Sodium in PDB 2frs: Crystal Structure of the F15W Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.51 Angstroms Resolution

The structure of Crystal Structure of the F15W Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.51 Angstroms Resolution, PDB code: 2frs was solved by S.Vaezeslami, J.H.Geiger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.90 / 1.51
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	34.582, 37.030, 58.693, 102.00, 106.12, 93.00
R / Rfree (%)	17.4 / 24

The binding sites of Sodium atom in the Crystal Structure of the F15W Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.51 Angstroms Resolution (pdb code 2frs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the F15W Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.51 Angstroms Resolution, PDB code: 2frs:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the F15W Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.51 Angstroms Resolution


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 F15W Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.51 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:48.0 occ:1.00 O A:THR75 2.1 30.9 1.0 O A:HOH700 2.2 44.9 1.0 NA A:NA503 3.0 35.1 1.0 C A:THR75 3.1 31.9 1.0 O A:GLN74 3.3 31.9 1.0 C A:GLN74 3.3 31.2 1.0 CB A:GLN74 3.3 31.8 1.0 N A:THR75 3.6 31.8 1.0 O A:HOH623 3.9 37.7 1.0 CA A:GLN74 3.9 31.0 1.0 O A:HOH585 3.9 33.0 1.0 O A:VAL76 3.9 32.3 1.0 CA A:THR75 3.9 32.0 1.0 N A:VAL76 3.9 31.8 1.0 CA A:GLY78 4.0 31.4 1.0 CA A:VAL76 4.1 31.8 1.0 C A:VAL76 4.2 32.2 1.0 N A:GLY78 4.2 32.1 1.0 O A:HOH715 4.3 33.8 1.0 O A:HOH698 4.5 15.8 0.5 O A:HOH698 4.6 13.1 0.5 CG A:GLN74 4.6 34.0 1.0 N A:GLN74 4.7 29.6 1.0 OE1 A:GLN74 4.8 41.7 1.0 C A:GLY78 4.8 31.0 1.0 CD A:GLN74 4.8 37.2 1.0 O A:HOH729 4.8 36.0 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the F15W Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.51 Angstroms Resolution


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 F15W Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.51 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:38.9 occ:1.00 O A:PRO105 2.1 27.2 1.0 O A:HOH716 2.4 31.3 1.0 C A:PRO105 3.2 27.8 1.0 O A:HOH649 3.4 49.9 1.0 N A:PRO105 3.5 30.7 1.0 CD A:PRO105 3.6 30.6 1.0 O A:HOH659 3.7 32.5 1.0 CG2 A:THR107 3.7 22.9 1.0 O A:HOH658 3.7 45.5 1.0 C A:GLY104 3.7 31.4 1.0 CG A:PRO105 3.8 30.7 1.0 CA A:PRO105 3.9 29.7 1.0 OG1 A:THR107 3.9 24.0 1.0 CA A:GLY104 4.0 31.9 1.0 N A:THR107 4.1 24.1 1.0 CG A:LEU99 4.2 28.4 1.0 N A:LYS106 4.3 27.2 1.0 O A:GLY104 4.3 31.5 1.0 CD1 A:LEU99 4.3 29.0 1.0 CB A:THR107 4.3 21.5 1.0 CB A:PRO105 4.4 30.1 1.0 CG2 A:THR75 4.4 34.5 1.0 C A:LYS106 4.5 25.5 1.0 CA A:LYS106 4.5 26.4 1.0 CD2 A:LEU99 4.7 28.2 1.0 N A:GLY104 4.8 32.5 1.0 CA A:THR107 4.8 22.3 1.0 OG1 A:THR75 4.9 34.0 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the F15W Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.51 Angstroms Resolution


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 F15W Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.51 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:35.1 occ:1.00 O A:HOH715 2.0 33.8 1.0 O A:HOH700 2.2 44.9 1.0 O A:VAL76 2.3 32.3 1.0 O A:HOH698 2.8 13.1 0.5 NA A:NA501 3.0 48.0 1.0 C A:VAL76 3.3 32.2 1.0 O A:HOH699 3.4 40.4 1.0 O A:THR75 3.6 30.9 1.0 O A:HOH698 3.7 15.8 0.5 O A:HOH711 3.8 19.7 0.5 CA A:VAL76 4.0 31.8 1.0 O A:HOH711 4.0 17.5 0.5 N A:GLY78 4.1 32.1 1.0 CA A:GLY78 4.3 31.4 1.0 N A:ASP77 4.4 32.3 1.0 C A:ASP77 4.4 32.5 1.0 C A:THR75 4.6 31.9 1.0 CA A:ASP77 4.7 32.6 1.0 N A:VAL76 4.8 31.8 1.0 CG1 A:VAL76 5.0 32.2 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the F15W Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.51 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the F15W Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.51 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:32.1 occ:1.00 O A:LEU22 2.2 25.7 1.0 O A:GLY23 2.6 29.4 1.0 O A:HOH573 2.7 44.9 1.0 C A:GLY23 3.1 30.1 1.0 C A:LEU22 3.2 25.9 1.0 CA A:GLY23 3.3 28.5 1.0 O A:LYS20 3.3 29.4 1.0 N A:GLY23 3.6 25.9 1.0 O A:LEU19 4.0 32.3 1.0 N A:VAL24 4.1 32.2 1.0 C A:LYS20 4.2 29.1 1.0 C A:VAL24 4.5 33.7 1.0 CA A:LEU22 4.5 25.4 1.0 CA A:LYS20 4.6 30.4 1.0 N A:LEU22 4.7 25.1 1.0 C A:VAL21 4.8 26.2 1.0 CA A:VAL24 4.9 33.1 1.0 O A:HOH564 4.9 37.6 1.0 O A:VAL21 4.9 25.9 1.0

S.Vaezeslami, E.Mathes, C.Vasileiou, B.Borhan, J.H.Geiger. The Structure of Apo-Wild-Type Cellular Retinoic Acid Binding Protein II at 1.4 A and Its Relationship to Ligand Binding and Nuclear Translocation. J.Mol.Biol. V. 363 687 2006.
ISSN: ISSN 0022-2836
PubMed: 16979656
DOI: 10.1016/J.JMB.2006.08.059