Zinc in PDB 7rjf: Mopd-1 Mutant-L47W

The structure of Mopd-1 Mutant-L47W, PDB code: 7rjf was solved by Y.Huawu, K.W.Conan, J.K.Gordon, M.C.Brett, H.Yen-Hua, J.C.David, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.35 / 1.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	41.377, 41.377, 127.399, 90, 90, 90
R / Rfree (%)	23.2 / 27.7

The binding sites of Zinc atom in the Mopd-1 Mutant-L47W (pdb code 7rjf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Mopd-1 Mutant-L47W, PDB code: 7rjf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Mopd-1 Mutant-L47W


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mopd-1 Mutant-L47W within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:24.4 occ:1.00 NE2 B:HIS30 2.1 22.5 1.0 ND1 A:HIS34 2.1 26.3 1.0 CE1 A:HIS34 2.9 26.7 1.0 HE1 A:HIS34 3.0 32.1 1.0 CD2 B:HIS30 3.0 24.9 1.0 CE1 B:HIS30 3.1 30.4 1.0 HD2 B:HIS30 3.2 30.0 1.0 CG A:HIS34 3.2 27.2 1.0 HE1 B:HIS30 3.2 36.5 1.0 HA A:HIS34 3.3 30.8 1.0 HB2 A:HIS34 3.4 29.4 1.0 CB A:HIS34 3.7 24.4 1.0 CA A:HIS34 3.9 25.6 1.0 H A:LYS35 3.9 32.9 1.0 NE2 A:HIS34 4.1 30.8 1.0 ND1 B:HIS30 4.2 24.8 1.0 CG B:HIS30 4.2 24.5 1.0 HE3 B:TRP47 4.2 32.5 1.0 CD2 A:HIS34 4.3 30.3 1.0 O B:HOH106 4.3 30.3 1.0 N A:LYS35 4.5 27.4 1.0 CE3 B:TRP47 4.6 27.0 1.0 HB3 A:HIS34 4.6 29.4 1.0 C A:HIS34 4.7 26.0 1.0 HB2 B:TRP47 4.7 30.8 1.0 HE2 A:HIS34 4.9 37.0 1.0 HZ3 B:TRP47 4.9 31.9 1.0 HD1 B:HIS30 4.9 29.8 1.0 O A:ILE33 5.0 27.5 1.0 O A:LYS35 5.0 35.1 1.0

Zinc binding site 2 out of 2 in the Mopd-1 Mutant-L47W


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mopd-1 Mutant-L47W within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:30.8 occ:1.00 O8 A:MLI104 1.9 32.2 1.0 O8 A:MLI103 2.1 40.9 1.0 NE2 A:HIS30 2.1 28.8 1.0 ND1 B:HIS34 2.2 34.0 1.0 C3 A:MLI104 2.6 34.2 1.0 O9 A:MLI104 2.7 33.2 1.0 C3 A:MLI103 2.8 39.5 1.0 O9 A:MLI103 2.8 38.0 1.0 CD2 A:HIS30 3.0 30.4 1.0 CE1 B:HIS34 3.0 44.7 1.0 CE1 A:HIS30 3.1 30.2 1.0 HD2 A:HIS30 3.1 36.6 1.0 HE1 B:HIS34 3.2 53.7 1.0 HB2 B:HIS34 3.2 36.5 1.0 CG B:HIS34 3.2 38.8 1.0 HE1 A:HIS30 3.4 36.4 1.0 HA B:HIS34 3.4 34.9 1.0 O A:HOH201 3.5 47.3 1.0 CB B:HIS34 3.6 30.3 1.0 H B:LYS35 3.7 53.9 1.0 HE3 A:TRP47 3.8 37.9 1.0 CA B:HIS34 4.0 29.0 1.0 C1 A:MLI104 4.1 35.6 1.0 HB2 A:TRP47 4.2 38.6 1.0 CG A:HIS30 4.2 23.3 1.0 NE2 B:HIS34 4.2 39.9 1.0 ND1 A:HIS30 4.2 28.7 1.0 C1 A:MLI103 4.2 51.6 1.0 CD2 B:HIS34 4.3 38.3 1.0 N B:LYS35 4.4 44.9 1.0 CE3 A:TRP47 4.4 31.5 1.0 H12 A:MLI103 4.5 62.0 1.0 HB3 B:HIS34 4.5 36.5 1.0 HA A:CYS29 4.5 34.2 1.0 H A:TRP47 4.5 40.5 1.0 C2 A:MLI104 4.5 53.6 1.0 H12 A:MLI104 4.6 42.8 1.0 C B:HIS34 4.7 40.7 1.0 H11 A:MLI104 4.7 42.8 1.0 O7 A:MLI103 4.7 54.5 1.0 H11 A:MLI103 4.8 62.0 1.0 HZ3 A:TRP47 4.8 32.4 1.0 O6 A:MLI104 4.8 51.5 1.0 O B:LYS35 4.9 52.3 1.0 O A:ASN28 4.9 34.1 1.0 HE2 B:HIS34 5.0 47.9 1.0 C2 A:MLI103 5.0 53.9 1.0 CZ3 A:TRP47 5.0 26.9 1.0 HD1 A:HIS30 5.0 34.5 1.0

H.Yin, X.Zhou, Y.H.Huang, G.J.King, B.M.Collins, Y.Gao, D.J.Craik, C.K.Wang. Rational Design of Potent Peptide Inhibitors of the Pd-1:Pd-L1 Interaction For Cancer Immunotherapy. J.Am.Chem.Soc. 2021.
ISSN: ESSN 1520-5126
PubMed: 34661406
DOI: 10.1021/JACS.1C08132