Magnesium in PDB 8po7: Structure of Escherichia Coli Hrpa in Complex with Adp and Dinucleotide Dcdc

All present enzymatic activity of Structure of Escherichia Coli Hrpa in Complex with Adp and Dinucleotide Dcdc:
3.6.4.13;

The structure of Structure of Escherichia Coli Hrpa in Complex with Adp and Dinucleotide Dcdc, PDB code: 8po7 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)	89.14 / 2.26
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.47, 106.124, 178.276, 90, 90, 90
R / Rfree (%)	19 / 23.2

The binding sites of Magnesium atom in the Structure of Escherichia Coli Hrpa in Complex with Adp and Dinucleotide Dcdc (pdb code 8po7). 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 Dinucleotide Dcdc, PDB code: 8po7:
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 Dinucleotide Dcdc


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 Dinucleotide Dcdc within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:18.4 occ:1.00 O A:HOH2113 2.1 18.4 1.0 O A:HOH2163 2.1 16.4 1.0 O1B A:ADP2001 2.2 23.8 1.0 O A:HOH2144 2.2 17.8 1.0 OG1 A:THR107 2.2 20.8 1.0 O A:HOH2137 2.3 13.7 1.0 CB A:THR107 3.2 21.6 1.0 PB A:ADP2001 3.3 20.1 1.0 O3B A:ADP2001 3.5 20.6 1.0 OE2 A:GLU198 3.7 22.6 1.0 OD1 A:ASP197 3.9 19.8 1.0 OD2 A:ASP197 4.0 18.8 1.0 O1A A:ADP2001 4.0 17.1 1.0 N A:THR107 4.0 20.4 1.0 O A:HOH2146 4.0 28.3 1.0 CA A:THR107 4.2 22.6 1.0 CG2 A:THR107 4.3 14.2 1.0 O A:HOH2143 4.3 15.6 1.0 CG A:ASP197 4.3 24.0 1.0 O2B A:ADP2001 4.4 20.6 1.0 O A:SER354 4.4 31.5 1.0 O3A A:ADP2001 4.4 13.2 1.0 O A:THR353 4.5 28.2 1.0 O A:HOH2101 4.6 42.2 1.0 CD A:GLU198 4.7 40.5 1.0 PA A:ADP2001 4.7 22.3 1.0 O A:HOH2255 4.7 31.0 1.0 NZ A:LYS106 4.8 16.5 1.0 CE A:LYS106 4.8 14.5 1.0 CB A:LYS106 4.8 15.6 1.0 O A:HOH2237 4.9 25.8 1.0

Magnesium binding site 2 out of 2 in the Structure of Escherichia Coli Hrpa in Complex with Adp and Dinucleotide Dcdc


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 Dinucleotide Dcdc within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:20.6 occ:1.00 O1B B:ADP2001 2.1 14.6 1.0 O B:HOH2105 2.1 19.7 1.0 OG1 B:THR107 2.1 19.4 1.0 O B:HOH2145 2.1 25.7 1.0 O B:HOH2186 2.2 15.6 1.0 O B:HOH2116 2.2 11.9 1.0 CB B:THR107 3.2 19.7 1.0 PB B:ADP2001 3.3 19.9 1.0 O3B B:ADP2001 3.5 23.6 1.0 OE2 B:GLU198 3.6 30.6 1.0 O2A B:ADP2001 3.9 15.3 1.0 OD1 B:ASP197 4.0 18.6 1.0 N B:THR107 4.0 16.7 1.0 O B:HOH2121 4.1 16.5 1.0 OD2 B:ASP197 4.1 20.0 1.0 O B:SER354 4.1 33.3 1.0 O B:HOH2129 4.1 23.5 1.0 CA B:THR107 4.2 16.9 1.0 CG2 B:THR107 4.2 18.8 1.0 O2B B:ADP2001 4.3 17.0 1.0 O3A B:ADP2001 4.4 22.3 1.0 O B:THR353 4.4 36.9 1.0 CG B:ASP197 4.4 22.0 1.0 O B:HOH2101 4.6 33.0 1.0 CD B:GLU198 4.6 37.5 1.0 PA B:ADP2001 4.7 20.9 1.0 NZ B:LYS106 4.7 17.1 1.0 O B:HOH2252 4.8 22.8 1.0 CE B:LYS106 4.9 19.9 1.0 CB B:LYS106 4.9 16.3 1.0 C B:SER354 4.9 29.2 1.0 CA B:SER354 4.9 30.9 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