Zinc in PDB 6knm: Apelin Receptor in Complex with Single Domain Antibody

The structure of Apelin Receptor in Complex with Single Domain Antibody, PDB code: 6knm was solved by Y.B.Ma, Y.Ding, X.Song, X.Ma, X.Li, N.Zhang, Y.Song, Y.Sun, Y.Shen, W.Zhong, L.A.Hu, Y.L.Ma, M.Y.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.64 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.780, 48.390, 350.100, 90.00, 90.00, 90.00
R / Rfree (%)	25.8 / 30.5

The binding sites of Zinc atom in the Apelin Receptor in Complex with Single Domain Antibody (pdb code 6knm). 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 Apelin Receptor in Complex with Single Domain Antibody, PDB code: 6knm:

Zinc binding site 1 out of 1 in the Apelin Receptor in Complex with Single Domain Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Apelin Receptor in Complex with Single Domain Antibody within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1101 b:90.8 occ:1.00 SG B:CYS1006 2.1 89.1 1.0 SG B:CYS1009 2.3 81.5 1.0 SG B:CYS1042 2.5 82.9 1.0 SG B:CYS1039 2.5 84.8 1.0 CB B:CYS1009 2.8 86.3 1.0 CB B:CYS1006 3.3 90.9 1.0 CB B:CYS1039 3.3 86.1 1.0 N B:CYS1009 3.4 90.9 1.0 CA B:CYS1009 3.6 88.6 1.0 CG2 B:VAL1044 3.8 80.8 1.0 CB B:CYS1042 3.8 81.8 1.0 N B:CYS1042 4.2 89.0 1.0 C B:CYS1009 4.3 86.8 1.0 N B:GLY1010 4.4 90.8 1.0 C B:VAL1008 4.6 91.3 1.0 CA B:CYS1042 4.6 90.6 1.0 CA B:CYS1006 4.6 88.7 1.0 CB B:VAL1008 4.7 84.2 1.0 CA B:CYS1039 4.8 81.9 1.0 N B:GLY1043 4.9 83.1 1.0 N B:VAL1008 4.9 87.2 1.0 CB B:LEU1041 4.9 83.8 1.0 C B:CYS1006 5.0 88.7 1.0 CA B:VAL1008 5.0 88.8 1.0

Y.B.Ma, Y.Ding, X.Song, X.Ma, X.Li, N.Zhang, Y.Song, Y.Sun, Y.Shen, W.Zhong, L.A.Hu, Y.L.Ma, M.Y.Zhang. Structure-Guided Discovery of A Single-Domain Antibody Agonist Against Human Apelin Receptor Sci Adv 2020.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.AAX7379