP10 3.2 27.9 1.0 OE1 A:GLU48 3.4 27.7 1.0 MG A:MG204 3.6 40.2 1.0 OD2 A:ASP10 3.8 33.8 1.0 O A:GLY11 3.9 21.6 1.0 OD1 A:ASP70 3.9 35.9 1.0 N A:GLY11 4.2 22.8 1.0 OD2 A:ASP70 4.2 40.0 1.0 ND2 A:ASN44 4.2 21.2 1.0 CG A:GLU48 4.3 21.0 1.0 CG A:ASP70 4.4 35.0 1.0 O A:HOH301 4.5 31.5 1.0 OD1 A:ASN44 4.5 28.4 1.0 CB A:ASP10 4.5 26.9 1.0 CA A:ASP10 4.6 21.7 1.0 C A:GLY11 4.8 22.8 1.0 CG A:ASN44 4.8 22.6 1.0 CB A:SER71 4.8 25.7 1.0 CA A:SER71 4.9 24.0 1.0 CA A:GLY11 5.0 18.6 1.0 C A:ASP10 5.0 19.7 1.0 NE2 A:HIS124 5.0 37.0 1.0 N A:SER71 5.0 27.8 1.0

Magnesium binding site 2 out of 4 in the E. Coli Ribonuclease Hi in Complex with Two MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Ribonuclease Hi in Complex with Two MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:40.2 occ:1.00 O A:GLY11 2.4 21.6 1.0 OD2 A:ASP10 2.5 33.8 1.0 O A:HOH336 2.5 24.7 1.0 OD1 A:ASP134 2.8 37.8 1.0 O A:HOH360 3.0 42.5 1.0 CG A:ASP10 3.0 27.9 1.0 OD1 A:ASP10 3.0 26.4 1.0 O A:HOH305 3.5 31.7 1.0 MG A:MG203 3.6 17.8 0.6 C A:GLY11 3.6 22.8 1.0 CG A:ASP134 3.9 37.6 1.0 O A:HOH367 4.0 54.0 1.0 CE1 A:HIS124 4.2 41.0 1.0 CA A:SER12 4.3 22.3 1.0 CB A:ASP10 4.4 26.9 1.0 CB A:ASP134 4.4 26.6 1.0 NE2 A:HIS124 4.4 37.0 1.0 CB A:SER12 4.4 22.6 1.0 N A:SER12 4.4 21.0 1.0 N A:GLY11 4.4 22.8 1.0 OD1 A:ASN44 4.5 28.4 1.0 OE2 A:GLU48 4.5 30.2 1.0 O A:HOH333 4.7 27.4 1.0 CA A:GLY11 4.7 18.6 1.0 CA A:ASP134 4.7 26.4 1.0 OD2 A:ASP134 4.9 36.7 1.0 OG A:SER12 4.9 33.1 1.0

Magnesium binding site 3 out of 4 in the E. Coli Ribonuclease Hi in Complex with Two MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E. Coli Ribonuclease Hi in Complex with Two MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:39.4 occ:1.00 OE2 B:GLU48 2.0 31.8 1.0 O B:HOH318 2.1 33.5 1.0 O B:HOH304 2.3 36.8 1.0 OD1 B:ASP10 2.4 35.2 1.0 O B:HOH303 2.7 48.5 1.0 CD B:GLU48 3.0 32.1 1.0 OE1 B:GLU48 3.5 37.2 1.0 CG B:ASP10 3.5 38.1 1.0 O B:GLY11 3.8 30.6 1.0 OD2 B:ASP70 3.9 57.5 1.0 MG B:MG202 3.9 56.0 1.0 OD1 B:ASP70 3.9 48.2 1.0 OD2 B:ASP10 4.0 46.5 1.0 CG B:ASP70 4.2 49.8 1.0 N B:GLY11 4.2 30.4 1.0 ND2 B:ASN44 4.3 34.2 1.0 CG B:GLU48 4.3 29.8 1.0 OD1 B:ASN44 4.4 30.8 1.0 CA B:SER71 4.7 33.4 1.0 C B:GLY11 4.8 30.4 1.0 CB B:ASP10 4.8 38.0 1.0 CG B:ASN44 4.8 28.6 1.0 CB B:SER71 4.9 29.9 1.0 CA B:ASP10 4.9 33.8 1.0 N B:SER71 4.9 36.1 1.0 CA B:GLY11 5.0 28.5 1.0

Magnesium binding site 4 out of 4 in the E. Coli Ribonuclease Hi in Complex with Two MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E. Coli Ribonuclease Hi in Complex with Two MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:56.0 occ:1.00 OD1 B:ASP134 2.4 53.1 1.0 O B:HOH318 2.6 33.5 1.0 O B:GLY11 2.7 30.6 1.0 OD2 B:ASP10 2.8 46.5 1.0 O B:HOH353 3.0 46.2 1.0 O B:HOH303 3.4 48.5 1.0 CG B:ASP10 3.4 38.1 1.0 OD1 B:ASP10 3.4 35.2 1.0 CG B:ASP134 3.6 48.7 1.0 C B:GLY11 3.9 30.4 1.0 MG B:MG201 3.9 39.4 1.0 CB B:SER12 4.2 29.9 1.0 CA B:SER12 4.3 30.5 1.0 CB B:ASP134 4.4 42.8 1.0 N B:SER12 4.5 22.6 1.0 O B:HOH327 4.6 32.4 1.0 OD2 B:ASP134 4.6 56.0 1.0 NE2 B:HIS124 4.6 65.7 1.0 CE1 B:HIS124 4.6 72.3 1.0 OD1 B:ASN44 4.6 30.8 1.0 CA B:ASP134 4.7 38.2 1.0 OG B:SER12 4.7 40.4 1.0 NE B:ARG138 4.7 47.7 1.0 CB B:ASP10 4.7 38.0 1.0 NH2 B:ARG138 4.8 52.1 1.0 N B:GLY11 4.8 30.4 1.0 OE2 B:GLU48 4.9 31.8 1.0 CA B:GLY11 5.0 28.5 1.0

Z.Liao, T.Oyama, Y.Kitagawa, K.Katayanagi, K.Morikawa, M.Oda. Pivotal Role of A Conserved Histidine in Escherichia Coli Ribonuclease Hi As Proposed By X-Ray Crystallography. Acta Crystallogr D Struct V. 78 390 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35234152
DOI: 10.1107/S2059798322000870