Sodium in PDB 2vdx: Crystal Structure of the Reactive Loop Cleaved Corticosteroid Binding Globulin

The structure of Crystal Structure of the Reactive Loop Cleaved Corticosteroid Binding Globulin, PDB code: 2vdx was solved by A.Zhou, Z.Wei, R.J.Read, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.47 / 1.84
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	39.941, 39.740, 112.113, 81.94, 84.06, 65.39
R / Rfree (%)	19.2 / 24.1

The binding sites of Sodium atom in the Crystal Structure of the Reactive Loop Cleaved Corticosteroid Binding Globulin (pdb code 2vdx). 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 Reactive Loop Cleaved Corticosteroid Binding Globulin, PDB code: 2vdx:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Reactive Loop Cleaved Corticosteroid Binding Globulin


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 Reactive Loop Cleaved Corticosteroid Binding Globulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1384 b:31.3 occ:1.00 O A:HOH2058 2.2 35.4 1.0 O A:HOH2098 2.3 28.7 1.0 O A:HOH2101 2.3 24.9 1.0 O A:GLY237 2.4 19.1 1.0 O A:TYR235 2.4 17.9 1.0 O A:HOH2099 3.0 38.5 1.0 C A:GLY237 3.5 19.1 1.0 C A:TYR235 3.6 17.4 1.0 N A:GLY237 3.6 19.2 1.0 CB A:ASN234 4.1 20.2 1.0 C A:VAL236 4.1 18.0 1.0 CA A:GLY237 4.1 19.0 1.0 CA A:VAL236 4.2 17.6 1.0 OG1 A:THR186 4.3 21.9 1.0 ND2 A:ASN234 4.3 22.1 1.0 N A:VAL236 4.3 17.0 1.0 CG A:ASN234 4.3 20.8 1.0 O A:GLY239 4.4 19.1 1.0 N A:TYR235 4.5 18.2 1.0 N A:ASN238 4.5 18.9 1.0 CA A:TYR235 4.7 18.0 1.0 CA A:ASN238 4.9 19.1 1.0 O A:VAL236 4.9 18.2 1.0 C A:ASN234 5.0 18.8 1.0 CA A:ASN234 5.0 19.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Reactive Loop Cleaved Corticosteroid Binding Globulin


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 Reactive Loop Cleaved Corticosteroid Binding Globulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1385 b:34.1 occ:1.00 O A:HOH2084 2.2 22.9 1.0 O A:SER215 2.5 21.7 1.0 OG A:SER216 2.6 20.9 1.0 C A:SER215 3.4 21.7 1.0 CB A:SER216 3.7 21.6 1.0 CA A:SER216 3.8 21.8 1.0 N A:SER216 4.0 21.6 1.0 N A:SER215 4.1 21.3 1.0 O A:HOH2060 4.1 26.6 1.0 CA A:SER215 4.4 22.1 1.0 CB A:GLN214 4.7 20.0 1.0 OE1 A:GLN214 4.8 20.9 1.0 O A:HOH2086 4.9 30.0 1.0 C A:GLN214 5.0 20.3 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Reactive Loop Cleaved Corticosteroid Binding Globulin


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 Reactive Loop Cleaved Corticosteroid Binding Globulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1386 b:40.8 occ:1.00 O A:HOH2029 2.2 31.8 1.0 O A:LEU93 2.2 32.0 1.0 O A:LYS96 2.4 34.0 1.0 C A:LEU93 3.4 32.3 1.0 C A:LYS96 3.5 33.4 1.0 CA A:PHE94 4.0 33.8 1.0 N A:LYS96 4.1 34.3 1.0 N A:PHE94 4.1 33.1 1.0 C A:PHE94 4.2 34.4 1.0 O A:LEU101 4.3 23.3 1.0 CA A:LYS96 4.3 33.9 1.0 OD1 A:ASP98 4.3 28.5 1.0 O A:MET103 4.4 23.4 1.0 CA A:LEU93 4.4 31.7 1.0 O A:PHE94 4.5 34.7 1.0 OD2 A:ASP98 4.5 30.3 1.0 N A:ALA95 4.6 34.2 1.0 N A:SER97 4.6 32.2 1.0 CG A:ASP98 4.6 29.6 1.0 CB A:LYS96 4.7 34.3 1.0 CA A:SER97 4.7 31.3 1.0 O A:GLN92 4.8 31.8 1.0 N A:ASP98 4.9 29.6 1.0 C A:SER97 5.0 30.6 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Reactive Loop Cleaved Corticosteroid Binding Globulin


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 Reactive Loop Cleaved Corticosteroid Binding Globulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1384 b:46.3 occ:1.00 O B:HOH2086 2.3 34.5 1.0 O B:HOH2023 2.4 41.8 1.0 O B:TYR235 2.4 27.6 1.0 O B:GLY237 2.4 29.2 1.0 O B:HOH2085 2.9 38.6 1.0 C B:GLY237 3.6 29.0 1.0 C B:TYR235 3.6 27.1 1.0 N B:GLY237 3.7 27.7 1.0 CB B:ASN234 4.0 28.5 1.0 OG1 B:THR186 4.1 27.2 1.0 CA B:VAL236 4.3 26.9 1.0 C B:VAL236 4.3 27.1 1.0 CA B:GLY237 4.3 28.4 1.0 N B:TYR235 4.4 27.0 1.0 N B:VAL236 4.4 26.8 1.0 CG B:ASN234 4.4 29.6 1.0 O B:GLY239 4.5 27.4 1.0 N B:ASN238 4.6 29.2 1.0 ND2 B:ASN234 4.6 31.9 1.0 CA B:TYR235 4.6 26.9 1.0 CA B:ASN238 4.8 29.8 1.0 C B:ASN234 4.8 27.6 1.0 CA B:ASN234 4.9 28.2 1.0

A.Zhou, Z.Wei, P.L.Stanley, R.J.Read, P.E.Stein, R.W.Carrell. The S-to-R Transition of Corticosteroid-Binding Globulin and the Mechanism of Hormone Release. J.Mol.Biol. V. 380 244 2008.
ISSN: ISSN 0022-2836
PubMed: 18513745
DOI: 10.1016/J.JMB.2008.05.012