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

Enzymatic activity of Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP)

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

Protein crystallography data

The structure of Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP), PDB code: 6jxj 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) 49.71 / 2.50
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.230, 103.230, 369.440, 90.00, 90.00, 120.00
R / Rfree (%) 21.4 / 27.3

Other elements in 6jxj:

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

Fluorine (F) 4 atoms
Magnesium (Mg) 1 atom
Aluminium (Al) 1 atom

Rubidium Binding Sites:

The binding sites of Rubidium atom in the Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP) (pdb code 6jxj). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 8 binding sites of Rubidium where determined in the Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP), PDB code: 6jxj:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Rubidium binding site 1 out of 8 in 6jxj

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Rubidium binding site 1 out of 8 in the Rb+-Bound E2-Alf 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-Alf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1108

b:82.7
occ:1.00
 O A:VAL456 2.8 55.3 1.0
O A:GLY458 2.9 66.6 1.0
O A:HOH1429 2.9 50.7 1.0
O A:HOH1471 3.0 30.3 1.0
OG1 A:THR463 3.2 55.1 1.0
O A:HOH1396 3.3 51.9 1.0
O A:HOH1394 3.6 59.0 1.0
C A:VAL456 3.9 62.8 1.0
C A:GLY458 4.0 52.0 1.0
N A:GLY458 4.1 63.0 1.0
CG2 A:VAL456 4.1 44.2 1.0
CB A:THR463 4.2 42.0 1.0
CG2 A:THR463 4.3 39.0 1.0
CA A:GLY458 4.6 51.8 1.0
N A:VAL456 4.6 63.3 1.0
O A:ASP459 4.7 34.3 1.0
CA A:VAL456 4.8 62.1 1.0
N A:ILE457 4.8 62.3 1.0
C A:ILE457 4.8 60.4 1.0
CA A:ILE457 4.9 61.1 1.0
C A:ASP459 4.9 50.5 1.0

Rubidium binding site 2 out of 8 in 6jxj

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Rubidium binding site 2 out of 8 in the Rb+-Bound E2-Alf 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-Alf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1109

b:45.8
occ:1.00
 OD2 A:ASP756 2.8 45.4 1.0
O A:ALA737 2.9 49.6 1.0
O A:LEU734 3.1 50.0 1.0
O A:LYS735 3.1 56.2 1.0
O A:HOH1266 3.1 19.5 1.0
C A:LYS735 3.7 34.0 1.0
CG A:ASP756 3.8 56.6 1.0
C A:ALA737 3.9 33.7 1.0
OD1 A:ASP756 3.9 63.9 1.0
RB A:RB1110 4.1 71.9 1.0
CA A:LYS735 4.1 42.8 1.0
C A:LEU734 4.2 37.5 1.0
N A:GLY740 4.3 33.6 1.0
C A:ASP738 4.3 37.1 1.0
O A:ASP738 4.3 36.8 1.0
N A:ALA737 4.4 46.5 1.0
CA A:ILE739 4.4 25.6 1.0
N A:ILE739 4.4 37.2 1.0
O A:HOH1441 4.5 67.0 1.0
N A:LYS736 4.5 26.2 1.0
C A:ILE739 4.6 31.3 1.0
CA A:ALA737 4.6 41.2 1.0
N A:LYS735 4.7 46.5 1.0
C A:LYS736 4.7 32.1 1.0
N A:ASP738 4.8 26.7 1.0
CA A:ASP738 4.8 30.5 1.0
CB A:ALA737 4.8 36.9 1.0
O A:ALA754 4.9 37.1 1.0

Rubidium binding site 3 out of 8 in 6jxj

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Rubidium binding site 3 out of 8 in the Rb+-Bound E2-Alf 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-Alf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1110

b:71.9
occ:1.00
 O A:ALA737 3.0 49.6 1.0
O A:HOH1359 3.2 46.1 1.0
O A:LYS735 3.2 56.2 1.0
O A:LYS736 3.3 30.8 1.0
C A:LYS736 3.6 32.1 1.0
OE1 A:GLU289 3.6 71.7 1.0
CA A:LYS736 3.9 34.0 1.0
C A:ALA737 3.9 33.7 1.0
O A:HOH1441 4.0 67.0 1.0
RB A:RB1109 4.1 45.8 1.0
CD A:GLU289 4.1 89.9 1.0
C A:LYS735 4.3 34.0 1.0
CB A:GLU289 4.3 73.4 1.0
N A:ALA737 4.4 46.5 1.0
N A:LYS736 4.5 26.2 1.0
OE2 A:GLU289 4.6 92.9 1.0
N A:ASP738 4.7 26.7 1.0
CA A:ASP738 4.7 30.5 1.0
CG A:GLU289 4.7 85.8 1.0
CG1 A:VAL286 4.7 51.1 1.0
CA A:ALA737 4.8 41.2 1.0
O A:GLU289 4.8 72.8 1.0
N A:GLU289 4.8 87.6 1.0
O A:GLU287 4.9 0.9 1.0

Rubidium binding site 4 out of 8 in 6jxj

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Rubidium binding site 4 out of 8 in the Rb+-Bound E2-Alf 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-Alf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1111

b:0.4
occ:1.00
 O A:ASP509 2.6 87.3 1.0
O A:ASP506 3.1 88.0 1.0
O A:LEU504 3.2 92.2 1.0
C A:ASP509 3.8 95.9 1.0
CG2 A:THR503 4.0 74.4 1.0
C A:LEU504 4.1 84.8 1.0
O A:PRO507 4.3 0.1 1.0
C A:ASP506 4.3 1.0 1.0
N A:LEU504 4.3 82.8 1.0
CA A:PRO510 4.3 99.4 1.0
N A:PRO510 4.4 94.7 1.0
CA A:LEU504 4.6 81.4 1.0
C A:PRO507 4.7 0.2 1.0
CA A:PRO507 4.7 0.3 1.0
CB A:LEU504 4.9 81.0 1.0
CA A:ASP509 4.9 0.9 1.0
N A:PRO507 5.0 0.4 1.0

Rubidium binding site 5 out of 8 in 6jxj

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Rubidium binding site 5 out of 8 in the Rb+-Bound E2-Alf 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-Alf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1112

b:41.2
occ:1.00
 O A:VAL341 2.6 33.5 1.0
O A:ALA339 2.6 52.0 1.0
OE1 A:GLU795 2.9 49.8 1.0
OE1 A:GLU343 3.1 35.1 1.0
O A:VAL338 3.1 46.5 1.0
CD A:GLU820 3.3 43.8 1.0
OE2 A:GLU820 3.4 49.6 1.0
CG A:GLU820 3.4 27.9 1.0
C A:ALA339 3.4 41.9 1.0
ND2 A:ASN792 3.5 27.5 1.0
C A:VAL341 3.7 39.2 1.0
CG2 A:ILE816 3.7 20.2 1.0
OE2 A:GLU343 3.7 40.2 1.0
CD A:GLU343 3.7 35.5 1.0
CD A:GLU795 3.8 46.3 1.0
O A:HOH1257 3.9 68.0 1.0
CA A:ALA339 3.9 37.6 1.0
OE1 A:GLU820 4.0 52.4 1.0
C A:VAL338 4.2 37.9 1.0
OE2 A:GLU795 4.2 26.1 1.0
N A:VAL341 4.4 39.8 1.0
CA A:PRO342 4.4 26.4 1.0
N A:TYR340 4.4 31.2 1.0
C A:TYR340 4.4 30.1 1.0
N A:PRO342 4.4 34.8 1.0
N A:GLU343 4.6 38.7 1.0
N A:ALA339 4.6 30.9 1.0
CG A:ASN792 4.6 39.1 1.0
CB A:GLU820 4.6 35.5 1.0
O A:TYR340 4.6 34.3 1.0
CA A:VAL341 4.7 35.1 1.0
CA A:TYR340 4.8 32.5 1.0
CB A:GLU795 4.9 43.9 1.0
CG A:GLU795 5.0 43.7 1.0

Rubidium binding site 6 out of 8 in 6jxj

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Rubidium binding site 6 out of 8 in the Rb+-Bound E2-Alf 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-Alf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1113

b:50.8
occ:1.00
 O A:ALA746 2.8 58.6 1.0
OG A:SER748 3.0 35.8 1.0
O A:HOH1376 3.1 41.5 1.0
OD2 A:ASP726 3.1 38.7 1.0
O A:ASP726 3.1 35.8 1.0
O A:HOH1479 3.1 50.4 1.0
O A:HOH1308 3.4 77.0 1.0
N A:SER748 3.7 43.9 1.0
CG A:ASP726 3.8 32.7 1.0
C A:ASP726 4.0 35.6 1.0
C A:ALA746 4.0 42.0 1.0
C A:GLY747 4.1 43.2 1.0
CB A:SER748 4.1 21.7 1.0
CA A:SER748 4.3 24.7 1.0
CA A:GLY727 4.3 39.0 1.0
CA A:GLY747 4.4 30.4 1.0
CB A:ASP726 4.5 23.9 1.0
OD1 A:ASP726 4.5 40.2 1.0
N A:GLY727 4.6 29.2 1.0
O A:GLY747 4.7 54.9 1.0
N A:GLY747 4.7 36.6 1.0
MG A:MG1101 4.8 33.7 1.0
CA A:ASP726 4.9 32.6 1.0

Rubidium binding site 7 out of 8 in 6jxj

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Rubidium binding site 7 out of 8 in the Rb+-Bound E2-Alf 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 7 of Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1114

b:0.1
occ:1.00
 OE1 A:GLN65 2.7 0.1 1.0
CD A:GLN65 3.5 0.6 1.0
NE2 A:GLN65 3.6 0.6 1.0
CG A:GLN65 4.9 85.7 1.0

Rubidium binding site 8 out of 8 in 6jxj

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Rubidium binding site 8 out of 8 in the Rb+-Bound E2-Alf 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 8 of Rb+-Bound E2-Alf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb308

b:93.5
occ:1.00
 O B:VAL269 3.0 78.0 1.0
O B:GLU267 3.0 70.4 1.0
O B:ALA266 3.2 62.8 1.0
C B:GLU267 3.8 63.1 1.0
C B:VAL269 4.0 68.4 1.0
CA B:GLU267 4.3 57.4 1.0
C B:ALA266 4.3 50.1 1.0
N B:VAL269 4.4 58.4 1.0
N B:HIS268 4.6 68.6 1.0
N B:GLU267 4.8 46.8 1.0
N B:SER270 4.8 57.7 1.0
CA B:VAL269 4.9 61.5 1.0
CA B:SER270 4.9 43.0 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 12:15:11 2024

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