Atomistry » Sodium » PDB 3k9g-3la1 » 3l8l
Atomistry »
  Sodium »
    PDB 3k9g-3la1 »
      3l8l »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy