Magnesium in PDB 8po8: Structure of Escherichia Coli Hrpa in Complex with Adp and Oligonucleotide Poly(Dc)11 Forming An I-Motif

All present enzymatic activity of Structure of Escherichia Coli Hrpa in Complex with Adp and Oligonucleotide Poly(Dc)11 Forming An I-Motif:
3.6.4.13;

The structure of Structure of Escherichia Coli Hrpa in Complex with Adp and Oligonucleotide Poly(Dc)11 Forming An I-Motif, PDB code: 8po8 was solved by B.G.Xin, L.G.Yuan, L.L.Zhang, S.M.Xie, N.N.Liu, X.Ai, H.H.Li, S.Rety, X.G.Xi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.98 / 2.52
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.26, 105.973, 177.552, 90, 90, 90
R / Rfree (%)	21.1 / 24.3

The binding sites of Magnesium atom in the Structure of Escherichia Coli Hrpa in Complex with Adp and Oligonucleotide Poly(Dc)11 Forming An I-Motif (pdb code 8po8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Escherichia Coli Hrpa in Complex with Adp and Oligonucleotide Poly(Dc)11 Forming An I-Motif, PDB code: 8po8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Escherichia Coli Hrpa in Complex with Adp and Oligonucleotide Poly(Dc)11 Forming An I-Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Escherichia Coli Hrpa in Complex with Adp and Oligonucleotide Poly(Dc)11 Forming An I-Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:37.7 occ:1.00 O A:HOH2126 2.0 31.6 1.0 OG1 A:THR107 2.0 33.3 1.0 O A:HOH2129 2.3 34.6 1.0 O A:HOH2120 2.3 32.8 1.0 O3B A:ADP2001 2.5 34.3 1.0 OE2 A:GLU198 2.7 36.3 1.0 CB A:THR107 3.2 33.1 1.0 OD1 A:ASP197 3.7 34.1 1.0 PB A:ADP2001 3.7 37.0 1.0 OD2 A:ASP197 3.8 32.1 1.0 CD A:GLU198 4.0 39.7 1.0 O1B A:ADP2001 4.0 40.1 1.0 CG A:ASP197 4.1 33.6 1.0 CG2 A:THR107 4.1 30.3 1.0 O2A A:ADP2001 4.1 39.1 1.0 CA A:THR107 4.2 32.7 1.0 N A:THR107 4.2 31.7 1.0 O A:SER354 4.2 46.3 1.0 O A:HOH2103 4.2 60.5 1.0 O A:THR353 4.5 43.3 1.0 O2B A:ADP2001 4.7 36.5 1.0 CA A:SER354 4.8 44.5 1.0 CG A:GLU198 4.8 34.5 1.0 OE1 A:GLU198 4.9 38.2 1.0 O3A A:ADP2001 4.9 36.7 1.0 C A:SER354 4.9 47.1 1.0

Magnesium binding site 2 out of 2 in the Structure of Escherichia Coli Hrpa in Complex with Adp and Oligonucleotide Poly(Dc)11 Forming An I-Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Escherichia Coli Hrpa in Complex with Adp and Oligonucleotide Poly(Dc)11 Forming An I-Motif within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:36.3 occ:1.00 O B:HOH2121 2.1 34.7 1.0 O B:HOH2113 2.1 38.5 1.0 O3B B:ADP2001 2.2 30.2 1.0 OG1 B:THR107 2.2 31.1 1.0 O B:HOH2115 2.3 31.5 1.0 OE2 B:GLU198 2.5 39.3 1.0 PB B:ADP2001 3.3 51.2 1.0 CB B:THR107 3.3 31.1 1.0 O1B B:ADP2001 3.6 35.3 1.0 CD B:GLU198 3.6 42.0 1.0 O B:HOH2139 3.9 34.6 1.0 OD1 B:ASP197 3.9 33.7 1.0 OE1 B:GLU198 4.0 41.9 1.0 O2A B:ADP2001 4.0 32.9 1.0 N B:THR107 4.1 29.3 1.0 OD2 B:ASP197 4.1 31.6 1.0 CA B:THR107 4.2 30.1 1.0 O2B B:ADP2001 4.3 33.9 1.0 O B:HOH2106 4.3 38.8 1.0 CG2 B:THR107 4.4 31.0 1.0 NZ B:LYS106 4.4 31.7 1.0 CG B:ASP197 4.4 33.0 1.0 O3A B:ADP2001 4.5 29.7 1.0 O B:SER354 4.6 50.6 1.0 O B:THR353 4.6 51.2 1.0 CE B:LYS106 4.6 31.4 1.0 PA B:ADP2001 4.8 32.2 1.0 CB B:LYS106 4.8 29.8 1.0 CG B:GLU198 4.9 34.8 1.0

B.G.Xin, L.Y.Huang, L.G.Yuan, N.N.Liu, H.H.Li, X.Ai, D.S.Lei, X.M.Hou, S.Rety, X.G.Xi. Structural Insights Into the N-Terminal Aphb Domain of Hrpa: Mediating Canonical and I-Motif Recognition. Nucleic Acids Res. V. 52 3406 2024.
ISSN: ESSN 1362-4962
PubMed: 38412313
DOI: 10.1093/NAR/GKAE138