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

Protein crystallography data

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

Zinc Binding Sites:

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 7rjf

Go back to Zinc Binding Sites List in 7rjf
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 7rjf

Go back to Zinc Binding Sites List in 7rjf
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

Reference:

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
Page generated: Fri Nov 5 17:00:12 2021

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