Iodine 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:

Potassium

(K)

6 atoms

The binding sites of Iodine atom in the Gramicidin D Complex with Ki (pdb code 2izq). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Gramicidin D Complex with Ki, PDB code: 2izq:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in the Gramicidin D Complex with Ki


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Gramicidin D Complex with Ki within 5.0Å range: probe atom residue distance (Å) B Occ A:I103 b:5.5 occ:0.20 I B:IOD101 0.5 4.7 0.2 O B:HOH203 1.9 5.5 0.0 CZ3 A:TRP9 1.9 8.9 0.2 CH2 A:TRP9 2.2 10.3 0.2 I B:IOD102 2.5 6.9 0.1 HE1 A:TRP9 2.6 10.9 0.8 CE3 A:TRP9 3.2 7.3 0.2 HD23 B:DLE14 3.3 21.5 0.3 HD1 B:TRP13 3.3 7.7 1.0 NE1 A:TRP9 3.4 9.1 0.8 CZ2 A:TRP9 3.5 9.8 0.2 HE1 B:TRP13 3.5 8.9 1.0 HD21 B:DLE14 3.6 21.5 0.3 HD11 B:DLE14 3.6 14.9 0.7 CD2 B:DLE14 3.9 14.3 0.3 CD1 B:TRP13 3.9 6.4 1.0 NE1 B:TRP13 4.0 7.4 1.0 CD1 A:TRP9 4.0 7.3 0.8 HZ2 A:TRP9 4.1 11.8 0.2 CD2 A:TRP9 4.2 6.9 0.2 HB3 B:DLE14 4.3 9.4 0.5 HD13 B:DLE14 4.3 14.9 0.7 CE2 A:TRP9 4.3 8.6 0.2 HD22 B:DLE14 4.4 21.5 0.3 CD1 B:DLE14 4.4 9.9 0.7 CE2 A:TRP9 4.5 8.8 0.8 HZ2 A:TRP9 4.7 14.0 0.8 HB2 B:DLE14 4.8 9.4 0.5 CB B:DLE14 4.9 7.8 1.0 HG11 A:DVA8 5.0 12.7 1.0 HD12 B:DLE14 5.0 14.9 0.7

Iodine binding site 2 out of 8 in the Gramicidin D Complex with Ki


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Gramicidin D Complex with Ki within 5.0Å range: probe atom residue distance (Å) B Occ A:I104 b:11.5 occ:0.10 HZ2 A:TRP13 1.7 18.4 0.3 I D:IOD101 2.0 10.8 0.1 O A:HOH229 2.1 11.0 0.4 CZ2 A:TRP13 2.6 15.3 0.3 HE1 A:TRP13 2.7 17.6 0.7 O A:HOH216 2.8 9.1 0.2 O C:HOH223 2.9 9.9 0.3 HE1 C:PHE11 3.0 14.8 0.7 HE2 C:PHE11 3.2 12.7 0.2 HE1 A:TRP13 3.2 15.7 0.3 CE2 A:TRP13 3.4 12.9 0.3 HE2 C:PHE11 3.4 13.1 0.1 NE1 A:TRP13 3.5 14.6 0.7 HD12 D:DLE4 3.6 19.7 0.4 CH2 A:TRP13 3.6 17.8 0.3 NE1 A:TRP13 3.6 13.1 0.3 HH2 A:TRP13 3.7 21.4 0.3 HD13 A:DLE12 3.7 25.2 0.3 NE1 C:PHE11 3.8 12.3 0.7 HD11 A:DLE12 3.8 25.2 0.3 OH C:PHE11 4.0 14.7 0.2 HD11 D:DLE4 4.0 19.7 0.4 CE2 C:PHE11 4.0 10.6 0.2 HZ2 C:PHE11 4.1 14.1 0.7 CE2 C:PHE11 4.2 10.9 0.1 HZ2 A:TRP13 4.2 20.4 0.7 CD1 A:DLE12 4.2 16.8 0.3 CD1 D:DLE4 4.3 13.2 0.4 HD1 A:TRP13 4.4 15.8 0.7 CD1 A:TRP13 4.4 13.2 0.7 CE2 A:TRP13 4.5 13.6 0.7 HZ3 B:TRP9 4.5 19.3 0.4 CZ C:PHE11 4.6 10.7 0.2 CE2 C:PHE11 4.7 9.9 0.7 HD13 D:DLE4 4.7 19.7 0.4 HH C:PHE11 4.7 22.1 0.2 CZ2 C:PHE11 4.7 11.8 0.7 HD12 A:DLE12 4.7 25.2 0.3 CD2 A:TRP13 4.7 12.4 0.3 HD23 A:DLE12 4.7 23.0 0.7 HZ C:PHE11 4.7 12.7 0.1 HD11 A:DLE12 4.7 25.3 0.7 CZ2 A:TRP13 4.8 17.0 0.7 HD22 D:DLE4 4.8 24.4 0.4 CD1 C:PHE11 4.8 11.2 0.7 CZ C:PHE11 4.9 10.6 0.1 HD1 C:PHE11 4.9 13.5 0.7 CZ3 A:TRP13 4.9 15.4 0.3 CD1 A:TRP13 5.0 12.5 0.3 HD2 C:PHE11 5.0 11.3 0.1

Iodine binding site 3 out of 8 in the Gramicidin D Complex with Ki


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Gramicidin D Complex with Ki within 5.0Å range: probe atom residue distance (Å) B Occ A:I105 b:11.3 occ:0.09 O A:ETA16 3.2 19.9 0.4 HB2 A:ETA16 3.4 17.3 0.4 HB1 A:ETA16 3.4 22.8 0.6 HA2 A:ETA16 3.7 17.9 0.6 CB A:ETA16 3.8 14.4 0.4 HO A:ETA16 3.8 29.9 0.4 HB1 A:ETA16 4.1 17.3 0.4 CB A:ETA16 4.2 19.0 0.6 HB2 A:ETA16 4.3 22.8 0.6 CA A:ETA16 4.4 14.9 0.6 HA1 A:ETA16 4.9 17.9 0.6

Iodine binding site 4 out of 8 in the Gramicidin D Complex with Ki


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Gramicidin D Complex with Ki within 5.0Å range: probe atom residue distance (Å) B Occ A:I109 b:8.0 occ:0.18 O D:HOH2016 0.4 5.7 0.2 O D:HOH2017 0.5 6.7 0.2 O D:HOH2014 0.5 5.0 0.2 O D:HOH2012 0.8 8.3 0.2 HD12 B:DLE12 2.0 13.3 0.3 HD11 B:DLE12 2.6 13.3 0.3 CD1 B:DLE12 2.7 8.9 0.3 HE1 D:TYR11 2.9 12.5 0.7 HD22 B:DLE12 2.9 19.2 0.3 HE2 D:TYR11 3.1 13.0 0.3 HH D:TYR11 3.1 20.9 0.3 HD22 A:DLE4 3.3 24.9 0.6 HB2 A:ALA3 3.3 12.0 1.0 HD21 A:DLE4 3.3 24.9 0.6 HD23 B:DLE12 3.3 19.2 0.3 HG A:DLE4 3.3 11.9 0.6 CD2 B:DLE12 3.4 12.8 0.3 HD22 A:DLE4 3.4 16.3 0.4 HD11 B:DLE12 3.4 18.0 0.7 HD13 B:DLE12 3.4 13.3 0.3 CG B:DLE12 3.5 9.9 0.3 HZ2 D:TYR11 3.6 11.3 0.7 HD21 A:DLE4 3.6 16.3 0.4 HB2 B:DLE12 3.6 9.5 0.7 CD2 A:DLE4 3.6 16.6 0.6 NE1 D:TYR11 3.7 10.4 0.7 O C:HOH208 3.7 16.6 0.2 HB3 A:DLE4 3.8 9.5 0.5 HG A:DLE4 3.8 10.0 0.4 OH D:TYR11 3.9 13.9 0.3 CE2 D:TYR11 3.9 10.8 0.3 CD2 A:DLE4 3.9 10.8 0.4 CG A:DLE4 3.9 9.9 0.6 HG B:DLE12 3.9 11.9 0.3 HD23 B:DLE12 4.1 30.7 0.7 CB A:ALA3 4.2 8.0 1.0 CZ2 D:TYR11 4.2 9.4 0.7 HD21 B:DLE12 4.3 19.2 0.3 CG A:DLE4 4.3 8.3 0.4 CE2 D:TYR11 4.3 8.1 0.7 CD1 B:DLE12 4.3 12.0 0.7 CZ D:TYR11 4.4 9.8 0.3 HB1 A:ALA3 4.4 12.0 1.0 HB3 C:ALA5 4.4 15.3 1.0 CB B:DLE12 4.5 7.9 0.7 HD23 A:DLE4 4.5 24.9 0.6 HB3 A:ALA3 4.5 12.0 1.0 CB A:DLE4 4.5 7.9 1.0 HB3 B:DLE12 4.7 9.5 0.7 HD13 B:DLE12 4.7 18.0 0.7 H A:DLE4 4.7 7.5 1.0 HB2 B:DLE12 4.7 9.9 0.3 CG B:DLE12 4.8 10.6 0.7 HD23 A:DLE4 4.8 16.3 0.4 CB B:DLE12 4.8 8.3 0.3 CD1 D:TYR11 4.8 8.9 0.7 CD2 B:DLE12 4.9 20.4 0.7 HD12 B:DLE12 5.0 18.0 0.7 N A:DLE4 5.0 6.3 1.0 CD2 D:TYR11 5.0 9.7 0.3

Iodine binding site 5 out of 8 in the Gramicidin D Complex with Ki


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Gramicidin D Complex with Ki within 5.0Å range: probe atom residue distance (Å) B Occ B:I101 b:4.7 occ:0.23 I A:IOD103 0.5 5.5 0.2 O B:HOH203 1.5 5.5 0.0 I B:IOD102 2.1 6.9 0.1 CZ3 A:TRP9 2.3 8.9 0.2 CH2 A:TRP9 2.6 10.3 0.2 HD23 B:DLE14 3.0 21.5 0.3 HE1 A:TRP9 3.1 10.9 0.8 HE1 B:TRP13 3.2 8.9 1.0 HD1 B:TRP13 3.2 7.7 1.0 HD11 B:DLE14 3.4 14.9 0.7 CE3 A:TRP9 3.5 7.3 0.2 HD21 B:DLE14 3.6 21.5 0.3 NE1 B:TRP13 3.7 7.4 1.0 CD2 B:DLE14 3.7 14.3 0.3 CD1 B:TRP13 3.8 6.4 1.0 NE1 A:TRP9 3.8 9.1 0.8 HD13 B:DLE14 3.9 14.9 0.7 CZ2 A:TRP9 4.0 9.8 0.2 CD1 B:DLE14 4.1 9.9 0.7 HB3 B:DLE14 4.1 9.4 0.5 HD22 B:DLE14 4.2 21.5 0.3 CD1 A:TRP9 4.4 7.3 0.8 HZ2 A:TRP9 4.5 11.8 0.2 HB2 B:DLE14 4.6 9.4 0.5 CD2 A:TRP9 4.6 6.9 0.2 HD12 B:DLE14 4.7 14.9 0.7 CB B:DLE14 4.7 7.8 1.0 CE2 A:TRP9 4.8 8.6 0.2 CG B:DLE14 4.9 8.6 0.3 CE2 A:TRP9 5.0 8.8 0.8

Iodine binding site 6 out of 8 in the Gramicidin D Complex with Ki


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Gramicidin D Complex with Ki within 5.0Å range: probe atom residue distance (Å) B Occ B:I102 b:6.9 occ:0.12 O B:HOH203 1.6 5.5 0.0 I B:IOD101 2.1 4.7 0.2 I A:IOD103 2.5 5.5 0.2 HE1 B:TRP13 2.9 8.9 1.0 NE1 B:TRP13 3.6 7.4 1.0 HD1 B:TRP13 4.3 7.7 1.0 HD23 B:DLE14 4.3 21.5 0.3 CD1 B:TRP13 4.3 6.4 1.0 CZ3 A:TRP9 4.4 8.9 0.2 HZ2 B:TRP13 4.6 10.8 1.0 HD13 B:DLE14 4.6 14.9 0.7 CE2 B:TRP13 4.6 7.2 1.0 CH2 A:TRP9 4.7 10.3 0.2 HD11 B:DLE14 4.8 14.9 0.7 CZ2 B:TRP13 5.0 9.0 1.0

Iodine binding site 7 out of 8 in the Gramicidin D Complex with Ki


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Gramicidin D Complex with Ki within 5.0Å range: probe atom residue distance (Å) B Occ D:I101 b:10.8 occ:0.12 O A:HOH229 0.5 11.0 0.4 O C:HOH223 1.6 9.9 0.3 HD12 D:DLE4 1.9 19.7 0.4 I A:IOD104 2.0 11.5 0.1 O A:HOH216 2.0 9.1 0.2 HD11 D:DLE4 2.1 19.7 0.4 CD1 D:DLE4 2.4 13.2 0.4 HD13 A:DLE12 2.6 25.2 0.3 HE1 C:PHE11 2.7 14.8 0.7 HZ2 A:TRP13 2.7 18.4 0.3 HD11 A:DLE12 2.8 25.2 0.3 HE1 A:TRP13 2.8 17.6 0.7 HE2 C:PHE11 2.9 12.7 0.2 CD1 A:DLE12 3.0 16.8 0.3 HD13 D:DLE4 3.0 19.7 0.4 HD22 D:DLE4 3.1 24.4 0.4 HD12 A:DLE12 3.1 25.2 0.3 HD23 D:DLE4 3.2 24.4 0.4 HD23 A:DLE12 3.2 23.0 0.7 HE2 C:PHE11 3.2 13.1 0.1 HE1 A:TRP13 3.3 15.7 0.3 CD2 D:DLE4 3.4 16.3 0.4 NE1 C:PHE11 3.4 12.3 0.7 CZ2 A:TRP13 3.5 15.3 0.3 CG D:DLE4 3.5 11.1 0.4 HB2 D:DLE4 3.6 10.8 0.3 HD1 C:PHE11 3.6 13.5 0.7 HB2 D:DLE4 3.6 12.7 0.3 NE1 A:TRP13 3.6 14.6 0.7 HD23 D:DLE4 3.6 20.5 0.3 CE2 C:PHE11 3.8 10.6 0.2 HD23 D:DLE4 3.8 18.8 0.3 NE1 A:TRP13 3.9 13.1 0.3 CD1 C:PHE11 3.9 11.2 0.7 HD2 C:PHE11 3.9 11.3 0.1 CE2 A:TRP13 4.0 12.9 0.3 CE2 C:PHE11 4.0 10.9 0.1 HZ2 A:TRP13 4.0 20.4 0.7 HG D:DLE4 4.0 13.3 0.4 HD11 D:DLE4 4.1 16.2 0.3 HD2 C:PHE11 4.1 10.8 0.2 CD2 A:DLE12 4.2 15.3 0.7 HD12 D:DLE4 4.2 19.7 0.3 HD11 A:DLE12 4.2 25.3 0.7 HD21 D:DLE4 4.3 24.4 0.4 CD2 C:PHE11 4.4 9.4 0.1 HB2 D:DLE4 4.4 10.7 0.4 CD2 C:PHE11 4.4 9.0 0.2 CG A:DLE12 4.4 15.2 0.3 CB D:DLE4 4.5 9.0 0.3 HD22 A:DLE12 4.5 23.0 0.7 HB2 A:DLE12 4.5 10.8 0.7 CE2 A:TRP13 4.5 13.6 0.7 CD2 D:DLE4 4.5 13.7 0.3 CB D:DLE4 4.5 10.6 0.3 HB3 D:DLE4 4.6 10.8 0.3 HD21 A:DLE12 4.6 23.0 0.7 HB3 D:ALA5 4.6 20.1 1.0 CD1 A:TRP13 4.6 13.2 0.7 CZ2 A:TRP13 4.6 17.0 0.7 CB D:DLE4 4.6 8.9 0.4 HD1 A:TRP13 4.6 15.8 0.7 CH2 A:TRP13 4.7 17.8 0.3 CD2 D:DLE4 4.7 12.6 0.3 CE2 C:PHE11 4.7 9.9 0.7 HG A:DLE12 4.7 18.2 0.3 HD21 D:DLE4 4.7 20.5 0.3 HB3 D:DLE4 4.8 12.7 0.3 HH2 A:TRP13 4.8 21.4 0.3 OH C:PHE11 4.8 14.7 0.2 HB2 A:DLE12 4.8 15.2 0.3 CZ C:PHE11 4.8 10.7 0.2 CD1 D:DLE4 4.9 10.8 0.3 CG D:DLE4 4.9 10.9 0.3 CD1 D:DLE4 4.9 13.2 0.3 HZ2 C:PHE11 4.9 14.1 0.7 CD1 A:DLE12 4.9 16.8 0.7 CG D:DLE4 4.9 9.5 0.3 CG A:DLE12 5.0 12.1 0.7

Iodine binding site 8 out of 8 in the Gramicidin D Complex with Ki


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Gramicidin D Complex with Ki within 5.0Å range: probe atom residue distance (Å) B Occ D:I102 b:9.6 occ:0.06 HH2 D:TRP9 1.3 20.4 0.3 HH2 D:TRP9 1.4 14.9 0.7 CH2 D:TRP9 2.0 12.4 0.7 CH2 D:TRP9 2.2 17.0 0.3 HZ2 D:TRP9 2.4 12.7 0.7 CZ2 D:TRP9 2.5 10.6 0.7 HZ2 D:TRP9 2.8 18.6 0.3 CZ2 D:TRP9 2.9 15.5 0.3 CZ3 D:TRP9 3.2 11.9 0.7 CZ3 D:TRP9 3.3 16.1 0.3 HZ3 D:TRP9 3.4 19.4 0.3 HZ3 D:TRP9 3.5 14.3 0.7 HG22 D:DVA8 3.5 20.5 0.4 CE2 D:TRP9 3.8 8.3 0.7 HG23 D:DVA8 4.0 20.5 0.4 HH2 C:TRP15 4.0 14.5 0.8 HG23 D:DVA8 4.0 9.8 0.5 HZ3 C:TRP15 4.0 12.7 0.8 CG2 D:DVA8 4.2 13.7 0.4 CE2 D:TRP9 4.2 12.1 0.3 HZ3 C:TRP15 4.2 13.0 0.2 CE3 D:TRP9 4.3 8.3 0.7 HG22 D:DVA8 4.3 9.8 0.5 HG23 D:DVA8 4.4 14.2 0.1 HG22 D:DVA8 4.5 14.2 0.1 CD2 D:TRP9 4.5 7.0 0.7 HG21 D:DVA8 4.5 20.5 0.4 HH2 C:TRP15 4.5 14.6 0.2 CE3 D:TRP9 4.5 12.8 0.3 HG11 D:DVA8 4.6 8.2 0.1 HG12 D:DVA8 4.6 8.2 0.1 CG2 D:DVA8 4.6 6.5 0.5 CH2 C:TRP15 4.6 12.1 0.8 CZ3 C:TRP15 4.6 10.5 0.8 HD23 C:DLE14 4.6 14.0 0.8 NE1 D:TRP9 4.8 10.1 0.7 CD2 D:TRP9 4.9 11.4 0.3 CG2 D:DVA8 4.9 9.5 0.1 HE1 D:TRP9 4.9 12.1 0.7 CZ3 C:TRP15 5.0 10.8 0.2

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