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Sodium in PDB 4c79: Crystal Structure of the Smoothened Crd, Native

Protein crystallography data

The structure of Crystal Structure of the Smoothened Crd, Native, PDB code: 4c79 was solved by S.Nachtergaele, D.M.Whalen, L.K.Mydock, Z.Zhao, T.Malinauskas, K.Krishnan, P.W.Ingham, D.F.Covey, R.Rohatgi, C.Siebold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.203 / 2.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.620, 68.620, 95.030, 90.00, 90.00, 90.00
R / Rfree (%) 21.36 / 25.99

Other elements in 4c79:

The structure of Crystal Structure of the Smoothened Crd, Native also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Smoothened Crd, Native (pdb code 4c79). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Smoothened Crd, Native, PDB code: 4c79:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4c79

Go back to Sodium Binding Sites List in 4c79
Sodium binding site 1 out of 2 in the Crystal Structure of the Smoothened Crd, Native


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Smoothened Crd, Native within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1160

b:26.5
occ:1.00
O A:SER74 2.3 34.0 1.0
O A:HOH2014 2.4 16.6 1.0
O A:ALA71 2.4 30.2 1.0
O A:LEU68 2.4 30.6 1.0
C A:ALA71 3.5 30.3 1.0
C A:LEU68 3.5 29.7 1.0
C A:SER74 3.6 34.4 1.0
O A:HOH2015 3.6 45.6 1.0
CB A:LEU68 4.1 28.8 1.0
CA A:GLU72 4.2 33.7 1.0
OE1 A:GLU75 4.2 42.1 1.0
N A:GLU72 4.3 31.9 1.0
N A:SER74 4.3 34.0 1.0
N A:ILE69 4.4 30.0 1.0
CA A:ILE69 4.4 30.1 1.0
CA A:LEU68 4.4 28.5 1.0
N A:GLU75 4.5 35.6 1.0
CA A:SER74 4.5 34.1 1.0
CA A:ALA71 4.5 28.8 1.0
CA A:GLU75 4.5 36.6 1.0
N A:ALA71 4.5 28.6 1.0
C A:ILE69 4.5 30.1 1.0
O A:ILE69 4.6 30.8 1.0
C A:GLU72 4.6 34.1 1.0
CD A:GLU75 4.8 42.0 1.0
CB A:ALA71 4.8 27.8 1.0
N A:ASP73 4.9 33.8 1.0

Sodium binding site 2 out of 2 in 4c79

Go back to Sodium Binding Sites List in 4c79
Sodium binding site 2 out of 2 in the Crystal Structure of the Smoothened Crd, Native


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Smoothened Crd, Native within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1159

b:36.2
occ:1.00
O B:LEU68 2.3 32.3 1.0
O B:ALA71 2.4 33.0 1.0
O B:SER74 2.4 25.2 1.0
O B:HOH2011 2.4 31.3 1.0
O B:HOH2012 2.4 24.6 1.0
C B:ALA71 3.4 31.9 1.0
C B:LEU68 3.5 31.8 1.0
O B:HOH2013 3.6 40.5 1.0
C B:SER74 3.6 25.4 1.0
CA B:ILE69 4.1 31.3 1.0
CA B:GLU72 4.1 32.9 1.0
N B:GLU72 4.2 32.3 1.0
CG B:GLU75 4.2 33.4 1.0
N B:ILE69 4.2 31.4 1.0
C B:ILE69 4.3 30.4 1.0
CB B:LEU68 4.3 30.5 1.0
CA B:GLU75 4.3 28.1 1.0
O B:ILE69 4.4 30.3 1.0
N B:ALA71 4.4 30.3 1.0
N B:GLU75 4.4 26.4 1.0
CA B:ALA71 4.4 30.9 1.0
CA B:LEU68 4.5 31.1 1.0
C B:GLU72 4.5 31.7 1.0
N B:SER74 4.5 26.9 1.0
CA B:SER74 4.7 25.5 1.0
O B:GLU72 4.8 32.2 1.0
CB B:GLU75 4.9 30.8 1.0
CB B:ALA71 4.9 30.8 1.0
N B:LEU70 4.9 29.6 1.0

Reference:

S.Nachtergaele, D.M.Whalen, L.K.Mydock, Z.Zhao, T.Malinauskas, K.Krishnan, P.W.Ingham, D.F.Covey, C.Siebold, R.Rohatgi. Structure and Function of the Smoothened Extracellular Domain in Vertebrate Hedgehog Signaling Elife V. 2 01340 2013.
ISSN: ISSN 2050-084X
PubMed: 24171105
DOI: 10.7554/ELIFE.01340
Page generated: Tue Dec 15 06:35:24 2020

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