Sodium in PDB 7nfb: Er-Prs*(+) (Y537S) in Complex with Genistein and Src-2 Coactivator Peptide

The structure of Er-Prs*(+) (Y537S) in Complex with Genistein and Src-2 Coactivator Peptide, PDB code: 7nfb was solved by M.Kriegel, Y.A.Muller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.73 / 1.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.854, 81.526, 58.464, 90, 108.46, 90
R / Rfree (%)	14.2 / 17.8

The structure of Er-Prs*(+) (Y537S) in Complex with Genistein and Src-2 Coactivator Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Er-Prs*(+) (Y537S) in Complex with Genistein and Src-2 Coactivator Peptide (pdb code 7nfb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Er-Prs*(+) (Y537S) in Complex with Genistein and Src-2 Coactivator Peptide, PDB code: 7nfb:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Er-Prs*(+) (Y537S) in Complex with Genistein and Src-2 Coactivator Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Er-Prs*(+) (Y537S) in Complex with Genistein and Src-2 Coactivator Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:25.7 occ:1.00 HE2 B:HIS501 2.0 22.8 1.0 HG A:LEU497 2.7 24.5 1.0 ND1 A:HIS501 2.7 18.7 1.0 HB3 A:HIS501 2.8 20.1 1.0 NE2 B:HIS501 2.9 19.0 1.0 O A:LEU497 2.9 19.0 1.0 HD12 A:LEU497 3.0 25.5 1.0 HD13 A:LEU497 3.0 25.5 1.0 CD1 A:LEU497 3.3 21.2 1.0 CG A:LEU497 3.4 20.4 1.0 CG A:HIS501 3.5 17.1 1.0 CB A:HIS501 3.5 16.8 1.0 H A:HIS501 3.5 19.6 1.0 C A:LEU497 3.7 18.3 1.0 CE1 A:HIS501 3.7 18.3 1.0 HG21 B:ILE487 3.7 23.2 1.0 HD11 B:LEU497 3.7 36.2 0.6 CE1 B:HIS501 3.8 18.9 1.0 HE1 B:HIS501 3.8 22.6 1.0 CD2 B:HIS501 3.9 18.9 1.0 HA A:GLN498 3.9 21.8 1.0 HE1 A:HIS501 3.9 22.0 1.0 HD2 B:HIS501 4.0 22.6 1.0 HD12 B:LEU497 4.1 36.2 0.6 HD22 B:LEU497 4.2 23.7 0.4 N A:HIS501 4.2 16.3 1.0 HD21 A:LEU497 4.2 25.6 1.0 HB2 A:GLN500 4.2 20.5 1.0 HB2 A:HIS501 4.2 20.1 1.0 HD12 B:ILE487 4.2 25.2 1.0 HD11 A:LEU497 4.3 25.5 1.0 CD1 B:LEU497 4.4 30.2 0.6 HA A:LEU497 4.4 22.4 1.0 CD2 A:LEU497 4.4 21.3 1.0 CA A:HIS501 4.4 16.7 1.0 CB A:LEU497 4.5 19.3 1.0 CA A:LEU497 4.5 18.7 1.0 N A:GLN498 4.5 17.9 1.0 HG13 B:ILE487 4.6 22.3 1.0 CA A:GLN498 4.6 18.2 1.0 CG2 B:ILE487 4.7 19.3 1.0 CD2 A:HIS501 4.7 16.9 1.0 HA A:HIS501 4.8 20.0 1.0 NE2 A:HIS501 4.8 18.2 1.0 HB3 A:LEU497 4.8 23.1 1.0 HG B:LEU497 4.8 33.1 0.6 HD23 A:LEU497 4.9 25.6 1.0 HG23 B:ILE487 4.9 23.2 1.0 HD21 B:LEU497 4.9 23.7 0.4 ND1 B:HIS501 4.9 19.6 1.0 CD2 B:LEU497 4.9 19.8 0.4 CD1 B:ILE487 5.0 21.0 1.0

Sodium binding site 2 out of 3 in the Er-Prs*(+) (Y537S) in Complex with Genistein and Src-2 Coactivator Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Er-Prs*(+) (Y537S) in Complex with Genistein and Src-2 Coactivator Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:23.9 occ:1.00 HE2 A:HIS356 2.1 21.7 1.0 O A:HOH829 2.8 19.7 1.0 NE2 A:HIS356 3.0 18.1 1.0 CL A:CL611 3.0 25.6 1.0 CD2 A:HIS356 3.8 17.6 1.0 HD2 A:HIS356 3.8 21.2 1.0 HD13 A:LEU327 4.0 23.9 1.0 CE1 A:HIS356 4.0 18.7 1.0 HD22 A:LEU327 4.0 25.0 1.0 HB3 A:ARG352 4.0 22.1 1.0 HD21 A:LEU327 4.1 25.0 1.0 HE1 A:HIS356 4.1 22.5 1.0 HD11 A:LEU327 4.3 23.9 1.0 HD2 A:ARG352 4.3 27.8 1.0 CD2 A:LEU327 4.5 20.8 1.0 CD1 A:LEU327 4.6 19.9 1.0 HG2 A:ARG352 4.6 25.3 1.0 O A:HOH907 4.7 25.8 1.0 O A:HOH917 4.7 41.0 1.0 HH11 A:ARG352 4.8 26.5 1.0 CB A:ARG352 4.9 18.4 1.0 O A:ARG352 4.9 17.5 1.0

Sodium binding site 3 out of 3 in the Er-Prs*(+) (Y537S) in Complex with Genistein and Src-2 Coactivator Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Er-Prs*(+) (Y537S) in Complex with Genistein and Src-2 Coactivator Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:41.8 occ:1.00 HA B:SER334 2.2 48.3 1.0 HB3 B:SER334 2.5 50.8 1.0 CA B:SER334 2.8 40.2 1.0 CB B:SER334 3.0 42.3 1.0 N B:SER334 3.1 38.7 1.0 HB2 B:SER334 3.1 50.8 1.0 HB2 B:PRO333 3.3 43.9 1.0 H B:SER334 3.4 46.4 1.0 C B:PRO333 3.5 38.0 1.0 O B:PRO333 3.6 41.4 1.0 C B:SER334 4.2 40.0 1.0 CB B:PRO333 4.2 36.6 1.0 OG B:SER334 4.3 45.0 1.0 CA B:PRO333 4.4 34.9 1.0 HG B:SER334 4.7 54.0 1.0 O B:SER334 4.7 40.9 1.0 HB3 B:PRO333 4.8 43.9 1.0 OD1 B:ASP332 4.9 32.9 1.0 HD2 B:PRO333 4.9 38.8 1.0

M.Kriegel, H.J.Wiederanders, S.Alkhashrom, J.Eichler, Y.A.Muller. A Pross-Designed Extensively Mutated Estrogen Receptor Alpha Variant Displays Enhanced Thermal Stability While Retaining Native Allosteric Regulation and Structure. Sci Rep V. 11 10509 2021.
ISSN: ESSN 2045-2322
PubMed: 34006920
DOI: 10.1038/S41598-021-89785-1