Zinc in PDB 4xnw: The Human P2Y1 Receptor in Complex with MRS2500

The structure of The Human P2Y1 Receptor in Complex with MRS2500, PDB code: 4xnw was solved by D.Zhang, Z.Gao, K.Jacobson, G.W.Han, R.Stevens, Q.Zhao, B.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.31 / 2.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	40.670, 64.970, 77.570, 101.82, 95.70, 100.85
R / Rfree (%)	21.8 / 26.7

The structure of The Human P2Y1 Receptor in Complex with MRS2500 also contains other interesting chemical elements:

Iodine

(I)

2 atoms

The binding sites of Zinc atom in the The Human P2Y1 Receptor in Complex with MRS2500 (pdb code 4xnw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Human P2Y1 Receptor in Complex with MRS2500, PDB code: 4xnw:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the The Human P2Y1 Receptor in Complex with MRS2500


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Human P2Y1 Receptor in Complex with MRS2500 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:42.0 occ:1.00 SG A:CYS1039 2.1 39.1 1.0 SG A:CYS1009 2.2 44.1 1.0 SG A:CYS1042 2.3 42.7 1.0 SG A:CYS1006 2.3 43.6 1.0 CB A:CYS1039 3.1 36.6 1.0 CB A:CYS1006 3.3 43.1 1.0 CB A:CYS1009 3.3 45.5 1.0 CB A:CYS1042 3.6 40.7 1.0 N A:CYS1009 3.8 44.9 1.0 N A:CYS1042 3.9 38.0 1.0 CA A:CYS1009 4.1 44.7 1.0 CG2 A:VAL1044 4.1 53.4 1.0 CA A:CYS1042 4.3 38.6 1.0 CB A:LEU1041 4.4 35.9 1.0 CA A:CYS1039 4.5 36.8 1.0 CB A:TYR1011 4.6 40.2 1.0 C A:LEU1041 4.7 36.0 1.0 C A:CYS1009 4.7 41.8 1.0 C A:VAL1008 4.7 43.1 1.0 CA A:CYS1006 4.7 41.7 1.0 CB A:VAL1008 4.8 44.1 1.0 N A:GLY1043 4.9 45.3 1.0 C A:CYS1042 4.9 39.3 1.0 N A:LEU1041 4.9 36.4 1.0 CA A:LEU1041 4.9 36.0 1.0 C A:CYS1039 5.0 36.2 1.0 N A:GLY1010 5.0 37.8 1.0

Zinc binding site 2 out of 2 in the The Human P2Y1 Receptor in Complex with MRS2500


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Human P2Y1 Receptor in Complex with MRS2500 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1102 b:76.4 occ:1.00 SG C:CYS1009 1.9 68.9 1.0 SG C:CYS1042 2.2 0.9 1.0 SG C:CYS1039 2.4 57.1 1.0 SG C:CYS1006 2.5 85.6 1.0 CB C:CYS1009 3.0 77.2 1.0 CB C:CYS1006 3.4 85.8 1.0 CB C:CYS1039 3.4 61.9 1.0 CB C:CYS1042 3.4 96.9 1.0 N C:CYS1009 3.6 81.4 1.0 CA C:CYS1009 3.8 83.4 1.0 N C:CYS1042 3.8 91.8 1.0 CA C:CYS1042 4.2 95.2 1.0 CB C:LEU1041 4.3 81.2 1.0 CG2 C:VAL1044 4.3 0.7 1.0 C C:CYS1009 4.4 90.0 1.0 C C:VAL1008 4.5 87.7 1.0 C C:LEU1041 4.6 86.9 1.0 CB C:TYR1011 4.6 69.1 1.0 CB C:VAL1008 4.7 98.3 1.0 N C:GLY1010 4.8 95.9 1.0 CA C:CYS1039 4.9 65.1 1.0 CA C:CYS1006 4.9 84.6 1.0 CA C:LEU1041 4.9 81.1 1.0 C C:CYS1042 4.9 97.8 1.0 N C:TYR1011 4.9 80.7 1.0 N C:GLY1043 5.0 93.5 1.0 N C:LEU1041 5.0 80.0 1.0

D.Zhang, Z.Gao, K.Zhang, E.Kiselev, S.Crane, J.Wang, S.Paoletta, C.Yi, L.Ma, W.Zhang, G.W.Han, H.Liu, V.Cherezov, V.Katritch, H.Jiang, R.Stevens, K.Jacobson, Q.Zhao, B.Wu. Two Disparate Ligand-Binding Sites in the Human P2Y1 Receptor Nature 2015.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE14287