Iodine in PDB 3l8l: Gramicidin D Complex with Sodium Iodide

The structure of Gramicidin D Complex with Sodium Iodide, PDB code: 3l8l was solved by A.Olczak, M.L.Glowka, M.Szczesio, J.Bojarska, Z.Wawrzak, W.L.Duax, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.74 / 1.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	29.816, 31.255, 51.667, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

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

Sodium

(Na)

4 atoms

The binding sites of Iodine atom in the Gramicidin D Complex with Sodium Iodide (pdb code 3l8l). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Gramicidin D Complex with Sodium Iodide, PDB code: 3l8l:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in the Gramicidin D Complex with Sodium Iodide


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 Sodium Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I1020 b:21.4 occ:0.27 O C:HOH2008 1.5 30.2 0.7 CD2 B:DLE4 3.5 27.4 1.0 NE1 C:TRP11 3.6 23.2 1.0 CG B:DLE4 4.2 20.8 1.0 CZ2 C:TRP11 4.2 20.9 1.0 CE2 C:TRP11 4.3 20.3 1.0 CD1 A:DLE12 4.4 24.8 1.0 CB B:ALA3 4.4 18.0 1.0 CD2 A:DLE12 4.5 28.0 1.0 CB A:DLE12 4.6 18.9 1.0 CB B:DLE4 4.7 18.9 1.0 CD1 C:TRP11 4.7 21.8 1.0 CG A:DLE12 4.8 20.9 1.0 CB D:ALA5 4.9 19.9 1.0

Iodine binding site 2 out of 7 in the Gramicidin D Complex with Sodium Iodide


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 Sodium Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I1021 b:13.6 occ:0.42 O A:HOH2005 0.2 12.7 0.6 I A:IOD1025 2.1 23.9 0.1 NE1 A:TRP15 3.4 26.7 1.0 CE2 A:TRP15 4.2 26.1 1.0 CZ2 A:TRP15 4.3 26.9 1.0 CD1 A:TRP15 4.4 25.9 1.0

Iodine binding site 3 out of 7 in the Gramicidin D Complex with Sodium Iodide


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 Sodium Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I1025 b:23.9 occ:0.09 I A:IOD1021 2.1 13.6 0.4 O A:HOH2005 2.3 12.7 0.6 NE1 A:TRP15 3.3 26.7 1.0 CD1 A:TRP15 3.6 25.9 1.0 CE2 A:TRP15 4.4 26.1 1.0 CG A:TRP15 4.9 23.5 1.0

Iodine binding site 4 out of 7 in the Gramicidin D Complex with Sodium Iodide


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 Sodium Iodide within 5.0Å range: probe atom residue distance (Å) B Occ B:I1026 b:26.6 occ:0.13 CH2 B:TRP15 2.4 32.5 0.8 O A:HOH2004 2.8 22.4 1.0 CZ2 B:TRP15 2.9 30.9 0.8 CZ3 B:TRP15 3.4 32.6 0.8 NE1 B:TRP15 3.6 25.0 0.1 CD2 B:DLE14 3.9 25.9 0.6 CE2 B:TRP15 4.2 26.6 0.8 CD1 B:DLE14 4.2 19.5 0.4 CD2 B:DLE14 4.4 29.1 0.4 CE2 B:TRP15 4.4 26.8 0.1 CZ2 B:TRP15 4.4 27.9 0.1 CE3 B:TRP15 4.5 28.3 0.8 CH2 A:TRP9 4.6 26.4 0.4 CZ3 A:TRP9 4.6 26.6 0.4 CD1 B:TRP15 4.7 24.1 0.1 CD2 B:TRP15 4.8 23.1 0.8 C B:MOH3002 4.8 27.5 0.5 CG B:DLE14 4.9 27.4 0.4

Iodine binding site 5 out of 7 in the Gramicidin D Complex with Sodium Iodide


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 Sodium Iodide within 5.0Å range: probe atom residue distance (Å) B Occ C:I1024 b:23.8 occ:0.12 CN C:FVA1 4.7 26.2 1.0

Iodine binding site 6 out of 7 in the Gramicidin D Complex with Sodium Iodide


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 Sodium Iodide within 5.0Å range: probe atom residue distance (Å) B Occ D:I1022 b:12.6 occ:0.08 NE1 D:TRP13 3.3 30.4 1.0 CD1 D:TRP13 4.1 28.1 1.0 CZ2 B:TRP11 4.2 20.5 0.6 CE2 D:TRP13 4.3 29.6 1.0 CZ B:TRP11 4.5 22.6 0.4 CZ2 D:TRP13 4.6 32.6 1.0 CD1 C:DLE10 4.7 26.6 1.0 NE1 B:TRP11 4.7 23.1 0.6 CE2 B:TRP11 4.8 19.7 0.6 CE2 B:TRP11 4.8 22.1 0.4

Iodine binding site 7 out of 7 in the Gramicidin D Complex with Sodium Iodide


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 Sodium Iodide within 5.0Å range:

A.Olczak, M.L.Glowka, M.Szczesio, J.Bojarska, Z.Wawrzak, W.L.Duax. The First Crystal Structure of A Gramicidin Complex with Sodium: High-Resolution Study of A Nonstoichiometric Gramicidin D-Nai Complex. Acta Crystallogr.,Sect.D V. 66 874 2010.
ISSN: ISSN 0907-4449
PubMed: 20693686
DOI: 10.1107/S0907444910019876