Zinc in PDB 5vbl: Structure of Apelin Receptor in Complex with Agonist Peptide

The structure of Structure of Apelin Receptor in Complex with Agonist Peptide, PDB code: 5vbl was solved by Y.Ma, Y.Yue, Y.Ma, Q.Zhang, Q.Zhou, Y.Song, Y.Shen, X.Li, X.Ma, C.Li, M.A.Hanson, G.W.Han, E.A.Sickmier, G.Swaminath, S.Zhao, R.C.Stevems, L.A.Hu, W.Zhong, M.Zhang, F.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.61 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	150.580, 44.300, 79.450, 90.00, 114.87, 90.00
R / Rfree (%)	23.9 / 25.6

The structure of Structure of Apelin Receptor in Complex with Agonist Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Structure of Apelin Receptor in Complex with Agonist Peptide (pdb code 5vbl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Structure of Apelin Receptor in Complex with Agonist Peptide, PDB code: 5vbl:

Zinc binding site 1 out of 1 in the Structure of Apelin Receptor in Complex with Agonist Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Apelin Receptor in Complex with Agonist Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1101 b:43.4 occ:1.00 SG B:CYS1042 2.2 52.7 1.0 SG B:CYS1039 2.3 51.2 1.0 SG B:CYS1006 2.4 52.7 1.0 SG B:CYS1009 2.4 53.0 1.0 CB B:CYS1039 3.2 47.4 1.0 CB B:CYS1006 3.4 48.5 1.0 CB B:CYS1042 3.4 48.9 1.0 CB B:CYS1009 3.5 49.6 1.0 N B:CYS1009 3.9 49.9 1.0 N B:CYS1042 3.9 48.4 1.0 CG2 B:VAL1044 4.1 52.4 1.0 CA B:CYS1042 4.2 48.5 1.0 CA B:CYS1009 4.2 49.6 1.0 CB B:TYR1011 4.5 50.3 1.0 CA B:CYS1039 4.6 47.1 1.0 CB B:VAL1008 4.7 53.9 1.0 N B:GLY1010 4.7 49.6 1.0 C B:LEU1041 4.8 51.9 1.0 CA B:CYS1006 4.8 48.4 1.0 N B:TYR1011 4.8 49.4 1.0 C B:CYS1042 4.9 52.2 1.0 N B:GLY1043 4.9 48.4 1.0 CB B:LEU1041 4.9 47.8 1.0 C B:VAL1008 4.9 53.9 1.0 CZ B:PHE1049 5.0 55.4 1.0

Y.Ma, Y.Yue, Y.Ma, Q.Zhang, Q.Zhou, Y.Song, Y.Shen, X.Li, X.Ma, C.Li, M.A.Hanson, G.W.Han, E.A.Sickmier, G.Swaminath, S.Zhao, R.C.Stevens, L.A.Hu, W.Zhong, M.Zhang, F.Xu. Structural Basis For Apelin Control of the Human Apelin Receptor Structure V. 25 858 2017.
ISSN: ISSN 1878-4186
PubMed: 28528775
DOI: 10.1016/J.STR.2017.04.008