Zinc in PDB 1f5f: Crystal Structure of the N-Terminal G-Domain of Shbg in Complex with Zinc

The structure of Crystal Structure of the N-Terminal G-Domain of Shbg in Complex with Zinc, PDB code: 1f5f was solved by V.A.Avvakumov, Y.A.Muller, G.L.Hammond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.70
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	104.020, 104.020, 84.710, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 25.9

The structure of Crystal Structure of the N-Terminal G-Domain of Shbg in Complex with Zinc also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the N-Terminal G-Domain of Shbg in Complex with Zinc (pdb code 1f5f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the N-Terminal G-Domain of Shbg in Complex with Zinc, PDB code: 1f5f:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the N-Terminal G-Domain of Shbg in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the N-Terminal G-Domain of Shbg in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn251 b:40.4 occ:1.00 NE2 A:HIS83 2.0 36.7 1.0 NE2 A:HIS136 2.1 55.6 1.0 OD1 A:ASP65 2.2 43.5 1.0 CG A:ASP65 2.7 34.1 1.0 OD2 A:ASP65 2.7 37.7 1.0 CD2 A:HIS136 2.9 54.9 1.0 CD2 A:HIS83 2.9 41.3 1.0 CE1 A:HIS83 3.1 37.3 1.0 CE1 A:HIS136 3.3 54.9 1.0 CG A:HIS83 4.1 38.6 1.0 CG A:HIS136 4.1 54.8 1.0 CB A:ASP64 4.1 49.4 1.0 ND1 A:HIS83 4.1 42.6 1.0 CB A:ASP65 4.2 28.6 1.0 ND1 A:HIS136 4.2 55.9 1.0 OD2 A:ASP64 4.5 54.0 1.0 CG A:ASP64 4.6 57.0 1.0 CB A:ASN61 4.9 49.0 1.0 O A:ASP64 5.0 34.8 1.0 OG1 A:THR60 5.0 42.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the N-Terminal G-Domain of Shbg in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the N-Terminal G-Domain of Shbg in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn252 b:47.2 occ:1.00 OD2 A:ASP117 1.7 41.0 1.0 ND1 A:HIS101 2.1 32.4 1.0 O A:HOH269 2.1 36.7 1.0 CG A:ASP117 2.5 37.5 1.0 O A:HOH312 2.6 43.9 1.0 OD1 A:ASP117 2.8 32.7 1.0 CE1 A:HIS101 2.9 31.4 1.0 CG A:HIS101 3.3 28.3 1.0 CB A:HIS101 3.7 29.9 1.0 CB A:ASP117 3.9 34.6 1.0 CA A:HIS101 4.0 30.4 1.0 O A:HOH272 4.0 37.1 1.0 NE2 A:HIS101 4.1 35.0 1.0 O A:TRP100 4.1 32.9 1.0 O A:HOH295 4.2 54.7 1.0 CD2 A:HIS101 4.3 30.8 1.0 NE2 A:GLN102 4.6 64.1 1.0 N A:HIS101 4.9 33.8 1.0 C A:TRP100 4.9 37.9 1.0 NH1 A:ARG99 4.9 70.3 1.0 CG1 A:VAL116 4.9 30.3 1.0

G.V.Avvakumov, Y.A.Muller, G.L.Hammond. Steroid-Binding Specificity of Human Sex Hormone-Binding Globulin Is Influenced By Occupancy of A Zinc-Binding Site. J.Biol.Chem. V. 275 25920 2000.
ISSN: ISSN 0021-9258
PubMed: 10859323
DOI: 10.1074/JBC.M004484200