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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 6jxh:

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

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

Potassium Binding Sites:

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

Potassium binding site 1 out of 6 in 6jxh

Go back to Potassium Binding Sites List in 6jxh
Potassium binding site 1 out of 6 in the K+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1107

b:0.1
occ:1.00
 O A:ALA746 3.5 62.6 1.0
O A:HOH1454 3.6 61.0 1.0
OD2 A:ASP726 3.6 64.5 1.0
O A:HOH1376 3.7 91.7 1.0
CB A:SER748 4.0 43.8 1.0
O A:HOH1346 4.1 61.4 1.0
O A:ASP726 4.1 49.2 1.0
N A:SER748 4.2 38.6 1.0
OG A:SER748 4.4 54.7 1.0
CA A:GLY727 4.5 54.6 1.0
CA A:SER748 4.6 41.1 1.0
O A:HOH1419 4.6 68.6 1.0
CG A:ASP726 4.7 50.1 1.0
C A:ASP726 4.8 51.7 1.0
C A:ALA746 4.8 59.6 1.0
C A:GLY747 4.8 48.7 1.0
O A:HOH1281 4.9 37.1 1.0

Potassium binding site 2 out of 6 in 6jxh

Go back to Potassium Binding Sites List in 6jxh
Potassium binding site 2 out of 6 in the K+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1108

b:91.9
occ:1.00
 O A:HOH1444 2.7 76.0 1.0
O A:HOH1492 2.8 54.7 1.0
O A:VAL456 2.9 87.3 1.0
OG1 A:THR463 3.1 66.0 1.0
O A:GLY458 3.2 61.1 1.0
O A:HOH1356 3.4 97.6 1.0
O A:HOH1361 3.4 71.9 1.0
CG2 A:THR463 3.9 45.4 1.0
CB A:THR463 3.9 46.2 1.0
C A:VAL456 3.9 82.8 1.0
C A:GLY458 4.1 57.1 1.0
N A:GLY458 4.3 65.4 1.0
CB A:VAL456 4.3 63.2 1.0
O A:ASP459 4.4 45.8 1.0
CA A:VAL456 4.5 76.2 1.0
N A:VAL456 4.6 76.5 1.0
C A:ASP459 4.7 56.6 1.0
CA A:GLY458 4.8 55.6 1.0
O A:HOH1446 4.9 79.2 1.0
N A:ILE457 4.9 71.2 1.0
CG1 A:VAL456 5.0 67.0 1.0

Potassium binding site 3 out of 6 in 6jxh

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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of K+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1109

b:63.6
occ:1.00
 O A:ALA737 2.7 44.6 1.0
OD1 A:ASP756 2.7 68.5 1.0
O A:LYS735 2.8 62.0 1.0
O A:LEU734 3.0 61.2 1.0
O A:HOH1247 3.1 53.1 1.0
O A:HOH1443 3.3 77.0 1.0
C A:LYS735 3.5 49.5 1.0
CG A:ASP756 3.7 60.8 1.0
C A:ALA737 3.8 52.9 1.0
CA A:LYS735 3.8 49.0 1.0
N A:GLY740 4.0 42.6 1.0
K A:K1110 4.1 0.1 1.0
C A:LEU734 4.1 47.2 1.0
OD2 A:ASP756 4.1 79.8 1.0
N A:ALA737 4.3 51.2 1.0
O A:HOH1411 4.3 0.3 1.0
N A:LYS736 4.5 41.8 1.0
CA A:ALA737 4.5 58.8 1.0
N A:LYS735 4.5 46.8 1.0
C A:ASP738 4.5 41.8 1.0
C A:ILE739 4.5 42.5 1.0
CA A:ILE739 4.6 37.2 1.0
N A:ILE739 4.6 30.5 1.0
O A:ASP738 4.6 49.9 1.0
C A:LYS736 4.7 45.8 1.0
CA A:GLY740 4.7 28.9 1.0
CB A:ALA737 4.7 49.5 1.0
O A:ALA754 4.8 39.5 1.0
N A:ASP738 4.8 39.0 1.0
CB A:ASP756 4.9 45.1 1.0
CA A:ASP738 4.9 34.3 1.0

Potassium binding site 4 out of 6 in 6jxh

Go back to Potassium Binding Sites List in 6jxh
Potassium binding site 4 out of 6 in the K+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of K+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1110

b:0.1
occ:1.00
 O A:HOH1347 2.8 78.6 1.0
O A:LYS735 2.9 62.0 1.0
O A:HOH1428 3.0 0.3 1.0
O A:LYS736 3.3 40.7 1.0
O A:ALA737 3.4 44.6 1.0
OE1 A:GLU289 3.4 0.9 1.0
C A:LYS736 3.7 45.8 1.0
O A:HOH1443 3.7 77.0 1.0
CA A:LYS736 3.9 41.5 1.0
C A:LYS735 4.0 49.5 1.0
K A:K1109 4.1 63.6 1.0
C A:ALA737 4.2 52.9 1.0
O A:HOH1411 4.2 0.3 1.0
CD A:GLU289 4.4 0.3 1.0
N A:LYS736 4.4 41.8 1.0
CB A:GLU289 4.5 0.3 1.0
N A:ALA737 4.5 51.2 1.0
O A:GLU287 4.6 0.4 1.0
N A:GLU289 4.6 0.4 1.0
CG1 A:VAL286 4.7 71.8 1.0
CD A:LYS736 4.8 49.0 1.0
N A:ASP738 4.9 39.0 1.0
CG A:GLU289 4.9 0.5 1.0
CA A:ASP738 4.9 34.3 1.0
O A:GLU289 4.9 90.2 1.0
CA A:ALA737 5.0 58.8 1.0

Potassium binding site 5 out of 6 in 6jxh

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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of K+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1111

b:0.4
occ:1.00
 O A:HOH1359 2.8 0.8 1.0
O A:LEU504 3.3 0.9 1.0
O A:HOH1227 3.3 92.9 1.0
O A:ASP509 3.7 0.8 1.0
CG2 A:THR503 3.8 0.2 1.0
O A:ASP506 3.8 0.9 1.0
O A:PRO507 4.4 0.2 1.0
C A:LEU504 4.5 0.8 1.0
N A:LEU504 4.6 97.7 1.0
CA A:PRO510 4.7 0.8 1.0
C A:ASP509 4.7 1.0 1.0
CA A:PRO507 4.8 0.5 1.0
C A:ASP506 4.8 0.4 1.0
C A:PRO507 4.9 0.6 1.0

Potassium binding site 6 out of 6 in 6jxh

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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of K+-Bound E2-Mgf State of the Gastric Proton Pump (TYR799TRP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1112

b:56.8
occ:1.00
 O A:VAL341 2.6 52.6 1.0
O A:ALA339 2.6 50.8 1.0
OE2 A:GLU795 2.8 63.2 1.0
O A:VAL338 2.9 54.5 1.0
OE1 A:GLU343 2.9 49.1 1.0
CG A:GLU820 3.2 36.2 1.0
CD A:GLU820 3.2 55.6 1.0
OE1 A:GLU820 3.3 67.8 1.0
ND2 A:ASN792 3.4 42.7 1.0
C A:ALA339 3.5 50.8 1.0
C A:VAL341 3.7 49.0 1.0
CD A:GLU343 3.7 56.6 1.0
OE2 A:GLU343 3.7 60.3 1.0
CD A:GLU795 3.8 55.1 1.0
OE2 A:GLU820 3.9 69.4 1.0
CG2 A:ILE816 3.9 51.3 1.0
CA A:ALA339 4.0 52.2 1.0
C A:VAL338 4.0 51.2 1.0
CA A:PRO342 4.2 51.0 1.0
N A:VAL341 4.3 55.9 1.0
OE1 A:GLU795 4.4 44.7 1.0
N A:PRO342 4.4 52.7 1.0
C A:TYR340 4.4 50.8 1.0
CB A:GLU820 4.4 45.0 1.0
CG A:ASN792 4.4 51.1 1.0
N A:GLU343 4.5 50.2 1.0
N A:TYR340 4.5 50.1 1.0
N A:ALA339 4.5 44.4 1.0
CA A:VAL341 4.6 47.0 1.0
O A:TYR340 4.7 46.8 1.0
CB A:GLU795 4.8 48.5 1.0
CG A:GLU795 4.8 53.1 1.0
CA A:TYR340 4.9 50.6 1.0
C A:PRO342 4.9 40.5 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: Mon Dec 14 00:44:10 2020

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