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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 6jxk:

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
Magnesium (Mg) 4 atoms

Potassium Binding Sites:

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

Potassium binding site 1 out of 6 in 6jxk

Go back to Potassium Binding Sites List in 6jxk
Potassium binding site 1 out of 6 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1104

b:0.8
occ:1.00
 O A:ALA746 3.9 0.9 1.0
CB A:SER748 4.0 0.4 1.0
O A:ASP726 4.4 0.8 1.0
N A:SER748 4.5 0.7 1.0
CA A:GLY727 4.6 87.3 1.0
OG A:SER225 4.6 0.2 1.0
CA A:SER748 4.7 0.6 1.0
OG A:SER748 4.8 0.8 1.0
ND2 A:ASN393 5.0 0.9 1.0
OD2 A:ASP726 5.0 0.2 1.0

Potassium binding site 2 out of 6 in 6jxk

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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1105

b:0.5
occ:1.00
 O A:LYS735 2.7 0.2 1.0
OD2 A:ASP756 2.7 0.3 1.0
OD1 A:ASP756 2.9 0.4 1.0
O A:ALA737 2.9 67.9 1.0
CG A:ASP756 3.1 0.6 1.0
O A:LEU734 3.6 0.2 1.0
C A:LYS735 3.7 0.7 1.0
C A:ALA737 4.1 73.1 1.0
CA A:LYS735 4.1 0.7 1.0
N A:GLY740 4.4 0.2 1.0
N A:ALA737 4.5 54.8 1.0
CB A:ASP756 4.6 98.7 1.0
C A:LEU734 4.6 0.4 1.0
CA A:ALA737 4.8 71.8 1.0
N A:LYS736 4.8 67.3 1.0
N A:LYS735 4.9 0.1 1.0
C A:ASP738 4.9 72.1 1.0
C A:LYS736 4.9 51.4 1.0
C A:ILE739 5.0 0.7 1.0
O A:ALA754 5.0 0.5 1.0
CA A:ILE739 5.0 86.2 1.0

Potassium binding site 3 out of 6 in 6jxk

Go back to Potassium Binding Sites List in 6jxk
Potassium binding site 3 out of 6 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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
A:K1106

b:0.8
occ:1.00
 OE2 A:GLU795 2.6 1.0 1.0
O A:VAL338 2.7 0.3 1.0
O A:VAL341 2.7 0.2 1.0
OE1 A:GLU343 2.7 1.0 1.0
CG A:GLU820 3.1 0.7 1.0
O A:ALA339 3.2 0.1 1.0
CD A:GLU820 3.5 0.3 1.0
OE1 A:GLU820 3.5 0.3 1.0
ND2 A:ASN792 3.6 0.4 1.0
CD A:GLU343 3.7 1.0 1.0
CD A:GLU795 3.7 0.9 1.0
C A:ALA339 3.7 0.7 1.0
C A:VAL341 3.8 0.4 1.0
CG2 A:ILE816 3.8 0.7 1.0
C A:VAL338 3.8 0.4 1.0
OE2 A:GLU343 3.9 0.8 1.0
CA A:ALA339 4.0 0.5 1.0
CA A:PRO342 4.2 0.9 1.0
OE1 A:GLU795 4.3 0.2 1.0
OE2 A:GLU820 4.3 0.9 1.0
CB A:GLU820 4.3 0.5 1.0
N A:ALA339 4.4 0.0 1.0
N A:PRO342 4.4 0.3 1.0
N A:GLU343 4.4 0.9 1.0
N A:VAL341 4.6 0.8 1.0
N A:TYR340 4.6 0.3 1.0
C A:TYR340 4.7 0.8 1.0
CA A:VAL341 4.8 1.0 1.0
CG A:GLU795 4.8 0.2 1.0
CB A:GLU795 4.8 0.9 1.0
C A:PRO342 4.9 0.4 1.0
CG A:ASN792 4.9 0.4 1.0
O A:TYR340 5.0 0.8 1.0
CA A:VAL338 5.0 0.9 1.0

Potassium binding site 4 out of 6 in 6jxk

Go back to Potassium Binding Sites List in 6jxk
Potassium binding site 4 out of 6 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type) within 5.0Å range:

Potassium binding site 5 out of 6 in 6jxk

Go back to Potassium Binding Sites List in 6jxk
Potassium binding site 5 out of 6 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 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:K1104

b:0.8
occ:1.00
 OD2 E:ASP756 2.7 0.1 1.0
O E:LYS735 2.7 0.6 1.0
O E:ALA737 2.9 0.4 1.0
OD1 E:ASP756 3.0 0.9 1.0
CG E:ASP756 3.2 0.2 1.0
O E:LEU734 3.4 0.2 1.0
C E:LYS735 3.5 0.5 1.0
CA E:LYS735 3.7 0.0 1.0
O E:ASP738 4.0 0.9 1.0
C E:ALA737 4.1 0.9 1.0
C E:LEU734 4.3 1.0 1.0
N E:LYS735 4.5 0.6 1.0
C E:ASP738 4.5 0.1 1.0
N E:LYS736 4.7 0.2 1.0
CB E:ASP756 4.7 1.0 1.0
N E:GLY740 4.7 0.7 1.0
N E:ALA737 4.8 0.6 1.0
CB E:LYS735 4.8 0.3 1.0
O E:ALA754 4.8 0.8 1.0
CD E:LYS735 4.9 0.7 1.0
C E:LYS736 4.9 0.7 1.0
CA E:ALA737 5.0 0.1 1.0

Potassium binding site 6 out of 6 in 6jxk

Go back to Potassium Binding Sites List in 6jxk
Potassium binding site 6 out of 6 in the Rb+-Bound E2-Mgf State of the Gastric Proton Pump (Wild-Type)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 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:K1105

b:0.6
occ:1.00
 OE2 E:GLU795 2.6 0.8 1.0
O E:VAL338 2.6 0.2 1.0
O E:VAL341 2.6 0.4 1.0
OE1 E:GLU343 2.7 0.7 1.0
O E:ALA339 2.7 0.4 1.0
CG E:GLU820 3.1 0.0 1.0
OE1 E:GLU820 3.3 0.6 1.0
CD E:GLU820 3.3 0.2 1.0
C E:ALA339 3.3 0.4 1.0
ND2 E:ASN792 3.4 0.9 1.0
CG2 E:ILE816 3.4 0.9 1.0
CD E:GLU343 3.4 0.6 1.0
OE2 E:GLU343 3.5 0.0 1.0
CA E:ALA339 3.6 0.8 1.0
C E:VAL338 3.7 0.9 1.0
CD E:GLU795 3.8 0.2 1.0
C E:VAL341 3.8 0.7 1.0
OE2 E:GLU820 4.1 0.5 1.0
N E:ALA339 4.1 0.9 1.0
CB E:GLU820 4.3 0.6 1.0
N E:TYR340 4.3 0.6 1.0
N E:VAL341 4.4 0.5 1.0
C E:TYR340 4.4 0.6 1.0
OE1 E:GLU795 4.4 0.9 1.0
N E:GLU343 4.6 0.4 1.0
CA E:PRO342 4.6 0.5 1.0
N E:PRO342 4.6 0.5 1.0
O E:TYR340 4.7 0.1 1.0
CA E:VAL341 4.7 0.5 1.0
CG E:ASN792 4.7 0.6 1.0
CB E:GLU795 4.7 0.6 1.0
CG E:GLU795 4.8 0.9 1.0
CA E:TYR340 4.9 0.7 1.0
CG E:GLU343 4.9 0.6 1.0
CB E:ILE816 4.9 0.3 1.0
CB E:ALA339 4.9 0.7 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 Aug 12 16:44:55 2024

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