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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 6jxi:

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

Fluorine (F) 4 atoms
Magnesium (Mg) 2 atoms

Rubidium Binding Sites:

The binding sites of Rubidium 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 Rubidium atom.
In total 6 binding sites of Rubidium where determined in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP), PDB code: 6jxi:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5; 6;

Rubidium binding site 1 out of 6 in 6jxi

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Rubidium binding site 1 out of 6 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP)


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb 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:Rb1106

b:75.9
occ:1.00
 O A:ALA746 2.9 48.5 1.0
OD2 A:ASP726 2.9 46.7 1.0
O A:ASP726 3.2 33.4 1.0
O A:HOH1326 3.5 72.0 1.0
N A:SER748 3.8 29.9 1.0
CG A:ASP726 3.9 41.0 1.0
O A:HOH1273 3.9 43.1 1.0
C A:ASP726 4.0 36.4 1.0
C A:ALA746 4.1 41.1 1.0
CB A:SER748 4.1 45.0 1.0
C A:GLY747 4.3 42.5 1.0
OG A:SER748 4.3 45.8 1.0
CA A:GLY727 4.3 38.2 1.0
CB A:ASP726 4.4 30.3 1.0
CA A:SER748 4.5 37.4 1.0
CA A:GLY747 4.5 27.6 1.0
N A:GLY727 4.6 37.9 1.0
O A:HOH1375 4.6 58.9 1.0
OD1 A:ASP726 4.7 49.5 1.0
N A:GLY747 4.8 38.0 1.0
CA A:ASP726 4.9 29.1 1.0
O A:HOH1322 4.9 60.5 1.0
O A:GLY747 4.9 62.9 1.0

Rubidium binding site 2 out of 6 in 6jxi

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Rubidium binding site 2 out of 6 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP)


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb 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:Rb1107

b:90.1
occ:1.00
 O A:HOH1315 2.8 57.1 1.0
O A:VAL456 2.8 78.2 1.0
O A:GLY458 3.0 55.8 1.0
O A:HOH1446 3.0 44.8 1.0
OG1 A:THR463 3.3 50.1 1.0
O A:HOH1367 3.4 58.7 1.0
O A:HOH1369 3.6 68.7 1.0
C A:VAL456 3.8 69.1 1.0
N A:GLY458 4.1 56.4 1.0
C A:GLY458 4.1 49.4 1.0
CG2 A:THR463 4.2 54.2 1.0
CB A:THR463 4.2 53.3 1.0
CB A:VAL456 4.4 48.8 1.0
CA A:VAL456 4.5 60.3 1.0
N A:VAL456 4.6 62.1 1.0
O A:ASP459 4.6 33.8 1.0
CA A:GLY458 4.7 53.0 1.0
N A:ILE457 4.7 66.6 1.0
CG1 A:VAL456 4.9 49.4 1.0
CA A:ILE457 4.9 68.7 1.0
C A:ILE457 4.9 61.5 1.0
C A:ASP459 4.9 42.6 1.0

Rubidium binding site 3 out of 6 in 6jxi

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Rubidium binding site 3 out of 6 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP)


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 3 of Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1108

b:48.8
occ:1.00
 O A:ALA737 2.7 32.9 1.0
O A:HOH1253 2.9 28.1 1.0
O A:LYS735 2.9 41.7 1.0
OD1 A:ASP756 3.0 47.7 1.0
O A:LEU734 3.1 40.7 1.0
C A:LYS735 3.6 36.9 1.0
CG A:ASP756 3.8 45.6 1.0
OD2 A:ASP756 3.8 56.8 1.0
C A:ALA737 3.9 26.7 1.0
RB A:RB1109 3.9 81.7 1.0
CA A:LYS735 3.9 28.8 1.0
C A:LEU734 4.1 40.8 1.0
N A:GLY740 4.3 23.6 1.0
N A:ALA737 4.3 33.4 1.0
C A:ASP738 4.5 30.4 1.0
O A:ASP738 4.5 37.2 1.0
N A:LYS735 4.5 30.3 1.0
CA A:ILE739 4.5 31.1 1.0
CA A:ALA737 4.5 32.0 1.0
N A:LYS736 4.6 22.9 1.0
C A:ILE739 4.6 35.7 1.0
N A:ILE739 4.6 33.0 1.0
O A:ALA754 4.7 38.0 1.0
C A:LYS736 4.8 28.9 1.0
CB A:ALA737 4.8 24.2 1.0
N A:ASP738 4.9 38.5 1.0
CD A:LYS735 4.9 49.9 1.0
CA A:ASP738 5.0 35.2 1.0
CA A:GLY740 5.0 25.3 1.0

Rubidium binding site 4 out of 6 in 6jxi

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Rubidium binding site 4 out of 6 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP)


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 4 of Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1109

b:81.7
occ:1.00
 O A:LYS735 2.9 41.7 1.0
O A:ALA737 3.1 32.9 1.0
O A:LYS736 3.3 27.6 1.0
OE1 A:GLU289 3.5 94.7 1.0
C A:LYS736 3.6 28.9 1.0
C A:ALA737 3.8 26.7 1.0
RB A:RB1108 3.9 48.8 1.0
CA A:LYS736 3.9 27.3 1.0
C A:LYS735 4.0 36.9 1.0
CB A:GLU289 4.1 89.0 1.0
N A:ALA737 4.2 33.4 1.0
CD A:GLU289 4.4 98.0 1.0
N A:LYS736 4.5 22.9 1.0
N A:ASP738 4.5 38.5 1.0
CA A:ASP738 4.6 35.2 1.0
CA A:ALA737 4.7 32.0 1.0
O A:GLU289 4.8 80.7 1.0
CG A:GLU289 4.9 93.1 1.0
OD1 A:ASP738 5.0 53.3 1.0
O A:GLU287 5.0 0.4 1.0

Rubidium binding site 5 out of 6 in 6jxi

Go back to Rubidium Binding Sites List in 6jxi
Rubidium binding site 5 out of 6 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP)


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 5 of Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1110

b:0.5
occ:1.00
 O A:ASP509 3.1 0.8 1.0
O A:ASP506 3.3 84.8 1.0
O A:LEU504 3.5 97.5 1.0
CG2 A:THR503 4.1 73.5 1.0
C A:LEU504 4.2 91.8 1.0
C A:ASP509 4.2 0.8 1.0
N A:LEU504 4.4 82.5 1.0
C A:ASP506 4.5 0.0 1.0
O A:PRO507 4.5 0.1 1.0
CA A:PRO510 4.6 0.3 1.0
CA A:LEU504 4.7 85.9 1.0
CB A:LEU504 4.8 91.6 1.0
N A:PRO510 4.9 0.4 1.0
C A:PRO507 4.9 0.3 1.0
CA A:PRO507 5.0 0.1 1.0

Rubidium binding site 6 out of 6 in 6jxi

Go back to Rubidium Binding Sites List in 6jxi
Rubidium binding site 6 out of 6 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP)


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 6 of Rb+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1111

b:45.5
occ:1.00
 O A:VAL341 2.6 46.4 1.0
O A:ALA339 2.7 46.4 1.0
OE2 A:GLU343 3.0 34.2 1.0
OE2 A:GLU795 3.0 44.2 1.0
O A:VAL338 3.0 42.6 1.0
OE2 A:GLU820 3.2 47.3 1.0
CD A:GLU820 3.3 40.4 1.0
CG A:GLU820 3.3 30.8 1.0
C A:ALA339 3.4 47.7 1.0
ND2 A:ASN792 3.5 30.5 1.0
OE1 A:GLU343 3.6 38.4 1.0
C A:VAL341 3.7 41.5 1.0
CG2 A:ILE816 3.7 31.3 1.0
CD A:GLU343 3.7 41.1 1.0
CD A:GLU795 3.8 35.3 1.0
OE1 A:GLU820 4.0 53.5 1.0
CA A:ALA339 4.0 51.6 1.0
C A:VAL338 4.1 40.3 1.0
CA A:PRO342 4.3 34.6 1.0
C A:TYR340 4.3 33.2 1.0
N A:PRO342 4.4 35.8 1.0
N A:VAL341 4.4 40.4 1.0
N A:TYR340 4.4 40.2 1.0
CG A:ASN792 4.5 38.4 1.0
OE1 A:GLU795 4.5 33.1 1.0
O A:TYR340 4.5 26.6 1.0
N A:GLU343 4.5 31.2 1.0
N A:ALA339 4.6 40.4 1.0
CB A:GLU820 4.6 30.9 1.0
CG A:GLU795 4.7 33.8 1.0
CA A:VAL341 4.7 34.0 1.0
CB A:GLU795 4.7 35.6 1.0
CA A:TYR340 4.8 36.7 1.0
C A:PRO342 5.0 30.4 1.0

Reference:

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
Page generated: Thu Oct 10 12:13:16 2024

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