Magnesium in PDB 6jxi: Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP)

All present enzymatic activity of Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP):
7.2.2.19;

The structure of Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP), PDB code: 6jxi was solved by K.Abe, K.Irie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.67 / 2.60
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.380, 103.380, 369.860, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 26.3

The structure of Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP) also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Rubidium	(Rb)	6 atoms

The binding sites of Magnesium atom in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP) (pdb code 6jxi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP), PDB code: 6jxi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:35.7 occ:1.00 MG A:MF41101 0.0 35.7 1.0 F4 A:MF41101 2.0 28.2 1.0 F3 A:MF41101 2.0 33.7 1.0 F1 A:MF41101 2.0 59.6 1.0 F2 A:MF41101 2.0 41.6 1.0 OD1 A:ASP385 2.5 44.8 1.0 CG A:ASP385 3.5 43.5 1.0 OG1 A:THR626 3.5 35.3 1.0 O A:THR228 3.5 26.6 1.0 N A:GLY627 3.6 25.8 1.0 N A:THR387 3.8 28.5 1.0 OD2 A:ASP385 3.8 40.6 1.0 MG A:MG1105 3.8 44.9 1.0 CB A:THR387 3.9 40.1 1.0 O A:HOH1285 3.9 27.6 1.0 OE1 A:GLU230 4.0 49.9 1.0 OG1 A:THR387 4.0 52.5 1.0 CA A:THR626 4.1 36.5 1.0 ND2 A:ASN729 4.2 27.2 1.0 CB A:THR626 4.2 28.4 1.0 NZ A:LYS707 4.2 33.7 1.0 CA A:GLY229 4.2 25.2 1.0 CA A:THR387 4.4 38.9 1.0 C A:THR626 4.4 41.2 1.0 N A:LYS386 4.4 45.4 1.0 O A:THR387 4.5 47.7 1.0 CA A:GLY627 4.6 27.2 1.0 C A:THR228 4.6 46.5 1.0 C A:GLY229 4.6 34.0 1.0 N A:ASP628 4.7 26.4 1.0 O A:GLY229 4.8 52.6 1.0 CB A:ASP385 4.8 36.8 1.0 N A:GLY229 4.9 41.5 1.0 CD A:GLU230 4.9 37.5 1.0 C A:LYS386 4.9 41.4 1.0 C A:THR387 4.9 41.7 1.0

Magnesium binding site 2 out of 2 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1105 b:44.9 occ:1.00 O A:THR387 1.9 47.7 1.0 F2 A:MF41101 1.9 41.6 1.0 O A:HOH1285 2.1 27.6 1.0 O A:HOH1273 2.1 43.1 1.0 OD1 A:ASP726 2.2 49.5 1.0 OD2 A:ASP385 2.4 40.6 1.0 C A:THR387 3.0 41.7 1.0 CG A:ASP726 3.2 41.0 1.0 CG A:ASP385 3.3 43.5 1.0 OD2 A:ASP726 3.5 46.7 1.0 OD1 A:ASP385 3.6 44.8 1.0 CA A:THR387 3.8 38.9 1.0 MG A:MF41101 3.8 35.7 1.0 CB A:THR387 3.8 40.1 1.0 N A:THR387 4.0 28.5 1.0 O A:GLY229 4.1 52.6 1.0 N A:GLY388 4.1 33.3 1.0 CG2 A:THR387 4.4 26.3 1.0 OD2 A:ASP730 4.4 51.5 1.0 OG1 A:THR389 4.4 38.4 1.0 CA A:GLY229 4.4 25.2 1.0 CB A:ASP726 4.5 30.3 1.0 CA A:GLY388 4.5 41.2 1.0 F3 A:MF41101 4.6 33.7 1.0 N A:THR389 4.6 40.5 1.0 CB A:ASP385 4.6 36.8 1.0 N A:GLY727 4.6 37.9 1.0 C A:GLY229 4.7 34.0 1.0 OD1 A:ASN729 4.8 25.6 1.0 F4 A:MF41101 4.8 28.2 1.0 N A:ASP726 4.9 29.0 1.0 C A:GLY388 4.9 39.3 1.0 C A:ASP726 5.0 36.4 1.0 C A:LYS386 5.0 41.4 1.0 F1 A:MF41101 5.0 59.6 1.0

K.Yamamoto, V.Dubey, K.Irie, H.Nakanishi, H.Khandelia, Y.Fujiyoshi, K.Abe. A Single K+-Binding Site in the Crystal Structure of the Gastric Proton Pump. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 31436534
DOI: 10.7554/ELIFE.47701