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Potassium in PDB 7oph: Nak S-Di Mutant with Na+ and K+

Protein crystallography data

The structure of Nak S-Di Mutant with Na+ and K+, PDB code: 7oph was solved by S.Minniberger, A.J.R.Plested, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.01 / 1.42
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 81.13, 88.021, 49.313, 90, 90, 90
R / Rfree (%) 15.3 / 17.9

Other elements in 7oph:

The structure of Nak S-Di Mutant with Na+ and K+ also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Nak S-Di Mutant with Na+ and K+ (pdb code 7oph). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Nak S-Di Mutant with Na+ and K+, PDB code: 7oph:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 7oph

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Potassium binding site 1 out of 8 in the Nak S-Di Mutant with Na+ and K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Nak S-Di Mutant with Na+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K201

b:20.0
occ:0.50
 OG1 A:THR63 2.7 18.0 1.0
OG1 B:THR63 2.8 17.7 1.0
O B:THR63 2.9 16.3 1.0
O A:THR63 2.9 16.6 1.0
HB A:THR63 3.0 21.4 1.0
HB B:THR63 3.0 21.4 1.0
CB A:THR63 3.4 17.8 1.0
CB B:THR63 3.4 17.8 1.0
HG1 A:THR63 3.4 21.6 1.0
HG1 B:THR63 3.5 21.3 1.0
K B:K201 3.6 17.4 0.5
C B:THR63 3.7 16.7 1.0
C A:THR63 3.7 15.2 1.0
CA B:THR63 4.2 16.7 1.0
CA A:THR63 4.2 16.2 1.0
HA B:VAL64 4.4 19.9 1.0
HG21 A:THR63 4.6 22.1 1.0
HA A:VAL64 4.6 18.3 1.0
N B:VAL64 4.6 17.8 1.0
CG2 A:THR63 4.6 18.4 1.0
HG21 B:THR63 4.6 25.0 1.0
HA B:THR63 4.7 20.1 1.0
CG2 B:THR63 4.7 20.8 1.0
HA A:THR63 4.7 19.5 1.0
N A:VAL64 4.7 15.5 1.0
CA B:VAL64 5.0 16.6 1.0

Potassium binding site 2 out of 8 in 7oph

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Potassium binding site 2 out of 8 in the Nak S-Di Mutant with Na+ and K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Nak S-Di Mutant with Na+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K202

b:58.4
occ:1.00
 O A:HOH335 2.7 55.7 1.0
OG A:SER69 2.8 29.1 1.0
O A:SER69 2.9 23.6 1.0
HG2 A:GLN71 3.0 55.4 1.0
O A:HOH327 3.0 37.8 1.0
HG A:SER69 3.2 35.0 1.0
O A:PRO70 3.3 26.0 1.0
HA A:GLN71 3.3 33.1 1.0
C A:SER69 3.6 24.0 1.0
H A:SER69 3.6 29.5 1.0
HG3 A:GLN71 3.7 55.4 1.0
C A:PRO70 3.7 24.6 1.0
CG A:GLN71 3.7 46.2 1.0
CB A:SER69 4.0 27.3 1.0
CA A:GLN71 4.1 27.6 1.0
N A:GLN71 4.1 23.6 1.0
O A:HOH328 4.1 56.3 1.0
CA A:SER69 4.1 24.1 1.0
N A:SER69 4.2 24.6 1.0
HB2 A:SER69 4.3 32.7 1.0
N A:PRO70 4.4 22.6 1.0
CB A:GLN71 4.5 36.3 1.0
CA A:PRO70 4.6 22.9 1.0
H A:GLN71 4.7 28.3 1.0
HB3 A:SER69 4.7 32.7 1.0
CD A:GLN71 4.9 55.4 1.0
HB3 A:GLN71 4.9 43.6 1.0
HA A:PRO70 4.9 27.5 1.0

Potassium binding site 3 out of 8 in 7oph

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Potassium binding site 3 out of 8 in the Nak S-Di Mutant with Na+ and K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Nak S-Di Mutant with Na+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K203

b:50.2
occ:0.37
 O B:HOH320 2.9 49.4 1.0
HA A:ASP67 3.2 26.0 1.0
K B:K202 3.3 40.7 0.4
HA B:ASP67 3.5 34.8 1.0
HB3 A:ASP67 3.5 29.1 1.0
HB2 A:ASP67 3.6 29.1 1.0
CB A:ASP67 3.9 24.2 1.0
CA A:ASP67 4.0 21.7 1.0
O B:ASP67 4.0 34.0 1.0
CA B:ASP67 4.3 29.0 1.0
C B:ASP67 4.5 30.8 1.0
O A:SER66 4.5 21.7 1.0
O B:SER66 4.6 29.7 0.6
O B:SER66 4.6 29.9 0.4
HB2 B:ASP67 4.6 39.0 1.0
K B:K202 4.8 32.2 0.6
O A:ASP67 4.8 24.5 1.0
C A:ASP67 4.9 21.6 1.0
N A:ASP67 4.9 21.6 1.0
O B:HOH305 5.0 33.6 1.0
CB B:ASP67 5.0 32.5 1.0

Potassium binding site 4 out of 8 in 7oph

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Potassium binding site 4 out of 8 in the Nak S-Di Mutant with Na+ and K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Nak S-Di Mutant with Na+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K204

b:37.1
occ:0.52
 K A:K204 0.0 37.1 0.5
K A:K204 2.1 47.4 0.5
O A:VAL64 2.8 19.0 1.0
K B:K202 2.8 32.2 0.6
HA3 B:GLY65 2.8 24.9 1.0
HA3 A:GLY65 2.9 21.3 1.0
O A:GLY65 3.1 20.8 1.0
C A:GLY65 3.2 18.4 1.0
CA A:GLY65 3.5 17.8 1.0
K B:K202 3.6 40.7 0.4
CA B:GLY65 3.7 20.8 1.0
O B:SER66 3.7 29.7 0.6
O B:SER66 3.7 29.9 0.4
C A:VAL64 3.7 18.7 1.0
HA2 B:GLY65 3.9 24.9 1.0
O B:HOH305 3.9 33.6 1.0
N A:SER66 3.9 18.1 1.0
N A:GLY65 4.0 17.5 1.0
C B:GLY65 4.0 24.9 1.0
H B:SER66 4.1 33.9 0.4
H B:SER66 4.1 34.4 0.6
HG12 A:VAL64 4.2 21.0 1.0
N B:SER66 4.2 28.2 0.4
N B:SER66 4.2 28.6 0.6
O A:SER66 4.3 21.7 1.0
H A:SER66 4.3 21.8 1.0
HA2 A:GLY65 4.3 21.3 1.0
O B:VAL64 4.4 17.7 1.0
C A:SER66 4.5 20.9 1.0
O A:HOH312 4.5 26.1 1.0
HG13 A:VAL64 4.6 21.0 1.0
CA A:SER66 4.6 20.7 1.0
HA A:SER66 4.6 24.9 1.0
K B:K201 4.6 17.4 0.5
C B:SER66 4.7 29.1 0.6
C B:SER66 4.7 29.0 0.4
O B:GLY65 4.7 24.6 1.0
H A:GLY65 4.8 21.1 1.0
N B:GLY65 4.8 18.8 1.0
CG1 A:VAL64 4.8 17.5 1.0

Potassium binding site 5 out of 8 in 7oph

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Potassium binding site 5 out of 8 in the Nak S-Di Mutant with Na+ and K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Nak S-Di Mutant with Na+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K204

b:47.4
occ:0.48
 K A:K204 0.0 47.4 0.5
K A:K204 2.1 37.1 0.5
H B:SER66 2.6 34.4 0.6
H B:SER66 2.6 33.9 0.4
O B:HOH305 2.8 33.6 1.0
HA3 B:GLY65 2.9 24.9 1.0
O A:GLY65 3.0 20.8 1.0
HA2 B:GLY65 3.1 24.9 1.0
N B:SER66 3.1 28.6 0.6
N B:SER66 3.1 28.2 0.4
O B:SER66 3.2 29.9 0.4
O B:SER66 3.2 29.7 0.6
HG12 A:VAL64 3.2 21.0 1.0
O B:HOH319 3.2 24.7 0.4
O A:HOH312 3.2 26.1 1.0
CA B:GLY65 3.3 20.8 1.0
O B:HOH319 3.4 23.6 0.6
HG B:SER66 3.5 40.4 0.4
O A:VAL64 3.5 19.0 1.0
C B:GLY65 3.6 24.9 1.0
HG13 A:VAL64 3.6 21.0 1.0
C A:GLY65 3.8 18.4 1.0
CG1 A:VAL64 3.8 17.5 1.0
O A:HOH309 3.9 23.8 1.0
K B:K202 3.9 32.2 0.6
OG B:SER66 3.9 33.6 0.4
C B:SER66 4.0 29.0 0.4
C B:SER66 4.0 29.1 0.6
CA B:SER66 4.1 30.0 0.6
CA B:SER66 4.1 29.6 0.4
C A:VAL64 4.2 18.7 1.0
HB3 B:SER66 4.2 38.9 0.6
HA3 A:GLY65 4.3 21.3 1.0
HG11 A:VAL64 4.3 21.0 1.0
CA A:GLY65 4.4 17.8 1.0
HA A:SER66 4.5 24.9 1.0
N A:GLY65 4.6 17.5 1.0
O B:GLY65 4.6 24.6 1.0
O B:ILE68 4.6 25.5 1.0
N A:SER66 4.7 18.1 1.0
CB B:SER66 4.7 32.4 0.6
CB B:SER66 4.7 32.0 0.4
N B:GLY65 4.7 18.8 1.0
HA B:SER66 4.9 35.6 0.4
HA B:SER66 4.9 36.0 0.6
HB2 B:SER66 4.9 38.9 0.6
CA A:SER66 5.0 20.7 1.0
K B:K202 5.0 40.7 0.4

Potassium binding site 6 out of 8 in 7oph

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Potassium binding site 6 out of 8 in the Nak S-Di Mutant with Na+ and K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Nak S-Di Mutant with Na+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K201

b:17.4
occ:0.50
 O B:VAL64 2.7 17.7 1.0
O B:THR63 2.8 16.3 1.0
O A:THR63 2.9 16.6 1.0
O A:VAL64 2.9 19.0 1.0
C B:VAL64 3.4 17.6 1.0
C A:VAL64 3.6 18.7 1.0
HA B:VAL64 3.6 19.9 1.0
K A:K201 3.6 20.0 0.5
HA A:VAL64 3.8 18.3 1.0
HA3 B:GLY65 3.8 24.9 1.0
C B:THR63 3.9 16.7 1.0
CA B:VAL64 4.0 16.6 1.0
HA3 A:GLY65 4.0 21.3 1.0
C A:THR63 4.1 15.2 1.0
N B:GLY65 4.2 18.8 1.0
CA A:VAL64 4.2 15.2 1.0
N A:GLY65 4.4 17.5 1.0
N B:VAL64 4.5 17.8 1.0
CA B:GLY65 4.5 20.8 1.0
K A:K204 4.6 37.1 0.5
N A:VAL64 4.6 15.5 1.0
CA A:GLY65 4.7 17.8 1.0
H B:GLY65 4.9 22.5 1.0
HB B:THR63 4.9 21.4 1.0
HB A:THR63 4.9 21.4 1.0

Potassium binding site 7 out of 8 in 7oph

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Potassium binding site 7 out of 8 in the Nak S-Di Mutant with Na+ and K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Nak S-Di Mutant with Na+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K202

b:32.2
occ:0.63
 K B:K202 0.0 32.2 0.6
K B:K202 1.9 40.7 0.4
K A:K204 2.8 37.1 0.5
O B:SER66 2.9 29.7 0.6
O B:SER66 2.9 29.9 0.4
O B:GLY65 3.4 24.6 1.0
HA3 B:GLY65 3.4 24.9 1.0
C B:GLY65 3.5 24.9 1.0
C B:SER66 3.6 29.1 0.6
C B:SER66 3.6 29.0 0.4
N B:SER66 3.9 28.2 0.4
N B:SER66 3.9 28.6 0.6
K A:K204 3.9 47.4 0.5
CA B:GLY65 4.0 20.8 1.0
O B:VAL64 4.0 17.7 1.0
HA B:ASP67 4.0 34.8 1.0
O B:HOH318 4.2 21.0 1.0
CA B:SER66 4.2 29.6 0.4
CA B:SER66 4.2 30.0 0.6
H B:SER66 4.3 33.9 0.4
H B:SER66 4.3 34.4 0.6
N B:ASP67 4.3 27.1 1.0
HA B:SER66 4.4 35.6 0.4
HA B:SER66 4.4 36.0 0.6
HA2 B:GLY65 4.6 24.9 1.0
CA B:ASP67 4.7 29.0 1.0
K A:K203 4.8 50.2 0.4
O B:HOH305 4.8 33.6 1.0
C B:VAL64 4.8 17.6 1.0
N B:GLY65 4.9 18.8 1.0
H B:ASP67 4.9 32.5 1.0
O A:VAL64 4.9 19.0 1.0

Potassium binding site 8 out of 8 in 7oph

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Potassium binding site 8 out of 8 in the Nak S-Di Mutant with Na+ and K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Nak S-Di Mutant with Na+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K202

b:40.7
occ:0.37
 K B:K202 0.0 40.7 0.4
K B:K202 1.9 32.2 0.6
K A:K203 3.3 50.2 0.4
K A:K204 3.6 37.1 0.5
O B:SER66 3.7 29.7 0.6
O B:SER66 3.8 29.9 0.4
HA B:ASP67 3.9 34.8 1.0
C B:SER66 4.6 29.1 0.6
C B:SER66 4.6 29.0 0.4
O A:SER66 4.8 21.7 1.0
CA B:ASP67 4.8 29.0 1.0
K A:K204 5.0 47.4 0.5

Reference:

S.Minniberger, S.Abdolvand, S.Braunbeck, H.Sun, A.J.R.Plested. Asymmetry and Ion Selectivity Properties in the Bacterial Channel Nak Mimicking Ionotropic Glutamate Receptors To Be Published.
Page generated: Mon Aug 12 19:42:34 2024

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