Magnesium in PDB 6jd5: Atpase

The structure of Atpase, PDB code: 6jd5 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)	38.71 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.449, 69.691, 75.963, 90.00, 100.57, 90.00
R / Rfree (%)	17.6 / 22.5

The binding sites of Magnesium atom in the Atpase (pdb code 6jd5). 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: 6jd5:
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:Mg1402 b:33.1 occ:1.00 O A:HOH1539 1.9 25.6 1.0 O1B A:ATP1401 2.0 26.2 1.0 O A:HOH1536 2.1 25.0 1.0 OG1 A:THR1191 2.1 27.1 1.0 O1G A:ATP1401 2.2 29.9 1.0 O A:HOH1528 2.4 32.6 1.0 PB A:ATP1401 3.1 26.6 1.0 CB A:THR1191 3.1 27.9 1.0 O3B A:ATP1401 3.3 29.5 1.0 PG A:ATP1401 3.3 31.2 1.0 N A:THR1191 3.7 26.5 1.0 O A:HOH1557 3.9 37.6 1.0 CA A:THR1191 4.0 26.2 1.0 O A:HOH1526 4.1 32.0 1.0 OD2 A:ASP1285 4.1 26.8 1.0 O1A A:ATP1401 4.1 30.7 1.0 O A:HOH1604 4.1 33.5 1.0 O2B A:ATP1401 4.2 27.5 1.0 OD1 A:ASP1286 4.2 29.9 1.0 O3A A:ATP1401 4.2 26.8 1.0 OD2 A:ASP1286 4.3 28.8 1.0 CG2 A:THR1191 4.3 25.6 1.0 O2G A:ATP1401 4.3 25.0 1.0 OD1 A:ASP1285 4.3 28.0 1.0 O3G A:ATP1401 4.3 31.4 1.0 CB A:ALA1220 4.5 30.7 1.0 PA A:ATP1401 4.5 31.1 1.0 CG A:ASP1285 4.6 29.9 1.0 CB A:LYS1190 4.7 26.2 1.0 CG A:ASP1286 4.7 29.8 1.0 O2A A:ATP1401 4.7 31.3 1.0 CE A:LYS1190 4.8 24.6 1.0 C A:LYS1190 4.8 29.1 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:Mg1402 b:32.6 occ:1.00 O B:HOH1553 2.0 23.0 1.0 OG1 B:THR1191 2.0 22.7 1.0 O B:HOH1534 2.0 29.7 1.0 O1B B:ATP1401 2.1 29.8 1.0 O B:HOH1516 2.1 29.4 1.0 O1G B:ATP1401 2.3 26.1 1.0 CB B:THR1191 3.1 28.0 1.0 PB B:ATP1401 3.2 29.0 1.0 PG B:ATP1401 3.4 28.6 1.0 O3B B:ATP1401 3.4 29.7 1.0 N B:THR1191 3.7 24.3 1.0 O B:HOH1575 3.9 37.0 1.0 CA B:THR1191 3.9 25.1 1.0 OD2 B:ASP1285 4.0 28.9 1.0 O B:HOH1514 4.1 30.3 1.0 OD1 B:ASP1286 4.1 31.4 1.0 OD1 B:ASP1285 4.1 30.4 1.0 O1A B:ATP1401 4.2 31.5 1.0 CG2 B:THR1191 4.2 26.6 1.0 O2B B:ATP1401 4.2 29.1 1.0 OD2 B:ASP1286 4.2 28.7 1.0 O2G B:ATP1401 4.4 27.6 1.0 O3A B:ATP1401 4.4 28.3 1.0 O3G B:ATP1401 4.4 28.6 1.0 CG B:ASP1285 4.5 30.8 1.0 CB B:ALA1220 4.6 32.7 1.0 PA B:ATP1401 4.6 30.3 1.0 CB B:LYS1190 4.6 26.6 1.0 CG B:ASP1286 4.6 33.2 1.0 O2A B:ATP1401 4.8 31.9 1.0 C B:LYS1190 4.8 30.2 1.0 CE B:LYS1190 4.8 25.4 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