Sodium in PDB 3mzg: Crystal Structure of A Human Prolactin Receptor Antagonist in Complex with the Extracellular Domain of the Human Prolactin Receptor

The structure of Crystal Structure of A Human Prolactin Receptor Antagonist in Complex with the Extracellular Domain of the Human Prolactin Receptor, PDB code: 3mzg was solved by M.V.Kulkarni, M.C.Tettamanzi, J.W.Murphy, C.Keeler, D.G.Myszka, N.E.Chayen, E.J.Lolis, M.E.Hodsdon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.07 / 2.10
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	123.874, 123.874, 72.468, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 23

The structure of Crystal Structure of A Human Prolactin Receptor Antagonist in Complex with the Extracellular Domain of the Human Prolactin Receptor also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of A Human Prolactin Receptor Antagonist in Complex with the Extracellular Domain of the Human Prolactin Receptor (pdb code 3mzg). 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 A Human Prolactin Receptor Antagonist in Complex with the Extracellular Domain of the Human Prolactin Receptor, PDB code: 3mzg:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of A Human Prolactin Receptor Antagonist in Complex with the Extracellular Domain of the Human Prolactin Receptor


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 A Human Prolactin Receptor Antagonist in Complex with the Extracellular Domain of the Human Prolactin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na211 b:35.4 occ:1.00 O B:HOH364 2.2 25.4 1.0 O B:LYS66 2.3 29.8 1.0 O B:THR69 2.4 27.4 1.0 O A:HOH265 2.4 35.2 1.0 O B:HOH321 2.6 36.6 1.0 OD1 A:ASP68 3.2 45.2 1.0 C B:LYS66 3.4 29.1 1.0 C B:THR69 3.6 27.8 1.0 CB A:ASP68 3.6 35.0 1.0 CG A:ASP68 3.7 37.6 1.0 O B:HOH313 3.9 33.6 1.0 CA B:LYS66 4.0 29.2 1.0 N B:THR69 4.1 25.6 1.0 CA B:THR69 4.3 26.8 1.0 CB B:LYS66 4.3 31.1 1.0 O B:HOH271 4.3 38.4 1.0 CB B:THR69 4.4 26.9 1.0 N B:GLN67 4.4 29.0 1.0 O B:GLU18 4.5 27.7 1.0 CA B:GLN67 4.6 31.6 1.0 N B:SER70 4.6 25.8 1.0 OE2 A:GLU70 4.7 48.3 1.0 C B:GLN67 4.8 30.6 1.0 CA B:SER70 4.8 27.0 1.0 O A:HOH238 4.8 46.4 1.0 OD2 A:ASP68 4.9 38.3 1.0 O B:HOH324 4.9 39.1 1.0 N B:TYR68 5.0 27.7 1.0 CB B:SER70 5.0 28.9 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of A Human Prolactin Receptor Antagonist in Complex with the Extracellular Domain of the Human Prolactin Receptor


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 A Human Prolactin Receptor Antagonist in Complex with the Extracellular Domain of the Human Prolactin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na213 b:38.4 occ:1.00 O B:HOH365 2.3 46.9 1.0 O B:SER61 2.8 26.1 1.0 O B:HOH345 2.8 30.0 1.0 N B:SER61 2.9 28.0 1.0 O B:TYR54 3.2 31.5 1.0 N B:ASN60 3.4 31.4 1.0 O B:HOH331 3.4 37.4 1.0 CA B:ASN60 3.6 28.9 1.0 C B:ASN60 3.6 26.7 1.0 C B:SER61 3.7 27.4 1.0 CH2 B:TRP24 3.7 26.1 1.0 O B:GLY58 3.7 42.0 1.0 CA B:SER61 3.8 26.8 1.0 CD2 B:TYR54 3.9 26.2 1.0 CZ2 B:TRP24 3.9 30.0 1.0 CB B:TYR54 3.9 28.8 1.0 O B:HOH238 4.0 56.3 1.0 C B:TYR54 4.0 30.7 1.0 OG B:SER61 4.0 27.6 1.0 CA B:TYR54 4.1 28.4 1.0 C B:PRO59 4.2 35.6 1.0 CG B:TYR54 4.4 27.3 1.0 CB B:SER61 4.5 24.9 1.0 CZ3 B:TRP24 4.6 30.1 1.0 CA B:PRO59 4.8 39.0 1.0 O B:ASN60 4.8 27.1 1.0 C B:GLY58 4.9 42.1 1.0 OD1 B:ASN60 4.9 36.0 1.0 CE2 B:TYR54 4.9 26.3 1.0 CE2 B:TRP24 5.0 29.8 1.0 N B:CYS62 5.0 26.0 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of A Human Prolactin Receptor Antagonist in Complex with the Extracellular Domain of the Human Prolactin Receptor


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 A Human Prolactin Receptor Antagonist in Complex with the Extracellular Domain of the Human Prolactin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na214 b:22.2 occ:1.00 OG1 B:THR21 3.1 25.7 1.0 OG1 B:THR19 3.2 26.0 1.0 O B:HOH362 3.2 53.3 1.0 O B:HOH274 3.4 39.5 1.0 C B:PHE20 3.4 22.7 1.0 CE1 B:HIS63 3.5 31.3 1.0 CA B:PHE20 3.5 21.2 1.0 ND1 B:HIS63 3.5 30.7 1.0 CD B:PRO15 3.6 23.2 1.0 N B:PHE20 3.6 23.2 1.0 O B:PHE20 3.8 22.1 1.0 N B:THR21 3.8 22.7 1.0 C B:THR19 3.8 23.9 1.0 CB B:THR19 4.0 26.8 1.0 CG B:PRO15 4.1 25.6 1.0 O B:THR19 4.1 24.8 1.0 CB B:THR21 4.1 23.6 1.0 O B:HOH284 4.2 40.5 1.0 O B:ARG13 4.5 25.9 1.0 CA B:THR21 4.5 23.0 1.0 CA B:THR19 4.6 25.8 1.0 O B:HOH269 4.8 44.3 1.0 NE2 B:HIS63 4.8 29.5 1.0 CG B:HIS63 4.9 26.1 1.0 CB B:PHE20 5.0 19.0 1.0 N B:PRO15 5.0 24.3 1.0

M.V.Kulkarni, M.C.Tettamanzi, J.W.Murphy, C.Keeler, D.G.Myszka, N.E.Chayen, E.J.Lolis, M.E.Hodsdon. Two Independent Histidines, One in Human Prolactin and One in Its Receptor, Are Critical For pH-Dependent Receptor Recognition and Activation. J.Biol.Chem. V. 285 38524 2010.
ISSN: ISSN 0021-9258
PubMed: 20889499
DOI: 10.1074/JBC.M110.172072