Atomistry » Rubidium » PDB 5aw4-7w49 » 6jxi
Atomistry »
  Rubidium »
    PDB 5aw4-7w49 »
      6jxi »

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

Go back to Rubidium Binding Sites List in 6jxi
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

Go back to Rubidium Binding Sites List in 6jxi
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

Go back to Rubidium Binding Sites List in 6jxi
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

Go back to Rubidium Binding Sites List in 6jxi
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy