Potassium in PDB 2izq: Gramicidin D Complex with Ki

The structure of Gramicidin D Complex with Ki, PDB code: 2izq was solved by A.Olczak, M.L.Glowka, M.Szczesio, J.Bojarska, W.L.Duax, B.M.Burkhart, Z.Wawrzak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.00 / 0.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	30.144, 31.319, 51.554, 90.00, 90.00, 90.00
R / Rfree (%)	11.1 / 12.2

The structure of Gramicidin D Complex with Ki also contains other interesting chemical elements:

Iodine

(I)

8 atoms

The binding sites of Potassium atom in the Gramicidin D Complex with Ki (pdb code 2izq). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Gramicidin D Complex with Ki, PDB code: 2izq:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in the Gramicidin D Complex with Ki


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Gramicidin D Complex with Ki within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:6.3 occ:0.17 O B:HOH210 0.4 6.2 0.2 O A:HOH215 1.8 7.0 0.3 O A:HOH221 1.8 8.6 0.4 O A:HOH211 1.9 8.0 0.4 O A:HOH210 2.2 5.8 0.2 O B:HOH202 2.4 4.8 0.1 O B:HOH211 2.5 8.1 0.2 O A:HOH202 2.6 8.9 0.2 O B:DVA8 2.7 7.8 1.0 O A:DVA6 2.8 11.7 0.5 H A:DVA8 3.0 7.7 1.0 O B:DLE10 3.1 9.1 0.4 H B:DLE10 3.1 8.7 1.0 HA A:VAL7 3.1 10.7 0.5 N A:DVA8 3.3 6.5 1.0 O A:DVA6 3.3 9.4 0.5 N B:DLE10 3.4 7.3 1.0 O A:DVA8 3.4 7.1 1.0 C B:DVA8 3.6 6.3 1.0 C B:DLE10 3.6 9.6 1.0 C A:VAL7 3.6 7.1 1.0 HA B:TRP9 3.7 8.9 0.5 C A:DVA8 3.7 5.7 1.0 CA A:VAL7 3.7 8.9 1.0 C A:DVA6 3.7 8.0 1.0 O B:HOH206 3.8 7.5 0.2 C B:TRP9 3.8 7.1 1.0 O A:HOH213 3.9 11.3 0.4 O A:HOH214 3.9 7.8 0.4 O B:DLE10 4.0 8.1 0.6 CA A:DVA8 4.0 6.1 1.0 CA B:TRP9 4.0 7.4 1.0 N A:VAL7 4.1 7.4 1.0 CA B:DLE10 4.1 8.6 1.0 H B:DVA8 4.1 7.6 1.0 HA B:DLE10 4.1 10.3 0.5 N B:TYR11 4.1 5.8 0.8 N B:TYR11 4.1 6.2 0.2 N B:TRP9 4.2 7.1 1.0 HA A:DVA8 4.2 7.3 1.0 O A:TRP9 4.2 8.9 1.0 H A:DVA6 4.3 9.2 1.0 O A:PHE11 4.3 6.1 0.1 N A:TRP9 4.4 5.8 1.0 H B:TYR11 4.4 6.9 0.8 H B:TYR11 4.4 7.4 0.2 C A:TRP9 4.4 6.1 1.0 HG21 B:DVA8 4.4 23.3 0.2 O A:VAL7 4.5 8.7 1.0 N B:DVA8 4.6 6.3 1.0 C B:TYR11 4.6 5.9 0.8 C B:TYR11 4.6 6.8 0.2 O B:TRP9 4.7 8.5 1.0 O B:TYR11 4.8 8.5 0.8 N A:DVA6 4.8 7.6 1.0 H A:TRP9 4.8 6.9 1.0 CA B:DVA8 4.8 6.8 1.0 H A:VAL7 4.8 8.9 1.0 CA B:TYR11 4.8 6.0 0.2 CA B:TYR11 4.8 5.6 0.8 N A:DLE10 4.8 6.1 1.0 O B:TYR11 4.8 4.7 0.2 N B:DLE12 4.9 6.0 1.0 O A:HOH206 4.9 12.0 0.4 HA B:TYR11 4.9 7.2 0.2 CA A:DVA6 4.9 7.5 1.0 HA B:TYR11 4.9 6.7 0.8 H B:TRP9 4.9 8.5 1.0 O A:PHE11 4.9 7.2 0.5 CA A:TRP9 4.9 5.4 1.0

Potassium binding site 2 out of 6 in the Gramicidin D Complex with Ki


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Gramicidin D Complex with Ki within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:6.3 occ:0.14 O A:HOH224 1.0 9.5 0.3 O A:HOH228 1.5 13.1 0.3 O A:HOH218 1.8 14.6 0.4 O A:HOH208 2.0 8.8 0.2 O A:HOH209 2.7 8.4 0.4 O A:HOH222 2.9 13.7 0.3 H A:GLY2 2.9 8.6 1.0 O A:GLY2 2.9 7.3 1.0 O B:DLE14 2.9 8.3 1.0 O A:HOH207 3.0 18.4 0.4 O1 A:FVA1 3.0 12.2 0.9 HN1 B:ETA16 3.3 10.8 1.0 N A:GLY2 3.3 7.1 1.0 C A:GLY2 3.4 6.3 1.0 HA B:TRP15 3.6 9.1 1.0 HA A:FVA1 3.6 10.7 0.5 C B:DLE14 3.6 6.9 1.0 N B:ETA16 3.6 9.0 1.0 H B:DLE14 3.8 7.2 1.0 CA A:GLY2 3.9 6.9 1.0 CN A:FVA1 3.9 10.0 0.9 C B:TRP15 3.9 7.8 1.0 CA B:TRP15 4.0 7.6 1.0 C A:FVA1 4.0 8.4 1.0 N B:TRP15 4.0 7.2 1.0 O A:ALA3 4.1 8.0 1.0 CA A:FVA1 4.1 8.9 1.0 N A:ALA3 4.1 6.2 1.0 HA1 B:ETA16 4.2 12.7 0.8 HO B:ETA16 4.2 32.0 0.2 C A:ALA3 4.2 6.2 1.0 HA3 A:GLY2 4.2 8.3 1.0 HA1 B:ETA16 4.3 14.4 0.2 CA B:ETA16 4.3 10.6 0.8 N A:FVA1 4.4 9.6 1.0 HA2 B:ETA16 4.4 12.7 0.8 O1 A:FVA1 4.4 9.1 0.1 N B:DLE14 4.4 6.0 1.0 O A:ALA5 4.5 9.3 1.0 HN A:FVA1 4.5 12.0 0.9 CA B:ETA16 4.6 12.0 0.2 H B:TRP15 4.6 8.6 1.0 CA A:ALA3 4.6 6.4 1.0 O A:HOH213 4.6 11.3 0.4 N A:DLE4 4.6 6.3 1.0 CN A:FVA1 4.7 9.7 0.1 H A:ALA3 4.7 7.4 1.0 HA A:ALA3 4.7 7.7 1.0 O B:TRP15 4.7 7.7 0.7 CA B:DLE14 4.7 6.7 1.0 O B:ETA16 4.7 21.4 0.2 HA2 A:GLY2 4.7 8.3 1.0 O B:TRP15 4.7 14.1 0.3 HA A:DLE4 4.7 7.9 1.0 O A:FVA1 4.8 10.3 0.7 O B:HOH206 4.9 7.5 0.2 H A:DLE4 4.9 7.5 1.0 O A:FVA1 5.0 7.3 0.3

Potassium binding site 3 out of 6 in the Gramicidin D Complex with Ki


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Gramicidin D Complex with Ki within 5.0Å range: probe atom residue distance (Å) B Occ A:K107 b:5.2 occ:0.19 O B:HOH209 0.3 5.5 0.3 O B:HOH208 1.4 8.3 0.2 O A:HOH206 1.5 12.0 0.4 O A:HOH214 2.6 7.8 0.4 O A:HOH217 2.7 8.4 0.3 O B:DLE4 2.7 7.7 0.5 O A:HOH220 2.8 10.6 0.2 O A:DLE10 3.0 9.3 1.0 H A:DLE12 3.0 8.6 0.5 O A:DLE12 3.0 11.6 1.0 N A:DLE12 3.4 7.2 1.0 H B:DVA6 3.4 8.1 1.0 C A:DLE12 3.5 8.1 1.0 N B:DVA6 3.5 6.7 1.0 O B:DLE4 3.5 8.3 0.5 HA A:PHE11 3.5 6.3 0.5 HA B:ALA5 3.6 10.0 1.0 O B:VAL7 3.6 9.8 0.3 C A:PHE11 3.6 6.3 0.1 C B:ALA5 3.7 8.0 1.0 HA A:PHE11 3.7 6.6 0.3 O A:HOH227 3.7 10.3 0.3 C B:DLE4 3.8 7.9 1.0 C A:PHE11 3.9 6.5 0.5 O B:VAL7 3.9 12.5 0.7 O A:HOH202 3.9 8.9 0.2 C B:DVA6 3.9 6.2 1.0 N B:VAL7 3.9 6.6 1.0 C A:DLE10 4.0 6.9 1.0 C A:PHE11 4.0 5.4 0.3 CA B:ALA5 4.0 8.3 1.0 H B:VAL7 4.0 7.9 1.0 H B:DLE4 4.0 9.7 1.0 C B:VAL7 4.0 7.0 1.0 CA A:DLE12 4.0 8.3 1.0 CA A:PHE11 4.0 5.2 0.5 CA A:PHE11 4.1 5.9 0.1 HA B:DVA6 4.1 8.2 1.0 N A:TRP13 4.1 8.2 0.7 N A:TRP13 4.1 7.6 0.3 CA B:DVA6 4.1 6.9 1.0 N B:ALA5 4.2 7.9 1.0 CA A:PHE11 4.2 5.5 0.3 O A:PHE11 4.2 6.1 0.1 O B:ALA5 4.2 10.7 0.5 O B:ALA5 4.3 12.2 0.5 N A:PHE11 4.4 6.0 0.5 N A:PHE11 4.4 6.3 0.1 N A:PHE11 4.4 5.2 0.3 O B:DVA6 4.4 7.2 1.0 C A:TRP13 4.4 8.0 1.0 CA B:VAL7 4.5 6.5 1.0 HA A:DLE12 4.5 9.9 0.5 HA B:VAL7 4.5 7.8 1.0 HA A:DLE14 4.6 10.0 0.5 N A:DLE14 4.6 8.0 1.0 N B:DLE4 4.6 8.1 1.0 O A:TRP15 4.6 10.0 1.0 CA A:TRP13 4.6 8.0 0.7 O A:HOH211 4.6 8.0 0.4 N B:DVA8 4.6 6.3 1.0 HA B:DVA8 4.7 8.2 1.0 O A:PHE11 4.7 7.2 0.5 O A:TRP13 4.7 9.0 1.0 H A:DLE14 4.7 9.6 1.0 H A:DLE10 4.7 7.3 1.0 CA A:TRP13 4.8 8.8 0.3 O A:HOH215 4.8 7.0 0.3 O B:HOH205 4.8 9.4 0.2 O A:PHE11 4.8 5.3 0.3 CA B:DLE4 4.8 8.0 1.0 HA A:TRP13 4.9 10.5 0.3 O A:HOH223 4.9 10.6 0.2 H B:ALA5 4.9 9.5 1.0 H A:TRP15 4.9 9.6 1.0

Potassium binding site 4 out of 6 in the Gramicidin D Complex with Ki


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Gramicidin D Complex with Ki within 5.0Å range: probe atom residue distance (Å) B Occ C:K105 b:6.2 occ:0.24 O C:HOH204 0.3 10.9 0.4 O D:HOH2002 0.8 9.4 0.3 O C:HOH207 1.9 8.9 0.2 K C:K106 1.9 5.7 0.2 O C:HOH203 2.5 9.6 0.4 O D:HOH2004 2.7 8.9 0.5 O C:TRP9 2.8 5.7 0.5 O C:HOH220 2.9 11.5 0.2 O D:DLE10 2.9 7.6 1.0 O D:TRP13 3.0 6.3 0.5 O C:TRP9 3.3 10.8 0.5 H D:TRP13 3.4 7.0 1.0 O C:DVA6 3.4 8.4 0.4 O C:DVA6 3.6 15.3 0.6 H D:DLE12 3.6 7.6 1.0 H C:TRP9 3.6 7.5 1.0 O C:HOH205 3.6 10.8 0.3 HA C:DVA8 3.6 7.4 1.0 C C:TRP9 3.7 6.5 1.0 N C:TRP9 3.7 6.3 1.0 C D:DLE10 3.7 6.6 1.0 N D:TRP13 3.7 5.8 1.0 N D:DLE12 3.7 6.4 1.0 O D:TRP13 3.8 6.5 0.5 N C:DVA8 3.8 6.0 1.0 C C:DVA8 3.8 5.6 1.0 H C:DVA8 3.9 7.2 1.0 C D:TRP13 3.9 6.8 1.0 H C:DVA6 3.9 8.7 1.0 CA C:DVA8 4.0 6.2 1.0 C C:DVA6 4.0 7.6 1.0 C D:TYR11 4.0 6.0 0.7 H D:DLE10 4.0 7.8 1.0 C C:VAL7 4.1 6.4 1.0 O C:DLE4 4.1 10.2 0.6 HA D:DLE12 4.1 8.5 1.0 HA C:DLE10 4.1 8.9 1.0 C D:DLE12 4.1 7.0 1.0 C D:TYR11 4.2 5.4 0.3 N D:TYR11 4.2 5.7 0.3 HA D:TYR11 4.2 6.8 0.7 O C:DLE4 4.2 9.6 0.4 N D:TYR11 4.2 5.7 0.7 CA D:DLE12 4.3 7.1 1.0 O C:VAL7 4.3 12.2 0.5 CA C:TRP9 4.3 6.4 1.0 O C:DVA8 4.3 9.6 1.0 N C:DVA6 4.4 7.3 1.0 HA D:DLE14 4.4 9.4 1.0 CA D:TYR11 4.4 5.6 0.7 CA D:TRP13 4.4 5.9 1.0 HA D:TYR11 4.4 7.0 0.3 O C:HOH216 4.4 5.9 0.1 N D:DLE10 4.4 6.5 1.0 N C:DLE10 4.5 6.3 1.0 N C:VAL7 4.5 6.9 1.0 O C:VAL7 4.5 5.6 0.5 N D:DLE14 4.5 6.2 1.0 O D:DVA8 4.5 7.2 1.0 O D:TYR11 4.6 7.2 0.7 CA D:TYR11 4.6 5.8 0.3 HA C:VAL7 4.6 8.2 0.5 H D:TYR11 4.7 6.9 0.3 CA C:VAL7 4.7 6.9 1.0 CA D:DLE10 4.7 7.0 1.0 HA C:ALA5 4.7 9.4 1.0 O D:TYR11 4.8 5.0 0.3 CA C:DVA6 4.8 7.3 1.0 HA C:TRP9 4.8 7.6 0.5 H D:TYR11 4.9 6.8 0.7 HA D:TRP13 4.9 7.1 1.0 CA C:DLE10 4.9 7.4 1.0 CA D:DLE14 4.9 7.9 1.0 O D:DLE12 4.9 10.0 1.0

Potassium binding site 5 out of 6 in the Gramicidin D Complex with Ki


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Gramicidin D Complex with Ki within 5.0Å range: probe atom residue distance (Å) B Occ C:K106 b:5.7 occ:0.16 O D:HOH2002 1.1 9.4 0.3 O D:HOH2004 1.4 8.9 0.5 K C:K105 1.9 6.2 0.2 O C:HOH204 2.0 10.9 0.4 O C:DVA6 2.6 8.4 0.4 O C:HOH205 2.6 10.8 0.3 O C:DVA6 2.7 15.3 0.6 H D:DLE10 2.7 7.8 1.0 O D:DVA8 2.8 7.2 1.0 H C:DVA8 3.0 7.2 1.0 O D:DLE10 3.0 7.6 1.0 N D:DLE10 3.1 6.5 1.0 O C:HOH207 3.3 8.9 0.2 O C:HOH216 3.3 5.9 0.1 N C:DVA8 3.3 6.0 1.0 C D:DLE10 3.4 6.6 1.0 HA D:TRP9 3.4 8.3 1.0 C D:TRP9 3.5 7.6 1.0 HA C:VAL7 3.5 8.2 0.5 C C:DVA6 3.6 7.6 1.0 C C:DVA8 3.6 5.6 1.0 O C:DVA8 3.7 9.6 1.0 C D:DVA8 3.7 6.2 1.0 CA D:DLE10 3.8 7.0 1.0 C C:VAL7 3.8 6.4 1.0 O C:TRP9 3.8 5.7 0.5 CA D:TRP9 3.8 6.9 1.0 H C:DVA6 4.0 8.7 1.0 CA C:VAL7 4.0 6.9 1.0 CA C:DVA8 4.0 6.2 1.0 O C:HOH220 4.0 11.5 0.2 O C:HOH203 4.0 9.6 0.4 N C:TRP9 4.1 6.3 1.0 HA C:DVA8 4.1 7.4 1.0 N D:TRP9 4.1 6.4 1.0 N C:VAL7 4.1 6.9 1.0 C C:TRP9 4.1 6.5 1.0 N D:TYR11 4.1 5.7 0.3 O D:HOH2011 4.2 10.3 0.5 HA D:DLE10 4.2 8.4 1.0 N D:TYR11 4.2 5.7 0.7 O C:TRP9 4.3 10.8 0.5 H D:DVA8 4.3 7.5 1.0 O D:TRP9 4.3 10.9 1.0 H C:TRP9 4.3 7.5 1.0 H D:TYR11 4.4 6.9 0.3 O C:VAL7 4.5 12.2 0.5 O D:TRP13 4.5 6.3 0.5 N C:DVA6 4.5 7.3 1.0 HA C:DLE10 4.5 8.9 1.0 CA C:TRP9 4.6 6.4 1.0 N C:DLE10 4.6 6.3 1.0 H D:TYR11 4.6 6.8 0.7 HG13 C:DVA6 4.7 16.0 0.5 O C:VAL7 4.7 5.6 0.5 CA C:DVA6 4.7 7.3 1.0 HA C:TRP9 4.8 7.6 0.5 O C:HOH214 4.8 14.8 0.3 N D:DVA8 4.8 6.3 1.0 H D:TRP9 4.8 7.7 1.0 H C:VAL7 4.9 8.2 1.0 CA D:DVA8 4.9 6.9 1.0 C D:TYR11 4.9 6.0 0.7 O C:PHE11 4.9 7.1 0.2 H C:DLE10 4.9 7.6 1.0 HB3 D:DLE10 5.0 9.4 1.0 HA D:TYR11 5.0 6.8 0.7 CA D:TYR11 5.0 5.6 0.7

Potassium binding site 6 out of 6 in the Gramicidin D Complex with Ki


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Gramicidin D Complex with Ki within 5.0Å range: probe atom residue distance (Å) B Occ C:K107 b:8.3 occ:0.21 O D:HOH2001 0.7 14.2 0.4 O C:HOH221 1.2 11.4 0.5 O D:HOH2007 1.9 11.4 0.2 O D:HOH2010 2.3 14.7 0.3 O C:HOH201 2.4 17.0 0.3 O C:HOH219 2.7 16.5 0.6 O D:HOH2009 2.8 10.2 0.3 O C:DLE14 2.8 8.3 1.0 O1 D:FVA1 2.9 12.9 0.5 HO C:ETA16 3.0 56.0 1.0 H D:GLY2 3.1 8.3 1.0 O D:GLY2 3.2 12.0 1.0 C D:GLY2 3.5 7.0 1.0 N D:GLY2 3.5 6.9 1.0 O D:ALA3 3.6 5.3 0.1 C C:DLE14 3.6 6.4 1.0 HN1 C:ETA16 3.7 17.1 1.0 CN D:FVA1 3.7 12.4 0.5 HA C:TRP15 3.7 9.0 1.0 H C:DLE14 3.8 7.3 1.0 O C:ETA16 3.8 37.3 1.0 N C:ETA16 3.8 14.3 1.0 O D:ALA3 3.8 13.5 0.9 HA D:FVA1 3.9 11.5 0.5 C C:TRP15 4.0 8.7 1.0 C D:ALA3 4.0 7.8 1.0 HA1 C:ETA16 4.0 23.7 1.0 CA D:GLY2 4.1 7.3 1.0 N D:ALA3 4.1 6.8 1.0 O D:HOH2006 4.2 12.0 0.5 O1 D:FVA1 4.2 14.4 0.5 CA C:TRP15 4.2 7.5 1.0 C D:FVA1 4.2 7.3 1.0 N C:TRP15 4.2 6.7 1.0 HN D:FVA1 4.3 14.9 0.5 CA D:FVA1 4.3 9.6 1.0 O D:ALA5 4.4 12.6 1.0 HA3 D:GLY2 4.4 8.8 1.0 O C:HOH217 4.4 15.6 0.2 CA C:ETA16 4.4 19.8 1.0 HA D:DLE4 4.4 10.1 1.0 N C:DLE14 4.4 6.1 1.0 N D:FVA1 4.4 11.5 1.0 N D:DLE4 4.5 7.5 1.0 CA D:ALA3 4.5 7.0 1.0 CN D:FVA1 4.5 13.8 0.5 O D:HOH2008 4.5 13.5 0.4 O C:TRP15 4.5 11.5 1.0 HA D:ALA3 4.6 8.3 1.0 H D:ALA3 4.6 8.2 1.0 CA C:DLE14 4.7 6.3 1.0 HG C:DLE14 4.7 12.1 0.2 H D:FVA1 4.8 13.8 0.5 H D:ALA5 4.8 11.5 1.0 CB C:ETA16 4.8 26.0 1.0 H D:DLE4 4.9 9.0 1.0 CA D:DLE4 4.9 8.4 1.0 O C:HOH213 4.9 28.7 0.4 H C:TRP15 4.9 8.1 1.0 HA2 D:GLY2 4.9 8.8 1.0

A.Olczak, M.L.Glowka, M.Szczesio, J.Bojarska, W.L.Duax, B.M.Burkhart, Z.Wawrzak. Nonstoichiometric Complex of Gramicidin D with Ki at 0.80 A Resolution. Acta Crystallogr.,Sect.D V. 63 319 2007.
ISSN: ISSN 0907-4449
PubMed: 17327669
DOI: 10.1107/S0907444906053649