Zinc in PDB 8vju: Structure of Human Neurolysin in Complex with Dynorphin A13 Peptide

All present enzymatic activity of Structure of Human Neurolysin in Complex with Dynorphin A13 Peptide:
3.4.24.16;

The structure of Structure of Human Neurolysin in Complex with Dynorphin A13 Peptide, PDB code: 8vju was solved by K.Shi, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.29 / 1.99
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	142.067, 60.257, 95.553, 90, 90, 90
R / Rfree (%)	19.5 / 21.8

The structure of Structure of Human Neurolysin in Complex with Dynorphin A13 Peptide also contains other interesting chemical elements:

Sodium	(Na)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Structure of Human Neurolysin in Complex with Dynorphin A13 Peptide (pdb code 8vju). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Human Neurolysin in Complex with Dynorphin A13 Peptide, PDB code: 8vju:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Human Neurolysin in Complex with Dynorphin A13 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Neurolysin in Complex with Dynorphin A13 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:119.8 occ:1.00 NE2 A:HIS478 2.4 49.2 1.0 OE1 A:GLU503 2.4 47.2 1.0 NE2 A:HIS474 2.6 50.6 1.0 O C:ARG6 2.6 71.5 1.0 OE2 A:GLU503 2.7 56.5 1.0 CD A:GLU503 2.9 50.9 1.0 CD2 A:HIS478 3.1 45.3 1.0 C C:ARG6 3.5 72.3 1.0 CD2 A:HIS474 3.5 51.3 1.0 CE1 A:HIS474 3.5 51.8 1.0 CE1 A:HIS478 3.5 48.3 1.0 OG A:SER506 3.9 43.8 1.0 N C:ARG7 4.0 74.1 1.0 CA C:ARG7 4.1 74.9 1.0 CB A:SER506 4.2 40.8 1.0 CE1 A:TYR613 4.3 40.0 1.0 N C:ARG6 4.3 72.3 1.0 CG A:HIS478 4.4 46.1 1.0 CG A:GLU503 4.4 47.4 1.0 OE2 A:GLU475 4.4 52.0 1.0 ND1 A:HIS478 4.5 47.1 1.0 CA C:ARG6 4.5 72.1 1.0 ND1 A:HIS474 4.6 53.1 1.0 CG A:HIS474 4.6 49.0 1.0 CB C:LEU5 4.6 76.7 1.0 OE1 A:GLU475 4.7 46.6 1.0 OH A:TYR613 4.8 41.3 1.0 C C:LEU5 4.8 75.0 1.0 OH A:TYR606 4.8 53.6 1.0 CB C:ARG7 4.9 77.2 1.0 CD A:GLU475 4.9 47.7 1.0

Zinc binding site 2 out of 2 in the Structure of Human Neurolysin in Complex with Dynorphin A13 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Neurolysin in Complex with Dynorphin A13 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1010 b:89.2 occ:1.00 NE2 A:GLN669 3.6 63.5 1.0 CZ3 A:TRP615 3.9 46.2 1.0 CH2 A:TRP615 4.0 46.0 1.0 CD1 A:PHE295 4.1 39.6 1.0 CE3 A:TRP615 4.1 41.6 1.0 CG1 A:VAL618 4.2 40.7 1.0 CE1 A:PHE295 4.2 37.8 1.0 CZ2 A:TRP615 4.3 41.4 1.0 CG2 A:VAL618 4.3 40.7 1.0 CD2 A:TRP615 4.4 37.9 1.0 CB A:VAL618 4.4 40.5 1.0 CE2 A:TRP615 4.4 39.3 1.0 CG A:GLN669 4.5 62.4 1.0 CD A:GLN669 4.6 64.4 1.0 CE1 A:PHE619 4.9 43.7 1.0 CG A:PHE295 5.0 38.6 1.0

K.Shi, S.Bagchi, J.Bickel, S.H.Esfahani, L.Yin, T.Cheng, V.T.Karamyan, H.Aihara. Structural Basis of Divergent Substrate Recognition and Inhibition of Human Neurolysin. Sci Rep V. 14 18420 2024.
ISSN: ESSN 2045-2322
PubMed: 39117724
DOI: 10.1038/S41598-024-67639-W