Sodium in PDB 3dav: Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate

The structure of Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate, PDB code: 3dav was solved by O.C.Ezezika, B.J.Nolen, T.D.Pollard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.20 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.873, 82.426, 39.742, 90.00, 92.59, 90.00
R / Rfree (%)	17.4 / 26

The binding sites of Sodium atom in the Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate (pdb code 3dav). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate, PDB code: 3dav:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in the Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na128 b:33.4 occ:1.00 O A:HOH133 3.1 21.3 1.0 CA A:GLY60 3.8 18.2 1.0 N A:GLY60 4.0 18.5 1.0 CD A:LYS67 4.1 17.9 1.0 O A:THR59 4.3 18.4 1.0 C A:THR59 4.4 18.6 1.0 O A:PHE57 4.4 18.0 1.0 O A:GLY58 4.5 19.0 1.0 O A:TYR68 4.5 18.5 1.0 CG A:LYS67 4.6 18.8 1.0 CA A:ILE69 4.6 17.9 1.0 CE A:LYS67 5.0 16.4 1.0

Sodium binding site 2 out of 9 in the Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na129 b:44.0 occ:1.00 CA A:LYS112 3.8 19.5 1.0 N A:LYS112 3.9 19.5 1.0 CB A:LYS112 4.1 19.5 1.0 O A:HOH205 4.4 41.2 1.0 C A:ALA111 4.4 19.5 1.0 CB A:ALA111 4.5 19.2 1.0 O A:GLY108 4.7 21.1 1.0 O A:ALA111 4.8 19.4 1.0 CG A:GLU115 4.8 17.5 1.0 CD A:LYS112 4.9 22.7 1.0

Sodium binding site 3 out of 9 in the Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na130 b:56.8 occ:1.00 OE1 A:GLU74 3.9 24.6 1.0 OH A:TYR79 3.9 17.6 1.0 OE2 A:GLU115 4.0 15.4 1.0 OG A:SER77 4.1 21.8 1.0 CD A:ARG72 4.2 19.4 1.0 OE2 A:GLU74 4.4 25.6 1.0 CD A:GLU115 4.5 16.2 1.0 NE A:ARG72 4.5 21.4 1.0 CB A:SER77 4.5 21.0 1.0 CD A:GLU74 4.5 23.9 1.0 NH1 A:ARG72 4.7 20.9 1.0 CZ A:ARG72 4.8 20.8 1.0 CZ A:TYR79 4.8 18.2 1.0 OE1 A:GLU115 4.9 16.7 1.0

Sodium binding site 4 out of 9 in the Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na128 b:23.3 occ:1.00 NA B:NA130 2.6 29.6 1.0 OE2 B:GLU42 2.8 19.7 1.0 CD B:GLU42 3.6 19.6 1.0 CG B:GLU42 3.7 20.1 1.0 CG2 B:ILE62 4.0 15.7 1.0 CA B:GLY65 4.2 16.2 1.0 N B:GLY65 4.4 16.0 1.0 OG B:SER39 4.5 21.0 1.0 OE1 B:GLU42 4.8 18.5 1.0

Sodium binding site 5 out of 9 in the Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na129 b:29.0 occ:1.00 N B:LYS67 3.1 18.0 1.0 O B:LYS67 3.6 18.6 1.0 CA B:LYS67 3.9 18.1 1.0 CD1 B:LEU82 3.9 23.6 1.0 CA B:GLN66 3.9 17.4 1.0 C B:GLN66 4.0 17.6 1.0 CB B:LYS67 4.0 18.2 1.0 CB B:GLN66 4.0 17.6 1.0 C B:LYS67 4.1 18.2 1.0 O B:HOH229 4.4 42.8 1.0 CD2 B:LEU82 4.4 23.4 1.0 O B:HOH160 4.4 50.7 1.0 CG B:GLN66 4.5 17.8 1.0 CG B:LEU82 4.8 23.4 1.0

Sodium binding site 6 out of 9 in the Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na130 b:29.6 occ:1.00 NA B:NA128 2.6 23.3 1.0 OG B:SER39 2.7 21.0 1.0 CB B:SER39 3.4 21.3 1.0 OE2 B:GLU42 3.9 19.7 1.0 CG B:GLU42 4.0 20.1 1.0 CD B:GLU42 4.1 19.6 1.0 CB B:GLN41 4.1 21.3 1.0 CD B:GLN41 4.1 24.7 1.0 OE1 B:GLN41 4.1 25.7 1.0 NE2 B:GLN41 4.3 25.9 1.0 N B:GLU42 4.5 20.9 1.0 CG B:GLN41 4.6 22.7 1.0 CA B:SER39 4.8 21.2 1.0 CB B:GLU42 4.9 20.8 1.0 OE1 B:GLU42 4.9 18.5 1.0 O B:HOH213 4.9 29.1 1.0 CA B:GLN41 5.0 21.3 1.0

Sodium binding site 7 out of 9 in the Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na131 b:25.2 occ:1.00 O B:HOH184 2.5 21.8 1.0 O B:PHE57 3.1 21.8 1.0 N B:THR70 3.3 19.4 1.0 CA B:GLY60 3.5 17.8 1.0 N B:GLY60 3.7 18.2 1.0 OG1 B:THR70 3.7 19.7 1.0 CB B:THR70 3.9 19.9 1.0 C B:PHE57 4.0 21.3 1.0 CA B:ILE69 4.0 18.7 1.0 CG2 B:ILE69 4.0 18.9 1.0 O B:MET56 4.1 22.8 1.0 C B:ILE69 4.1 19.2 1.0 CA B:THR70 4.1 20.0 1.0 CA B:PHE57 4.3 21.7 1.0 O B:THR70 4.5 20.4 1.0 O B:TYR68 4.6 18.1 1.0 C B:THR59 4.6 18.4 1.0 CB B:ILE69 4.6 18.6 1.0 C B:THR70 4.8 20.5 1.0 C B:GLY60 4.9 17.6 1.0

Sodium binding site 8 out of 9 in the Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na132 b:49.5 occ:1.00 O B:HOH271 2.6 46.0 1.0 O B:HOH270 3.7 55.3 1.0

Sodium binding site 9 out of 9 in the Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Schizosaccharomyces Pombe Profilin Crystallized From Sodium Formate within 5.0Å range:

O.C.Ezezika, N.S.Younger, J.Lu, D.A.Kaiser, Z.A.Corbin, B.J.Nolen, D.R.Kovar, T.D.Pollard. Incompatibility with Formin CDC12P Prevents Human Profilin From Substituting For Fission Yeast Profilin: Insights From Crystal Structures of Fission Yeast Profilin. J.Biol.Chem. V. 284 2088 2009.
ISSN: ISSN 0021-9258
PubMed: 19028693
DOI: 10.1074/JBC.M807073200