Zinc in PDB 7mk3: Crystal Structure of NPR1

The structure of Crystal Structure of NPR1, PDB code: 7mk3 was solved by J.Cheng, Q.Wu, P.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.42 / 3.06
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.98, 78.98, 395.37, 90, 90, 90
R / Rfree (%)	24.4 / 27

The structure of Crystal Structure of NPR1 also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Zinc atom in the Crystal Structure of NPR1 (pdb code 7mk3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of NPR1, PDB code: 7mk3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of NPR1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of NPR1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:79.0 occ:1.00 ND1 A:HIS157 2.1 88.6 1.0 SG A:CYS150 2.3 80.7 1.0 SG A:CYS155 2.3 80.4 1.0 SG A:CYS160 2.3 78.3 1.0 CE1 A:HIS157 2.9 88.8 1.0 CB A:CYS160 3.0 80.2 1.0 CB A:CYS155 3.1 85.6 1.0 CB A:CYS150 3.2 86.8 1.0 CG A:HIS157 3.3 82.7 1.0 CA A:HIS157 3.4 79.7 1.0 N A:HIS157 3.6 94.5 1.0 N A:CYS150 3.6 89.7 1.0 CB A:HIS157 3.7 82.7 1.0 CA A:CYS150 3.9 93.8 1.0 NE2 A:HIS157 4.1 94.1 1.0 CD2 A:HIS157 4.3 88.6 1.0 CA A:CYS155 4.3 87.9 1.0 C A:CYS155 4.4 91.8 1.0 CA A:CYS160 4.4 76.5 1.0 O A:CYS155 4.5 89.1 1.0 C A:CYS150 4.5 96.0 1.0 O A:ASP152 4.7 94.6 1.0 C A:HIS157 4.7 77.7 1.0 C A:GLU149 4.7 87.5 1.0 O A:CYS150 4.8 89.6 1.0 N A:CYS160 4.8 77.3 1.0 C A:CYS156 4.8 85.4 1.0 N A:CYS156 4.9 91.1 1.0 CA A:GLU149 5.0 89.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of NPR1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of NPR1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:80.0 occ:1.00 ND1 B:HIS157 2.1 91.4 1.0 SG B:CYS150 2.3 82.5 1.0 SG B:CYS155 2.3 78.3 1.0 SG B:CYS160 2.3 76.6 1.0 CE1 B:HIS157 2.9 90.0 1.0 CB B:CYS155 3.0 87.4 1.0 CB B:CYS160 3.0 89.1 1.0 CB B:CYS150 3.2 83.7 1.0 CG B:HIS157 3.2 82.5 1.0 CA B:HIS157 3.4 86.6 1.0 N B:HIS157 3.6 92.4 1.0 N B:CYS150 3.6 79.0 1.0 CB B:HIS157 3.7 85.6 1.0 CA B:CYS150 3.9 82.7 1.0 NE2 B:HIS157 4.1 88.2 1.0 CD2 B:HIS157 4.3 87.7 1.0 CA B:CYS155 4.3 87.8 1.0 C B:CYS155 4.4 92.1 1.0 CA B:CYS160 4.5 74.7 1.0 C B:CYS150 4.5 89.8 1.0 O B:CYS155 4.5 92.8 1.0 O B:CYS150 4.7 93.2 1.0 O B:ASP152 4.7 87.7 1.0 C B:GLU149 4.7 89.2 1.0 C B:HIS157 4.7 82.5 1.0 N B:CYS160 4.8 82.3 1.0 C B:CYS156 4.8 87.6 1.0 N B:CYS156 4.8 91.5 1.0 CA B:GLU149 5.0 96.2 1.0 CG B:GLN371 5.0 80.0 1.0

S.Kumar, R.Zavaliev, Q.Wu, Y.Zhou, J.Cheng, L.Dillard, J.Powers, J.Withers, J.Zhao, Z.Guan, M.J.Borgnia, A.Bartesaghi, X.Dong, P.Zhou. Structural Basis of NPR1 in Activating Plant Immunity. Nature V. 605 561 2022.
ISSN: ESSN 1476-4687
PubMed: 35545668
DOI: 10.1038/S41586-022-04699-W