Sodium in PDB 2r25: Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-

All present enzymatic activity of Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-:
2.7.13.3;

The structure of Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-, PDB code: 2r25 was solved by D.M.Copeland, X.Zhao, A.S.Soares, A.H.West, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.75 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.013, 75.544, 98.392, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24

The structure of Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3- also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Magnesium	(Mg)	1 atom

The binding sites of Sodium atom in the Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3- (pdb code 2r25). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-, PDB code: 2r25:

Sodium binding site 1 out of 1 in the Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3- within 5.0Å range: probe atom residue distance (Å) B Occ B:Na5 b:39.7 occ:0.75 OH B:TYR1165 2.2 38.6 1.0 O B:TYR1138 2.5 41.9 1.0 O B:PRO1168 2.6 28.8 1.0 CA B:MET1140 3.1 34.3 1.0 O B:ASN1139 3.2 40.8 1.0 CZ B:TYR1165 3.2 39.1 1.0 N B:MET1140 3.3 33.9 1.0 CE1 B:TYR1165 3.3 34.2 1.0 C B:MET1140 3.3 32.5 1.0 CB B:SER1167 3.3 32.5 1.0 C B:ASN1139 3.4 38.2 1.0 N B:ILE1141 3.4 27.8 1.0 C B:TYR1138 3.6 38.6 1.0 N B:PRO1168 3.7 31.2 1.0 C B:PRO1168 3.7 29.9 1.0 C B:SER1167 3.7 30.3 1.0 CG1 B:ILE1141 3.8 27.6 1.0 CD B:PRO1168 4.0 31.2 1.0 O B:MET1140 4.0 30.1 1.0 CB B:TYR1138 4.1 35.6 1.0 O B:SER1167 4.1 28.1 1.0 CA B:SER1167 4.1 30.2 1.0 CA B:PRO1168 4.2 29.5 1.0 CD1 B:ILE1141 4.3 27.8 1.0 CA B:TYR1138 4.4 38.9 1.0 N B:ASN1139 4.4 36.1 1.0 CB B:ILE1141 4.4 30.0 1.0 CA B:ASN1139 4.4 36.1 1.0 CA B:ILE1141 4.5 31.1 1.0 OG B:SER1167 4.5 39.9 1.0 CE2 B:TYR1165 4.5 36.0 1.0 N B:TYR1138 4.6 45.4 1.0 CB B:MET1140 4.6 37.1 1.0 CD1 B:TYR1165 4.7 34.7 1.0 N B:ILE1169 4.8 29.1 1.0 CB B:PRO1168 4.8 31.8 1.0

X.Zhao, D.M.Copeland, A.S.Soares, A.H.West. Crystal Structure of A Complex Between the Phosphorelay Protein YPD1 and the Response Regulator Domain of SLN1 Bound to A Phosphoryl Analog J.Mol.Biol. V. 375 1141 2008.
ISSN: ISSN 0022-2836
PubMed: 18076904
DOI: 10.1016/J.JMB.2007.11.045