Zinc in PDB 6qba: Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold

The structure of Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold, PDB code: 6qba was solved by G.Mlynek, C.U.Brey, K.Djinovic-Carugo, D.Puehringer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.25 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.456, 77.614, 80.509, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.1

The structure of Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold (pdb code 6qba). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold, PDB code: 6qba:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold


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 Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn208 b:31.5 occ:1.00 HN3 A:IMD203 1.0 77.2 1.0 N3 A:IMD203 1.7 64.4 1.0 OD1 A:ASP140 2.0 29.1 1.0 OD2 A:ASP140 2.4 28.7 1.0 C4 A:IMD203 2.4 38.0 1.0 H4 A:IMD203 2.5 45.7 1.0 CG A:ASP140 2.6 25.2 1.0 C2 A:IMD203 3.0 51.0 1.0 H2 A:IMD203 3.4 61.2 1.0 HB2 A:ASN142 3.5 32.0 1.0 C5 A:IMD203 3.7 51.5 1.0 N1 A:IMD203 3.9 77.0 1.0 CB A:ASP140 4.1 25.7 1.0 H A:ASN142 4.2 31.2 1.0 HB2 A:ASP140 4.4 30.8 1.0 HD22 A:ASN142 4.4 34.6 1.0 CB A:ASN142 4.4 26.6 1.0 HB3 A:ASP140 4.5 30.8 1.0 H5 A:IMD203 4.5 61.8 1.0 HD2 A:PRO141 4.5 30.4 1.0 H A:GLY143 4.8 44.8 1.0 HB3 A:ASN142 4.8 32.0 1.0 HN1 A:IMD203 4.9 92.4 1.0 O A:HOH337 4.9 57.9 1.0 HA A:ASP140 5.0 29.3 1.0 N A:ASN142 5.0 26.0 1.0 ND2 A:ASN142 5.0 28.8 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold


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 Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn209 b:49.7 occ:1.00 HN3 A:IMD205 1.3 71.3 1.0 HN3 A:IMD202 1.7 64.6 1.0 OE2 A:GLU13 2.0 58.6 1.0 N3 A:IMD205 2.1 59.4 1.0 N3 A:IMD202 2.3 53.9 1.0 H2 A:IMD202 2.3 48.3 1.0 C2 A:IMD202 2.6 40.2 1.0 C4 A:IMD205 2.7 56.9 1.0 H4 A:IMD205 2.7 68.3 1.0 CD A:GLU13 2.8 54.9 1.0 OE1 A:GLU13 3.0 54.1 1.0 C2 A:IMD205 3.2 83.4 1.0 C4 A:IMD202 3.6 40.0 1.0 H2 A:IMD205 3.6 0.1 1.0 HH21 A:ARG10 3.8 65.9 1.0 N1 A:IMD202 3.9 45.1 1.0 C5 A:IMD205 4.0 89.6 1.0 NH2 A:ARG10 4.0 54.9 1.0 H4 A:IMD202 4.1 48.0 1.0 N1 A:IMD205 4.2 80.8 1.0 HH22 A:ARG10 4.2 65.9 1.0 CG A:GLU13 4.3 50.6 1.0 HH22 A:ARG155 4.3 48.9 1.0 C5 A:IMD202 4.4 37.6 1.0 HH21 A:ARG155 4.4 48.9 1.0 NH2 A:ARG155 4.4 40.7 1.0 HG2 A:GLU13 4.5 60.7 1.0 CZ A:ARG10 4.5 57.1 1.0 O A:HOH338 4.5 62.3 1.0 HE A:ARG10 4.5 69.0 1.0 H A:GLU13 4.6 48.5 1.0 HN1 A:IMD202 4.6 54.1 1.0 HG3 A:GLU13 4.7 60.7 1.0 NE A:ARG10 4.7 57.5 1.0 H5 A:IMD205 4.8 0.6 1.0 CZ A:ARG155 5.0 42.0 1.0 OD1 A:ASP108 5.0 35.5 1.0 OD2 A:ASP108 5.0 36.6 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn210 b:33.8 occ:1.00 HN3 A:IMD204 1.3 48.8 1.0 HN3 A:IMD206 1.4 65.1 1.0 N3 A:IMD204 2.0 40.6 1.0 NE2 A:HIS170 2.0 28.0 1.0 OD2 A:ASP175 2.0 43.5 1.0 N3 A:IMD206 2.1 54.2 1.0 OD1 A:ASP175 2.3 43.1 1.0 H4 A:IMD204 2.3 42.2 1.0 C4 A:IMD204 2.4 35.1 1.0 CG A:ASP175 2.5 42.1 1.0 H4 A:IMD206 2.6 72.1 1.0 C4 A:IMD206 2.7 60.0 1.0 CE1 A:HIS170 2.8 27.6 1.0 HE1 A:HIS170 2.9 33.1 1.0 CD2 A:HIS170 3.1 27.1 1.0 C2 A:IMD204 3.3 60.8 1.0 C2 A:IMD206 3.4 69.4 1.0 HD2 A:HIS170 3.4 32.4 1.0 HA2 A:GLY172 3.5 35.2 1.0 H2 A:IMD204 3.8 73.0 1.0 C5 A:IMD204 3.8 79.7 1.0 H2 A:IMD206 3.8 83.3 1.0 C5 A:IMD206 4.0 94.5 1.0 ND1 A:HIS170 4.0 26.7 1.0 CB A:ASP175 4.1 45.5 1.0 N1 A:IMD204 4.1 89.3 1.0 CG A:HIS170 4.2 26.2 1.0 H A:GLY172 4.3 33.6 1.0 N1 A:IMD206 4.3 92.0 1.0 CA A:GLY172 4.4 29.4 1.0 HB2 A:ASP175 4.4 54.6 1.0 HB3 A:ASP175 4.4 54.6 1.0 H5 A:IMD204 4.6 95.7 1.0 HE1 A:TYR25 4.6 34.8 1.0 N A:GLY172 4.6 28.0 1.0 O A:HOH358 4.6 29.1 1.0 HA3 A:GLY172 4.7 35.2 1.0 O A:HOH439 4.7 38.7 1.0 H5 A:IMD206 4.7 0.4 1.0 HD1 A:HIS170 4.8 32.0 1.0 O A:ASP175 4.8 64.4 1.0 H A:ASP175 5.0 50.8 1.0

C.Brey, G.Mlynek, C.U.Brey, K.Djinovic-Carugo, D.Puehringer. N/A N/A.