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

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

The structure of K+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP), PDB code: 6jxh 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 / 2.50
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.370, 103.370, 370.010, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 25.7

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

Fluorine	(F)	4 atoms
Potassium	(K)	6 atoms

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

Magnesium binding site 1 out of 2 in the K+-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 K+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:45.3 occ:1.00 MG A:MF41101 0.0 45.3 1.0 F3 A:MF41101 2.0 50.4 1.0 F4 A:MF41101 2.0 41.2 1.0 F2 A:MF41101 2.0 49.3 1.0 F1 A:MF41101 2.0 54.9 1.0 OD1 A:ASP385 2.5 53.2 1.0 N A:GLY627 3.5 40.2 1.0 CG A:ASP385 3.5 55.2 1.0 OG1 A:THR626 3.6 38.5 1.0 OD2 A:ASP385 3.7 47.3 1.0 O A:THR228 3.7 36.5 1.0 N A:THR387 3.9 49.9 1.0 CB A:THR387 4.0 55.0 1.0 O A:HOH1219 4.0 38.8 1.0 MG A:MG1102 4.1 49.6 1.0 CA A:THR626 4.1 40.2 1.0 NZ A:LYS707 4.1 39.3 1.0 OG1 A:THR387 4.1 66.0 1.0 OE1 A:GLU230 4.2 73.5 1.0 CA A:GLY229 4.2 38.6 1.0 ND2 A:ASN729 4.3 39.4 1.0 CB A:THR626 4.3 47.0 1.0 C A:THR626 4.3 50.7 1.0 CA A:GLY627 4.3 32.4 1.0 N A:LYS386 4.5 60.7 1.0 CA A:THR387 4.5 53.0 1.0 O A:THR387 4.5 56.3 1.0 C A:GLY229 4.6 43.7 1.0 O A:GLY229 4.6 62.5 1.0 N A:ASP628 4.6 33.0 1.0 C A:THR228 4.7 59.8 1.0 CB A:ASP385 4.8 49.6 1.0 C A:LYS386 4.9 54.6 1.0 C A:GLY627 4.9 51.0 1.0 OD1 A:ASN729 4.9 40.8 1.0 N A:GLY229 5.0 50.2 1.0

Magnesium binding site 2 out of 2 in the K+-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 K+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:49.6 occ:1.00 O A:THR387 2.0 56.3 1.0 O A:HOH1346 2.0 61.4 1.0 F2 A:MF41101 2.1 49.3 1.0 O A:HOH1219 2.1 38.8 1.0 OD1 A:ASP726 2.2 44.5 1.0 OD2 A:ASP385 2.5 47.3 1.0 C A:THR387 3.1 50.4 1.0 CG A:ASP726 3.2 50.1 1.0 OD2 A:ASP726 3.5 64.5 1.0 CG A:ASP385 3.7 55.2 1.0 O A:GLY229 3.7 62.5 1.0 CB A:THR387 3.8 55.0 1.0 CA A:THR387 3.9 53.0 1.0 MG A:MF41101 4.1 45.3 1.0 N A:GLY388 4.1 41.4 1.0 OD1 A:ASP385 4.1 53.2 1.0 CG2 A:THR387 4.2 46.4 1.0 N A:THR387 4.3 49.9 1.0 CA A:GLY388 4.5 46.1 1.0 CA A:GLY229 4.5 38.6 1.0 N A:GLY727 4.5 52.3 1.0 C A:GLY229 4.5 43.7 1.0 OG1 A:THR389 4.5 48.9 1.0 CB A:ASP726 4.6 39.7 1.0 OD2 A:ASP730 4.6 74.5 1.0 OD1 A:ASN729 4.7 40.8 1.0 CA A:GLY727 4.8 54.6 1.0 N A:THR389 4.8 42.8 1.0 N A:ASP726 4.9 50.1 1.0 CB A:ASP385 4.9 49.6 1.0 C A:ASP726 5.0 51.7 1.0 C A:GLY388 5.0 38.7 1.0 F1 A:MF41101 5.0 54.9 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