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

Protein crystallography data

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

Other elements in 3l8l:

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

Iodine (I) 7 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 4 in 3l8l

Go back to Sodium Binding Sites List in 3l8l
Sodium binding site 1 out of 4 in the Gramicidin D Complex with Sodium Iodide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Gramicidin D Complex with Sodium Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1001

b:17.0
occ:0.50
 NA B:NA1000 0.7 17.4 0.2
O B:HOH2009 2.1 18.4 0.2
O B:HOH2006 2.3 20.8 0.7
O B:HOH2010 2.4 17.4 0.4
O B:DVA6 2.5 20.9 1.0
O A:DVA8 2.6 17.2 1.0
O B:HOH2005 2.8 20.8 0.4
N A:DLE10 3.0 15.6 1.0
O A:DLE10 3.2 22.8 1.0
C A:DLE10 3.4 15.7 1.0
N B:DVA8 3.4 14.8 1.0
C B:DVA6 3.4 16.6 1.0
C A:TRP9 3.5 14.9 1.0
C A:DVA8 3.5 15.2 1.0
CA B:VAL7 3.7 18.1 1.0
CA A:TRP9 3.7 14.4 1.0
CA A:DLE10 3.7 17.5 1.0
C B:VAL7 3.7 16.1 1.0
O B:DVA8 3.8 15.2 1.0
N A:TRP9 3.8 15.3 1.0
N B:VAL7 3.9 16.9 1.0
O B:HOH2003 4.0 28.8 0.8
C B:DVA8 4.0 14.0 1.0
N A:TRP11 4.1 13.5 1.0
CA B:DVA8 4.2 14.3 1.0
O A:TRP9 4.4 16.3 1.0
N B:DVA6 4.5 18.5 1.0
O B:TRP11 4.5 14.4 0.4
CA B:DVA6 4.6 17.7 1.0
O B:VAL7 4.6 18.0 1.0
O B:TRP9 4.6 16.2 1.0
N B:TRP9 4.7 14.4 1.0
CA A:DVA8 4.7 14.8 1.0
O B:HOH2007 4.7 16.5 0.5
N A:DVA8 4.7 14.2 1.0
C A:TRP11 4.8 14.9 1.0
O B:HOH2011 4.8 17.9 0.3
C B:TRP9 4.8 14.3 1.0
CA A:TRP11 4.8 14.5 1.0
CB A:DLE10 4.9 23.5 0.5

Sodium binding site 2 out of 4 in 3l8l

Go back to Sodium Binding Sites List in 3l8l
Sodium binding site 2 out of 4 in the Gramicidin D Complex with Sodium Iodide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Gramicidin D Complex with Sodium Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1000

b:17.4
occ:0.16
 NA A:NA1001 0.7 17.0 0.5
O B:HOH2006 2.0 20.8 0.7
O A:DVA8 2.3 17.2 1.0
O B:HOH2009 2.5 18.4 0.2
N B:DVA8 2.7 14.8 1.0
O B:DVA6 2.7 20.9 1.0
O B:HOH2010 2.8 17.4 0.4
O B:HOH2005 2.9 20.8 0.4
C B:VAL7 3.1 16.1 1.0
O B:DVA8 3.2 15.2 1.0
CA B:VAL7 3.3 18.1 1.0
C B:DVA8 3.4 14.0 1.0
C A:DVA8 3.4 15.2 1.0
C B:DVA6 3.4 16.6 1.0
CA B:DVA8 3.5 14.3 1.0
N A:DLE10 3.6 15.6 1.0
N B:VAL7 3.7 16.9 1.0
O A:DLE10 3.8 22.8 1.0
O B:HOH2003 4.0 28.8 0.8
N A:TRP9 4.0 15.3 1.0
C A:TRP9 4.0 14.9 1.0
CA A:TRP9 4.0 14.4 1.0
O B:VAL7 4.0 18.0 1.0
C A:DLE10 4.1 15.7 1.0
N B:TRP9 4.2 14.4 1.0
N A:DVA8 4.4 14.2 1.0
CA A:DLE10 4.4 17.5 1.0
O B:TRP9 4.5 16.2 1.0
CA A:DVA8 4.5 14.8 1.0
C B:TRP9 4.6 14.3 1.0
CB B:VAL7 4.6 22.0 0.6
CA B:DVA6 4.7 17.7 1.0
N A:TRP11 4.7 13.5 1.0
CB B:VAL7 4.7 19.3 0.4
N B:DVA6 4.8 18.5 1.0
O B:HOH2007 4.8 16.5 0.5
CA B:TRP9 4.9 14.1 1.0
CG2 A:DVA8 4.9 27.9 0.4
O A:TRP9 4.9 16.3 1.0
CB B:DVA8 5.0 16.3 1.0

Sodium binding site 3 out of 4 in 3l8l

Go back to Sodium Binding Sites List in 3l8l
Sodium binding site 3 out of 4 in the Gramicidin D Complex with Sodium Iodide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Gramicidin D Complex with Sodium Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1011

b:13.7
occ:0.39
 O D:HOH2007 1.8 13.8 0.2
O D:HOH2008 2.2 12.8 0.4
O C:HOH2005 2.2 18.2 0.2
O C:HOH2007 2.2 15.7 0.1
O D:HOH2011 2.4 17.0 0.5
O D:DVA6 2.4 18.3 1.0
O C:DVA8 2.7 17.6 1.0
O D:HOH2009 2.9 18.1 0.2
NA D:NA1010 3.0 18.2 0.2
N C:DLE10 3.0 15.2 1.0
O C:DLE10 3.0 17.5 1.0
N D:DVA8 3.3 15.0 1.0
C C:DLE10 3.3 15.2 1.0
C D:DVA6 3.4 15.7 1.0
C C:TRP9 3.5 16.3 1.0
C C:DVA8 3.6 15.2 1.0
CA C:DLE10 3.7 16.0 1.0
C D:VAL7 3.7 16.0 1.0
CA C:TRP9 3.7 16.4 1.0
O D:DVA8 3.8 15.7 1.0
CA D:VAL7 3.8 16.3 1.0
C D:DVA8 3.9 13.8 1.0
N D:VAL7 3.9 16.7 1.0
N C:TRP9 4.0 14.8 1.0
O D:HOH2004 4.0 19.0 0.4
CA D:DVA8 4.1 15.2 1.0
N C:TRP11 4.1 14.6 1.0
O C:HOH2003 4.2 17.6 0.2
O C:TRP9 4.3 18.1 1.0
N D:DVA6 4.4 16.6 1.0
O C:HOH2006 4.5 18.3 0.2
CA D:DVA6 4.5 17.0 1.0
O D:TRP9 4.5 15.6 1.0
N D:TRP9 4.5 14.2 1.0
O D:VAL7 4.6 18.2 1.0
C D:TRP9 4.7 13.4 1.0
N C:DVA8 4.8 15.0 1.0
CA C:DVA8 4.8 15.5 1.0
CA C:TRP11 4.9 14.2 1.0
C C:TRP11 4.9 13.5 1.0
O D:HOH2013 4.9 17.4 0.2
O D:TRP11 4.9 14.6 0.6
CG1 C:DVA8 5.0 26.3 0.5
CB C:DLE10 5.0 20.2 1.0

Sodium binding site 4 out of 4 in 3l8l

Go back to Sodium Binding Sites List in 3l8l
Sodium binding site 4 out of 4 in the Gramicidin D Complex with Sodium Iodide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Gramicidin D Complex with Sodium Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1010

b:18.2
occ:0.22
 O C:HOH2007 1.4 15.7 0.1
O D:HOH2004 1.5 19.0 0.4
O D:HOH2008 2.3 12.8 0.4
O D:HOH2007 2.3 13.8 0.2
O C:DLE10 2.3 17.5 1.0
O D:DLE4 2.7 18.4 1.0
O D:HOH2003 2.8 18.9 0.2
NA C:NA1011 3.0 13.7 0.4
N D:DVA6 3.0 16.6 1.0
O D:DVA6 3.3 18.3 1.0
C C:DLE10 3.3 15.2 1.0
N C:DLE12 3.4 15.4 1.0
C D:DVA6 3.5 15.7 1.0
C D:ALA5 3.5 17.4 1.0
CA D:ALA5 3.7 17.3 1.0
CA D:DVA6 3.7 17.0 1.0
C D:DLE4 3.7 18.6 1.0
CA C:TRP11 3.8 14.2 1.0
C C:TRP11 3.8 13.5 1.0
N C:TRP11 3.9 14.6 1.0
O D:HOH2001 4.0 20.2 0.3
C C:DLE12 4.1 15.1 1.0
N D:ALA5 4.2 17.7 1.0
N D:VAL7 4.2 16.7 1.0
O C:DLE12 4.2 19.0 1.0
CA C:DLE12 4.3 15.1 1.0
O D:ALA5 4.3 21.0 1.0
N C:TRP13 4.3 14.2 1.0
O D:HOH2011 4.5 17.0 0.5
N C:DLE10 4.5 15.2 1.0
CA C:DLE10 4.5 16.0 1.0
C D:VAL7 4.6 16.0 1.0
C C:TRP13 4.7 14.3 1.0
O D:TRP9 4.7 15.6 1.0
O C:TRP11 4.7 15.4 1.0
N D:DVA8 4.8 15.0 1.0
O D:VAL7 4.8 18.2 1.0
N C:DLE14 4.8 15.9 1.0
O C:TRP13 4.9 15.8 1.0
CA D:VAL7 4.9 16.3 1.0
O C:HOH2005 4.9 18.2 0.2
CA D:DLE4 5.0 20.1 1.0
N D:DLE4 5.0 16.9 1.0
CA C:TRP13 5.0 13.9 1.0

Reference:

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
Page generated: Mon Oct 7 11:17:46 2024

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