Magnesium in PDB 6jd4: Atpase

The structure of Atpase, PDB code: 6jd4 was solved by S.H.Wang, J.Li, Z.H.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.72 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.220, 77.314, 106.011, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.6

The binding sites of Magnesium atom in the Atpase (pdb code 6jd4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Atpase, PDB code: 6jd4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:6.9 occ:1.00 O1G A:ATP602 2.0 10.5 1.0 O1B A:ATP602 2.0 5.3 1.0 O A:HOH716 2.1 8.3 1.0 OG1 A:THR383 2.1 9.9 1.0 O A:HOH774 2.1 2.8 1.0 O A:HOH728 2.2 6.1 1.0 PB A:ATP602 3.2 7.7 1.0 PG A:ATP602 3.3 11.0 1.0 CB A:THR383 3.4 13.3 1.0 O3B A:ATP602 3.6 10.3 1.0 O A:HOH747 3.9 17.0 1.0 O A:HOH733 3.9 5.2 1.0 OD1 A:ASP477 3.9 13.2 1.0 O2G A:ATP602 4.0 12.4 1.0 N A:THR383 4.0 9.5 1.0 OD2 A:ASP477 4.0 12.5 1.0 OD2 A:ASP476 4.1 22.1 1.0 O2B A:ATP602 4.1 7.0 1.0 CA A:THR383 4.2 13.9 1.0 O2A A:ATP602 4.3 7.9 1.0 CG2 A:THR383 4.3 8.9 1.0 CG A:ASP477 4.4 12.4 1.0 OD1 A:ASP476 4.5 17.8 1.0 O3A A:ATP602 4.5 9.5 1.0 O3G A:ATP602 4.5 9.6 1.0 CG A:ASP476 4.7 21.4 1.0 NE A:ARG410 4.7 7.0 1.0 PA A:ATP602 4.8 11.3 1.0 CB A:LYS382 4.8 10.1 1.0 CE A:LYS382 4.9 17.4 1.0 O A:HOH769 5.0 11.7 1.0 CD A:ARG410 5.0 7.1 1.0

Magnesium binding site 2 out of 2 in the Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Atpase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:8.5 occ:1.00 O2G B:ATP602 2.0 10.1 1.0 OG1 B:THR383 2.0 9.0 1.0 O2B B:ATP602 2.0 8.7 1.0 O B:HOH774 2.1 3.3 1.0 O B:HOH715 2.1 8.9 1.0 O B:HOH741 2.3 6.6 1.0 PB B:ATP602 3.2 6.1 1.0 PG B:ATP602 3.3 9.4 1.0 CB B:THR383 3.3 7.3 1.0 O3B B:ATP602 3.5 9.9 1.0 O B:HOH768 3.9 4.8 1.0 O B:HOH734 3.9 17.1 1.0 OD1 B:ASP477 3.9 17.7 1.0 N B:THR383 4.0 9.9 1.0 OD2 B:ASP477 4.0 13.8 1.0 O3G B:ATP602 4.0 12.4 1.0 O1B B:ATP602 4.1 10.6 1.0 OD2 B:ASP476 4.1 13.3 1.0 O2A B:ATP602 4.2 8.2 1.0 CA B:THR383 4.2 7.3 1.0 CG2 B:THR383 4.3 5.6 1.0 CG B:ASP477 4.4 13.1 1.0 O1G B:ATP602 4.5 12.6 1.0 O3A B:ATP602 4.5 7.0 1.0 OD1 B:ASP476 4.5 10.8 1.0 NE B:ARG410 4.7 7.9 1.0 CG B:ASP476 4.7 12.2 1.0 PA B:ATP602 4.8 10.3 1.0 O B:HOH737 4.9 13.6 1.0 CB B:LYS382 4.9 11.5 1.0 CE B:LYS382 5.0 16.7 1.0

S.Wang, K.Zhou, X.Yang, B.Zhang, Y.Zhao, Y.Xiao, X.Yang, H.Yang, L.W.Guddat, J.Li, Z.Rao. Structural Insights Into Substrate Recognition By the Type VII Secretion System. Protein Cell 2019.
ISSN: ESSN 1674-8018
PubMed: 31758528
DOI: 10.1007/S13238-019-00671-Z