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Potassium in PDB 1gmk: Gramicidin/Kscn Complex

Protein crystallography data

The structure of Gramicidin/Kscn Complex, PDB code: 1gmk was solved by D.A.Doyle, B.A.Wallace, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 32.060, 51.800, 31.040, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / n/a

Potassium Binding Sites:

The binding sites of Potassium atom in the Gramicidin/Kscn Complex (pdb code 1gmk). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Gramicidin/Kscn Complex, PDB code: 1gmk:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 1gmk

Go back to Potassium Binding Sites List in 1gmk
Potassium binding site 1 out of 4 in the Gramicidin/Kscn Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Gramicidin/Kscn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K17

b:21.4
occ:0.50
 O1 B:FVA1 2.1 29.4 1.0
O A:TRP13 2.9 4.6 1.0
CN B:FVA1 3.2 4.3 1.0
CA A:DLE14 3.3 39.3 1.0
CB A:ETA16 3.6 12.8 1.0
N A:ETA16 3.6 6.7 1.0
N A:TRP15 3.6 7.7 1.0
O A:MOH22 3.7 20.7 1.0
C A:TRP13 3.7 36.1 1.0
N B:FVA1 3.8 25.0 1.0
O B:GLY2 3.8 37.2 1.0
N A:DLE14 3.9 48.1 1.0
C A:DLE14 4.0 39.1 1.0
CA A:ETA16 4.0 18.8 1.0
C A:MOH22 4.2 2.0 1.0
CB A:DLE14 4.2 35.0 1.0
O A:ETA16 4.6 18.5 1.0
C A:TRP15 4.6 6.5 1.0
CA B:FVA1 4.7 16.4 1.0
C B:FVA1 4.7 40.7 1.0
CA A:TRP15 4.8 20.4 1.0
C B:GLY2 4.9 3.3 1.0
N B:GLY2 4.9 18.1 1.0
CA A:TRP13 5.0 29.1 1.0

Potassium binding site 2 out of 4 in 1gmk

Go back to Potassium Binding Sites List in 1gmk
Potassium binding site 2 out of 4 in the Gramicidin/Kscn Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Gramicidin/Kscn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K17

b:36.6
occ:1.00
 O B:DVA6 2.0 20.8 1.0
C B:DVA6 3.1 42.2 1.0
O B:DVA8 3.1 50.3 1.0
N B:DVA8 3.2 16.5 1.0
C B:VAL7 3.3 21.8 1.0
C A:TRP9 3.4 2.0 1.0
C B:DVA8 3.5 19.1 1.0
N A:TRP9 3.6 32.7 1.0
O A:TRP9 3.6 18.4 1.0
CA A:TRP9 3.7 2.0 1.0
CA B:DVA8 3.7 6.5 1.0
O A:DLE10 3.7 28.3 1.0
O B:VAL7 3.7 22.6 1.0
N B:VAL7 3.7 2.0 1.0
CA B:VAL7 3.8 2.0 1.0
N A:DLE10 3.8 18.9 1.0
O A:VAL7 4.0 7.3 1.0
C A:DLE10 4.1 28.7 1.0
O B:DLE10 4.1 24.6 1.0
CA B:DVA6 4.2 12.1 1.0
C A:DVA8 4.3 26.7 1.0
N A:DLE12 4.3 31.2 1.0
N B:TRP9 4.3 43.5 1.0
O A:DLE12 4.4 36.2 1.0
CA A:DLE10 4.4 15.9 1.0
S A:SCN18 4.7 25.5 1.0
N B:DVA6 4.7 37.4 1.0
O A:DVA8 4.8 28.5 1.0
N B:DLE10 4.8 8.9 1.0
C A:VAL7 4.9 45.6 1.0
C A:DLE12 4.9 30.8 1.0
N A:TRP11 4.9 40.3 1.0
O B:ALA5 4.9 38.7 1.0
CA A:DVA8 4.9 47.3 1.0
CA B:TRP9 4.9 2.0 1.0
CA A:DLE12 5.0 7.2 1.0

Potassium binding site 3 out of 4 in 1gmk

Go back to Potassium Binding Sites List in 1gmk
Potassium binding site 3 out of 4 in the Gramicidin/Kscn Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Gramicidin/Kscn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K17

b:28.5
occ:0.70
 O1 D:FVA1 2.8 8.3 1.0
CB C:ETA16 3.0 16.6 1.0
CN D:FVA1 3.5 23.5 1.0
O D:MOH21 3.8 13.9 1.0
O C:ETA16 3.9 3.9 1.0
N C:ETA16 3.9 11.3 1.0
CA C:ETA16 4.0 18.1 1.0
N D:FVA1 4.0 60.0 1.0
C C:TRP15 4.4 30.1 1.0
N C:TRP15 4.4 41.4 1.0
O D:GLY2 4.6 27.0 1.0
O C:TRP13 4.6 9.3 1.0
O C:TRP15 4.7 25.3 1.0
CA D:FVA1 5.0 47.8 1.0

Potassium binding site 4 out of 4 in 1gmk

Go back to Potassium Binding Sites List in 1gmk
Potassium binding site 4 out of 4 in the Gramicidin/Kscn Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Gramicidin/Kscn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K17

b:33.9
occ:1.00
 O D:DVA6 2.4 29.7 1.0
O D:DVA8 2.8 26.6 1.0
C D:DVA6 3.3 18.7 1.0
C D:VAL7 3.3 34.3 1.0
O C:TRP9 3.5 2.0 1.0
O D:ALA5 3.5 16.3 1.0
O D:VAL7 3.5 29.2 1.0
N D:DVA8 3.6 16.0 1.0
C C:TRP9 3.6 5.2 1.0
N C:TRP11 3.7 43.4 1.0
C D:DVA8 3.7 33.1 1.0
CA D:VAL7 3.7 32.5 1.0
N D:VAL7 3.8 18.9 1.0
O C:VAL7 3.9 21.7 1.0
C C:DLE10 4.0 7.8 1.0
N C:DLE10 4.0 3.2 1.0
CA C:TRP11 4.0 17.7 1.0
O C:DLE12 4.1 41.9 1.0
N C:DLE12 4.1 37.4 1.0
N C:TRP9 4.1 14.3 1.0
CA D:DVA8 4.1 26.3 1.0
CA C:TRP9 4.2 12.1 1.0
C D:ALA5 4.2 25.0 1.0
C C:TRP11 4.2 32.6 1.0
CA D:DVA6 4.3 2.0 1.0
CA C:DLE10 4.3 2.9 1.0
O D:DLE4 4.4 24.4 1.0
C C:DLE12 4.5 21.0 1.0
O C:DLE10 4.6 33.4 1.0
N D:DVA6 4.6 2.0 1.0
C C:DVA8 4.6 2.0 1.0
N D:TRP9 4.8 34.6 1.0
C D:DLE4 4.9 35.3 1.0
N C:TRP13 4.9 36.1 1.0
CA C:DLE12 4.9 27.7 1.0
O C:TRP11 5.0 30.3 1.0
O C:DVA8 5.0 19.8 1.0
C C:VAL7 5.0 35.6 1.0

Reference:

D.A.Doyle, B.A.Wallace. Crystal Structure of the Gramicidin/Potassium Thiocyanate Complex. J.Mol.Biol. V. 266 963 1997.
ISSN: ISSN 0022-2836
PubMed: 9086274
DOI: 10.1006/JMBI.1996.0837
Page generated: Sun Dec 13 22:43:00 2020

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