Sodium in PDB 2wft: Crystal Structure of the Human Hip Ectodomain

The structure of Crystal Structure of the Human Hip Ectodomain, PDB code: 2wft was solved by B.Bishop, A.R.Aricescu, K.Harlos, C.A.O'callaghan, E.Y.Jones, C.Siebold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.89 / 2.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.976, 100.976, 305.916, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 23.8

The structure of Crystal Structure of the Human Hip Ectodomain also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of the Human Hip Ectodomain (pdb code 2wft). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Human Hip Ectodomain, PDB code: 2wft:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Human Hip Ectodomain


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 Human Hip Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1672 b:83.5 occ:1.00 O A:ARG241 3.0 52.9 1.0 OE1 A:GLU558 3.1 77.3 1.0 OG A:SER235 3.1 51.0 1.0 OG A:SER239 3.2 45.9 1.0 N A:ARG241 3.2 29.0 1.0 N A:SER235 3.3 56.7 1.0 OD1 A:ASP237 3.4 55.8 1.0 N A:GLN240 3.6 38.5 1.0 CB A:ARG241 3.6 42.8 1.0 CA A:ARG241 3.7 42.2 1.0 C A:ARG241 3.7 43.3 1.0 CB A:HIS234 3.8 47.9 1.0 CB A:SER235 3.9 59.9 1.0 C A:GLN240 4.0 42.8 1.0 CA A:GLN240 4.0 44.7 1.0 CA A:SER235 4.1 57.2 1.0 CA A:HIS234 4.1 51.4 1.0 CD A:GLU558 4.1 80.1 1.0 CE1 A:PHE243 4.2 44.4 1.0 C A:SER239 4.2 66.6 1.0 C A:HIS234 4.2 59.4 1.0 CG A:ASP237 4.3 64.8 1.0 N A:GLY236 4.3 60.0 1.0 N A:SER239 4.3 46.4 1.0 CB A:SER239 4.4 45.6 1.0 C A:SER235 4.4 54.1 1.0 NE A:ARG241 4.5 64.5 1.0 CA A:SER239 4.5 51.8 1.0 N A:ASP237 4.6 45.5 1.0 CG A:ARG241 4.6 46.0 1.0 OD2 A:ASP237 4.7 74.8 1.0 O A:HOH2004 4.8 54.4 1.0 CG A:HIS234 4.9 67.0 1.0 OE2 A:GLU558 4.9 81.4 1.0 CD1 A:PHE243 4.9 38.5 1.0 ND1 A:HIS234 4.9 51.4 1.0 CG A:GLU558 4.9 67.2 1.0 CB A:GLU558 5.0 43.9 1.0 N A:LEU242 5.0 45.9 1.0 O A:GLN240 5.0 56.1 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Human Hip Ectodomain


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 Human Hip Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1673 b:0.2 occ:1.00 O A:ASP443 3.4 0.3 1.0 O A:HIS440 3.6 0.1 1.0 O A:ILE446 3.8 99.8 1.0 OD1 A:ASN447 3.9 0.4 1.0 CA A:ILE444 4.2 0.5 1.0 O A:ILE444 4.4 97.5 1.0 C A:ASP443 4.4 0.2 1.0 C A:ILE444 4.6 0.8 1.0 CA A:ASN447 4.7 98.5 1.0 N A:ILE444 4.8 0.1 1.0 C A:HIS440 4.8 0.4 1.0 C A:ILE446 4.8 0.5 1.0 CG A:ASN447 4.9 0.5 1.0 O A:ASN447 5.0 87.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Human Hip Ectodomain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Human Hip Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1671 b:75.3 occ:1.00 OE1 B:GLU558 3.0 59.4 1.0 OG B:SER235 3.1 46.3 1.0 O B:ARG241 3.1 36.5 1.0 N B:SER235 3.2 46.3 1.0 N B:ARG241 3.3 34.2 1.0 OD1 B:ASP237 3.5 36.1 1.0 OG B:SER239 3.5 40.8 1.0 N B:GLN240 3.5 39.5 1.0 CB B:HIS234 3.6 35.3 1.0 C B:ARG241 3.9 35.1 1.0 CA B:ARG241 3.9 35.1 1.0 CD B:GLU558 3.9 79.2 1.0 CB B:SER235 3.9 56.9 1.0 CA B:GLN240 4.0 42.4 1.0 CB B:ARG241 4.0 30.1 1.0 CA B:SER235 4.0 55.6 1.0 C B:GLN240 4.0 38.9 1.0 CA B:HIS234 4.0 47.2 1.0 C B:HIS234 4.1 56.5 1.0 N B:GLY236 4.1 52.4 1.0 C B:SER239 4.3 58.8 1.0 C B:SER235 4.3 50.2 1.0 CE1 B:PHE243 4.3 42.3 1.0 N B:SER239 4.3 37.1 1.0 CG B:ASP237 4.4 68.0 1.0 N B:ASP237 4.4 47.3 1.0 CB B:SER239 4.5 37.3 1.0 CA B:SER239 4.6 43.9 1.0 CG B:HIS234 4.6 64.8 1.0 O B:HOH2016 4.6 56.4 1.0 OE2 B:GLU558 4.7 79.0 1.0 CG B:GLU558 4.7 74.2 1.0 ND1 B:HIS234 4.7 54.4 1.0 CB B:GLU558 4.7 48.7 1.0 NE B:ARG241 4.8 58.7 1.0 OD2 B:ASP237 4.8 71.2 1.0 CG B:ARG241 4.9 42.1 1.0 CD1 B:PHE243 5.0 34.6 1.0 CA B:GLY236 5.0 45.9 1.0

B.Bishop, A.R.Aricescu, K.Harlos, C.A.O'callaghan, E.Y.Jones, C.Siebold. Structural Insights Into Hedgehog Ligand Sequestration By the Human Hedgehog-Interacting Protein Hip Nat.Struct.Mol.Biol. V. 16 698 2009.
ISSN: ISSN 1545-9993
PubMed: 19561611
DOI: 10.1038/NSMB.1607