Magnesium in PDB 6jxk: Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)

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

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

Resolution Low / High (Å)	47.79 / 4.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	191.510, 106.430, 250.960, 90.00, 107.79, 90.00
R / Rfree (%)	26.3 / 33.8

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

Fluorine	(F)	8 atoms
Potassium	(K)	6 atoms

The binding sites of Magnesium atom in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type) (pdb code 6jxk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type), PDB code: 6jxk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)


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 (Wild-Type) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:0.1 occ:1.00 MG A:MF41101 0.0 0.1 1.0 F3 A:MF41101 2.0 0.0 1.0 F2 A:MF41101 2.0 93.7 1.0 F4 A:MF41101 2.0 0.8 1.0 F1 A:MF41101 2.0 0.8 1.0 OD1 A:ASP385 2.7 91.5 1.0 OG1 A:THR626 3.1 93.4 1.0 OG1 A:THR387 3.1 0.7 1.0 O A:THR228 3.2 0.3 1.0 OD2 A:ASP385 3.2 97.0 1.0 CG A:ASP385 3.3 0.8 1.0 ND2 A:ASN729 3.4 0.5 1.0 N A:GLY627 3.7 96.2 1.0 CB A:THR387 3.7 0.4 1.0 CA A:GLY229 3.9 1.0 1.0 N A:THR387 4.0 0.1 1.0 O A:GLY229 4.1 0.3 1.0 C A:GLY229 4.1 0.8 1.0 CB A:THR626 4.2 94.4 1.0 C A:THR228 4.2 93.0 1.0 CA A:THR626 4.2 0.7 1.0 MG A:MG1102 4.3 80.3 1.0 CA A:THR387 4.5 0.2 1.0 N A:LYS386 4.5 0.6 1.0 C A:THR626 4.5 88.3 1.0 N A:GLY229 4.5 95.2 1.0 N A:ASP628 4.5 0.7 1.0 CA A:GLY627 4.6 0.7 1.0 CG A:ASN729 4.7 0.7 1.0 NZ A:LYS707 4.7 0.4 1.0 CB A:ASP385 4.7 0.2 1.0 N A:GLU230 4.9 0.8 1.0 O A:THR387 4.9 0.8 1.0 CG A:GLU230 5.0 0.6 1.0 CG2 A:THR387 5.0 0.5 1.0 C A:GLY627 5.0 0.5 1.0

Magnesium binding site 2 out of 4 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)


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 (Wild-Type) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:80.3 occ:1.00 OD2 A:ASP726 2.1 0.2 1.0 F2 A:MF41101 2.4 93.7 1.0 O A:THR387 2.4 0.8 1.0 OD1 A:ASP726 2.5 0.4 1.0 CG A:ASP726 2.7 0.2 1.0 OD2 A:ASP385 3.0 97.0 1.0 C A:THR387 3.1 0.1 1.0 CB A:THR387 3.3 0.4 1.0 O A:GLY229 3.4 0.3 1.0 CA A:THR387 3.7 0.2 1.0 CG A:ASP385 3.8 0.8 1.0 CG2 A:THR387 4.0 0.5 1.0 N A:GLY388 4.0 0.4 1.0 OD1 A:ASP385 4.1 91.5 1.0 CB A:ASP726 4.2 0.5 1.0 C A:GLY229 4.2 0.8 1.0 MG A:MF41101 4.3 0.1 1.0 CA A:GLY229 4.3 1.0 1.0 OG1 A:THR387 4.3 0.7 1.0 N A:THR387 4.3 0.1 1.0 N A:GLY727 4.4 0.3 1.0 CA A:GLY388 4.5 0.3 1.0 OD2 A:ASP730 4.5 0.3 1.0 OG1 A:THR389 4.6 0.2 1.0 CA A:GLY727 4.6 87.3 1.0 C A:GLY388 4.7 0.5 1.0 C A:ASP726 4.8 0.2 1.0 OD1 A:ASN729 4.8 0.7 1.0 F3 A:MF41101 4.9 0.0 1.0 CB A:ASP385 4.9 0.2 1.0

Magnesium binding site 3 out of 4 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1101 b:0.3 occ:1.00 MG E:MF41101 0.0 0.3 1.0 F3 E:MF41101 2.0 0.4 1.0 F2 E:MF41101 2.0 0.5 1.0 F1 E:MF41101 2.0 0.3 1.0 F4 E:MF41101 2.0 0.8 1.0 OD1 E:ASP385 3.0 0.1 1.0 O E:THR228 3.1 0.2 1.0 OG1 E:THR626 3.1 0.8 1.0 OG1 E:THR387 3.2 0.2 1.0 N E:GLY627 3.2 0.9 1.0 ND2 E:ASN729 3.6 0.1 1.0 CG E:ASP385 3.8 0.2 1.0 CA E:THR626 4.0 0.1 1.0 OD2 E:ASP385 4.0 0.8 1.0 CA E:GLY627 4.0 0.2 1.0 CB E:THR626 4.1 0.6 1.0 C E:THR626 4.1 0.6 1.0 C E:THR228 4.2 0.1 1.0 NZ E:LYS707 4.3 0.4 1.0 C E:GLY627 4.4 0.9 1.0 CA E:GLY229 4.4 0.9 1.0 N E:THR387 4.4 0.8 1.0 CB E:THR387 4.4 0.4 1.0 MG E:MG1102 4.5 0.5 1.0 N E:ASP628 4.6 1.0 1.0 N E:LYS386 4.6 0.1 1.0 CG E:ASN729 4.6 0.3 1.0 N E:GLY229 4.7 0.6 1.0 CG2 E:THR387 4.7 0.7 1.0 OD1 E:ASN729 4.8 0.6 1.0 O E:GLY627 4.9 0.6 1.0 C E:GLY229 5.0 0.1 1.0

Magnesium binding site 4 out of 4 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1102 b:0.5 occ:1.00 OD1 E:ASP726 2.0 0.5 1.0 OG1 E:THR387 2.0 0.2 1.0 O E:THR387 2.5 0.9 1.0 CB E:THR387 2.5 0.4 1.0 CG E:ASP726 2.6 0.4 1.0 OD2 E:ASP726 2.6 0.8 1.0 C E:THR387 2.9 0.7 1.0 OD2 E:ASP385 2.9 0.8 1.0 F2 E:MF41101 3.2 0.5 1.0 CA E:THR387 3.2 0.6 1.0 CG E:ASP385 3.7 0.2 1.0 N E:THR387 3.8 0.8 1.0 O E:GLY229 3.8 0.6 1.0 OD1 E:ASP385 3.8 0.1 1.0 CG2 E:THR387 3.9 0.7 1.0 N E:GLY388 3.9 0.9 1.0 CB E:ASP726 4.0 0.3 1.0 N E:GLY727 4.3 1.0 1.0 CA E:GLY229 4.5 0.9 1.0 MG E:MF41101 4.5 0.3 1.0 C E:GLY229 4.6 0.1 1.0 F3 E:MF41101 4.6 0.4 1.0 CA E:GLY388 4.6 0.1 1.0 CA E:GLY727 4.6 0.3 1.0 CA E:ASP726 4.8 0.6 1.0 C E:ASP726 4.8 0.5 1.0 OD2 E:ASP730 4.9 0.4 1.0 N E:ASP726 4.9 0.3 1.0 C E:LYS386 4.9 0.8 1.0 C E:GLY388 5.0 0.8 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