Sodium in PDB 3ncc: A Human Prolactin Receptor Antagonist in Complex with the Mutant Extracellular Domain H188A of the Human Prolactin Receptor

The structure of A Human Prolactin Receptor Antagonist in Complex with the Mutant Extracellular Domain H188A of the Human Prolactin Receptor, PDB code: 3ncc 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)	32.03 / 2.50
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	123.411, 123.411, 73.148, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 24.1

The structure of A Human Prolactin Receptor Antagonist in Complex with the Mutant Extracellular Domain H188A of the Human Prolactin Receptor also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the A Human Prolactin Receptor Antagonist in Complex with the Mutant Extracellular Domain H188A of the Human Prolactin Receptor (pdb code 3ncc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the A Human Prolactin Receptor Antagonist in Complex with the Mutant Extracellular Domain H188A of the Human Prolactin Receptor, PDB code: 3ncc:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the A Human Prolactin Receptor Antagonist in Complex with the Mutant Extracellular Domain H188A 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 A Human Prolactin Receptor Antagonist in Complex with the Mutant Extracellular Domain H188A of the Human Prolactin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na211 b:22.2 occ:1.00 OG1 B:THR19 3.0 23.8 1.0 OG1 B:THR21 3.1 21.5 1.0 O B:HOH255 3.2 50.4 1.0 CD B:PRO15 3.4 20.8 1.0 CA B:PHE20 3.5 20.3 1.0 C B:PHE20 3.5 21.3 1.0 CE1 B:HIS63 3.5 23.7 1.0 ND1 B:HIS63 3.6 23.3 1.0 N B:PHE20 3.6 20.3 1.0 CG B:PRO15 3.8 20.0 1.0 O B:PHE20 3.9 22.6 1.0 N B:THR21 3.9 21.4 1.0 CB B:THR19 3.9 22.9 1.0 C B:THR19 3.9 21.7 1.0 O B:HOH265 4.1 45.5 1.0 CB B:THR21 4.1 21.8 1.0 O B:THR19 4.2 21.3 1.0 O B:ARG13 4.4 25.1 1.0 CA B:THR21 4.6 21.5 1.0 CA B:THR19 4.6 21.9 1.0 N B:PRO15 4.8 21.6 1.0 NE2 B:HIS63 4.8 23.3 1.0 CB B:PHE20 4.9 20.2 1.0 CG B:HIS63 5.0 24.2 1.0 O B:HOH250 5.0 49.9 1.0

Sodium binding site 2 out of 3 in the A Human Prolactin Receptor Antagonist in Complex with the Mutant Extracellular Domain H188A 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 A Human Prolactin Receptor Antagonist in Complex with the Mutant Extracellular Domain H188A of the Human Prolactin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na212 b:28.1 occ:1.00 O B:THR69 2.2 27.2 1.0 O B:LYS66 2.3 28.9 1.0 O A:HOH244 2.3 33.4 1.0 O B:HOH331 2.3 26.4 1.0 O A:HOH238 2.3 35.0 1.0 C B:THR69 3.3 27.6 1.0 OD1 A:ASP68 3.3 45.9 1.0 C B:LYS66 3.4 29.4 1.0 CB A:ASP68 3.8 37.6 1.0 N B:THR69 3.9 26.1 1.0 CG A:ASP68 3.9 41.6 1.0 O B:HOH292 4.0 35.6 1.0 CA B:THR69 4.0 27.1 1.0 CA B:LYS66 4.1 29.4 1.0 CB B:THR69 4.2 26.8 1.0 N B:SER70 4.4 27.1 1.0 O B:HOH252 4.5 32.1 1.0 N B:GLN67 4.5 29.7 1.0 O B:GLU18 4.5 27.0 1.0 CA B:SER70 4.6 27.1 1.0 CB B:LYS66 4.7 29.7 1.0 CA B:GLN67 4.7 30.2 1.0 CB B:SER70 4.8 27.9 1.0 O B:HOH302 4.8 31.1 1.0 C B:GLN67 4.8 29.0 1.0 CG2 B:THR69 4.8 23.5 1.0 O A:HOH230 4.9 40.3 1.0 N B:TYR68 4.9 28.1 1.0 OE2 A:GLU70 5.0 52.7 1.0

Sodium binding site 3 out of 3 in the A Human Prolactin Receptor Antagonist in Complex with the Mutant Extracellular Domain H188A 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 A Human Prolactin Receptor Antagonist in Complex with the Mutant Extracellular Domain H188A of the Human Prolactin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na214 b:38.0 occ:1.00 O B:SER61 2.8 27.4 1.0 N B:SER61 2.9 29.2 1.0 O B:TYR54 3.0 31.5 1.0 O B:HOH309 3.1 43.5 1.0 O B:HOH319 3.2 20.8 1.0 N B:ASN60 3.3 34.0 1.0 O B:GLY58 3.4 41.2 1.0 CA B:ASN60 3.6 31.3 1.0 C B:SER61 3.7 28.5 1.0 C B:ASN60 3.7 30.6 1.0 CA B:SER61 3.8 28.1 1.0 OG B:SER61 3.9 24.3 1.0 CH2 B:TRP24 3.9 28.4 1.0 C B:TYR54 3.9 30.6 1.0 CD2 B:TYR54 4.0 22.6 1.0 C B:PRO59 4.0 36.1 1.0 CB B:TYR54 4.1 29.8 1.0 CA B:TYR54 4.1 29.9 1.0 CZ2 B:TRP24 4.1 26.8 1.0 CB B:SER61 4.2 26.1 1.0 C B:GLY58 4.5 38.6 1.0 CG B:TYR54 4.6 28.3 1.0 CA B:PRO59 4.6 37.5 1.0 CZ3 B:TRP24 4.7 26.2 1.0 O B:HOH240 4.8 24.0 1.0 O B:PRO59 4.8 36.5 1.0 O B:ASN60 5.0 29.1 1.0 N B:CYS62 5.0 27.7 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