Magnesium in PDB 7vsc: E. Coli Ribonuclease Hi in Complex with One MG2+ (1)

All present enzymatic activity of E. Coli Ribonuclease Hi in Complex with One MG2+ (1):
3.1.26.4;

The structure of E. Coli Ribonuclease Hi in Complex with One MG2+ (1), PDB code: 7vsc 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)	49.04 / 1.83
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	61.998, 61.998, 80.138, 90, 90, 90
R / Rfree (%)	20.3 / 25

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

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


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+ (1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:29.9 occ:0.50 OE2 A:GLU48 1.9 33.6 1.0 OD1 A:ASP10 2.1 39.0 1.0 O A:HOH313 2.1 44.9 1.0 O A:HOH301 2.3 34.1 1.0 O A:HOH331 2.3 34.0 1.0 O A:HOH307 2.4 44.1 1.0 CD A:GLU48 2.9 31.8 1.0 CG A:ASP10 3.1 38.7 1.0 OE1 A:GLU48 3.3 36.3 1.0 MG A:MG202 3.3 45.3 1.0 OD1 A:ASP70 3.5 42.3 1.0 OD2 A:ASP10 3.6 38.6 1.0 O A:GLY11 3.7 30.2 1.0 N A:GLY11 3.9 27.9 1.0 OD2 A:ASP70 4.2 54.3 1.0 CG A:ASP70 4.2 43.4 1.0 CG A:GLU48 4.3 28.2 1.0 CB A:ASP10 4.4 31.2 1.0 OD1 A:ASN44 4.5 30.0 1.0 ND2 A:ASN44 4.5 31.0 1.0 CA A:ASP10 4.5 30.2 1.0 C A:GLY11 4.5 28.9 1.0 O A:HOH381 4.5 44.5 1.0 CA A:GLY11 4.7 30.3 1.0 C A:ASP10 4.8 29.2 1.0 CB A:SER71 4.8 32.5 1.0 O A:HOH358 4.8 32.8 1.0 CA A:SER71 4.8 33.7 1.0 CG A:ASN44 4.9 27.7 1.0 N A:SER71 5.0 36.9 1.0

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


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+ (1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:45.3 occ:1.00 O A:GLY11 2.3 30.2 1.0 O A:HOH331 2.4 34.0 1.0 OD1 A:ASP134 2.5 45.6 1.0 OD2 A:ASP10 2.6 38.6 1.0 OD1 A:ASP10 2.9 39.0 1.0 CG A:ASP10 3.1 38.7 1.0 O A:HOH369 3.2 47.1 1.0 MG A:MG201 3.3 29.9 0.5 O A:HOH307 3.4 44.1 1.0 C A:GLY11 3.5 28.9 1.0 CG A:ASP134 3.8 42.5 1.0 CA A:SER12 4.2 27.6 1.0 CB A:SER12 4.2 29.8 1.0 OD1 A:ASN44 4.3 30.0 1.0 N A:SER12 4.3 28.8 1.0 N A:GLY11 4.3 27.9 1.0 NE2 A:HIS124 4.4 51.7 1.0 CB A:ASP10 4.4 31.2 1.0 CB A:ASP134 4.5 35.7 1.0 OE2 A:GLU48 4.5 33.6 1.0 O A:HOH381 4.5 44.5 1.0 CA A:GLY11 4.6 30.3 1.0 O A:HOH334 4.6 31.9 1.0 OG A:SER12 4.7 34.2 1.0 OD2 A:ASP134 4.7 44.4 1.0 O A:HOH313 4.8 44.9 1.0 CA A:ASP134 4.8 32.4 1.0 CE1 A:HIS124 4.9 47.4 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