Magnesium in PDB 7vsd: E. Coli Ribonuclease Hi in Complex with One MG2+ (2)

All present enzymatic activity of E. Coli Ribonuclease Hi in Complex with One MG2+ (2):
3.1.26.4;

The structure of E. Coli Ribonuclease Hi in Complex with One MG2+ (2), PDB code: 7vsd 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)	47.69 / 1.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.363, 85.363, 77.798, 90, 90, 90
R / Rfree (%)	18.6 / 23

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

Magnesium binding site 1 out of 3 in the E. Coli Ribonuclease Hi in Complex with One MG2+ (2)


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 One MG2+ (2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:38.1 occ:1.00 O A:GLY11 2.5 24.6 1.0 OD1 A:ASN44 2.6 26.5 1.0 OE2 A:GLU48 2.8 32.2 1.0 MG A:MG203 3.2 46.9 1.0 CG A:ASN44 3.5 27.5 1.0 OD2 A:ASP10 3.6 33.5 1.0 C A:GLY11 3.7 22.1 1.0 O A:HOH305 3.7 47.6 1.0 CD A:GLU48 3.8 25.9 1.0 ND2 A:ASN44 3.8 29.1 1.0 O A:HOH326 3.9 29.7 1.0 CG A:GLU48 4.1 21.9 1.0 O A:HOH319 4.2 41.9 1.0 CA A:SER12 4.4 18.5 1.0 N A:SER12 4.5 18.7 1.0 CG A:ASP10 4.5 38.1 1.0 N A:GLY11 4.5 19.0 1.0 CA A:GLY11 4.7 18.3 1.0 O A:HOH301 4.7 42.8 1.0 OD1 A:ASP10 4.8 35.4 1.0 OE1 A:GLU48 4.8 28.6 1.0 CB A:ASN44 4.9 17.5 1.0

Magnesium binding site 2 out of 3 in the E. Coli Ribonuclease Hi in Complex with One MG2+ (2)


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 One MG2+ (2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:46.9 occ:1.00 O A:HOH305 2.6 47.6 1.0 OD1 A:ASP134 2.7 31.1 1.0 O A:GLY11 3.0 24.6 1.0 OD1 A:ASP10 3.0 35.4 1.0 MG A:MG202 3.2 38.1 1.0 O A:HOH319 3.2 41.9 1.0 CG A:ASP10 3.5 38.1 1.0 OD2 A:ASP10 3.6 33.5 1.0 CB A:SER12 3.7 24.0 1.0 CG A:ASP134 3.9 35.8 1.0 C A:GLY11 3.9 22.1 1.0 OG A:SER12 4.0 32.5 1.0 CA A:SER12 4.1 18.5 1.0 NE A:ARG138 4.2 33.6 1.0 NH2 A:ARG138 4.2 38.8 1.0 CB A:ASP134 4.4 22.8 1.0 N A:SER12 4.4 18.7 1.0 CZ A:ARG138 4.5 44.4 1.0 CA A:ASP134 4.6 26.3 1.0 CB A:ASP10 4.8 24.5 1.0 N A:GLY11 4.8 19.0 1.0 OD2 A:ASP134 4.9 31.7 1.0 CG A:ARG138 4.9 20.5 1.0 O A:HOH326 5.0 29.7 1.0 O A:ASP134 5.0 19.7 1.0 CA A:GLY11 5.0 18.3 1.0

Magnesium binding site 3 out of 3 in the E. Coli Ribonuclease Hi in Complex with One MG2+ (2)


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 One MG2+ (2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:40.3 occ:1.00 O B:HOH327 2.2 42.5 1.0 O B:HOH302 2.2 30.4 1.0 OD2 B:ASP10 2.3 35.9 1.0 OD1 B:ASP70 2.7 41.2 1.0 CG B:ASP10 2.7 34.3 1.0 N B:GLY11 3.1 19.7 1.0 O B:GLY11 3.1 26.8 1.0 OD1 B:ASP10 3.2 38.2 1.0 O B:HOH306 3.3 40.2 1.0 O B:HOH301 3.4 37.2 1.0 OE2 B:GLU48 3.5 32.7 1.0 CA B:ASP10 3.5 21.5 1.0 CG B:ASP70 3.5 43.1 1.0 OD2 B:ASP70 3.6 50.9 1.0 CB B:ASP10 3.7 23.3 1.0 C B:ASP10 3.8 18.2 1.0 CG B:GLU48 3.9 20.0 1.0 C B:GLY11 4.0 26.2 1.0 O B:HOH313 4.0 37.1 1.0 CD B:GLU48 4.1 28.4 1.0 CA B:GLY11 4.1 16.0 1.0 O B:HOH316 4.4 46.4 1.0 N B:ASP10 4.9 19.6 1.0 O B:THR9 4.9 23.7 1.0 CB B:ASP70 4.9 34.3 1.0 O B:ASP10 5.0 19.0 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