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Zinc in PDB 8vjv: Structure of Human Neurolysin in Complex with Dynorphin A8(1-8) Peptide

Enzymatic activity of Structure of Human Neurolysin in Complex with Dynorphin A8(1-8) Peptide

All present enzymatic activity of Structure of Human Neurolysin in Complex with Dynorphin A8(1-8) Peptide:
3.4.24.16;

Protein crystallography data

The structure of Structure of Human Neurolysin in Complex with Dynorphin A8(1-8) Peptide, PDB code: 8vjv 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) 95.73 / 2.12
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 143.168, 60.116, 95.734, 90, 90, 90
R / Rfree (%) 21.3 / 24.9

Other elements in 8vjv:

The structure of Structure of Human Neurolysin in Complex with Dynorphin A8(1-8) Peptide also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human Neurolysin in Complex with Dynorphin A8(1-8) Peptide (pdb code 8vjv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Structure of Human Neurolysin in Complex with Dynorphin A8(1-8) Peptide, PDB code: 8vjv:

Zinc binding site 1 out of 1 in 8vjv

Go back to Zinc Binding Sites List in 8vjv
Zinc binding site 1 out of 1 in the Structure of Human Neurolysin in Complex with Dynorphin A8(1-8) 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 A8(1-8) Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:142.0
occ:1.00
 OE1 A:GLU503 2.0 72.8 1.0
OE2 A:GLU503 2.0 74.9 1.0
NE2 A:HIS478 2.1 72.9 1.0
NE2 A:HIS474 2.1 67.0 1.0
CD A:GLU503 2.3 66.8 1.0
CE1 A:HIS474 2.9 60.8 1.0
CD2 A:HIS478 3.0 59.7 1.0
CE1 A:HIS478 3.1 62.3 1.0
CD2 A:HIS474 3.2 57.7 1.0
C D:GLY3 3.2 97.3 0.6
C D:GLY3 3.2 97.8 0.4
CA D:GLY3 3.3 90.6 0.6
CA D:GLY3 3.3 92.0 0.4
O D:GLY3 3.4 95.1 0.6
O D:GLY3 3.4 96.2 0.4
OG A:SER506 3.4 49.3 1.0
N D:GLY3 3.6 93.3 0.4
N D:PHE4 3.7 108.4 1.0
CG A:GLU503 3.8 54.8 1.0
CB A:SER506 3.9 47.2 1.0
ND1 A:HIS474 4.1 53.8 1.0
N D:GLY3 4.1 92.0 0.6
ND1 A:HIS478 4.2 54.2 1.0
CG A:HIS478 4.2 54.2 1.0
CG A:HIS474 4.2 57.0 1.0
C D:GLY2 4.4 87.4 0.4
CA D:PHE4 4.4 106.4 1.0
CE1 A:TYR613 4.5 59.6 1.0
OE2 A:GLU475 4.5 50.4 1.0
CD1 D:PHE4 4.6 109.3 1.0
CB A:GLU503 4.6 48.3 1.0
C D:GLY2 4.8 87.6 0.6
O D:GLY2 4.8 86.1 0.6
CA A:GLU503 4.8 43.7 1.0
OE1 A:GLU475 4.8 47.4 1.0
O D:GLY2 4.8 86.2 0.4

Reference:

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
Page generated: Fri Aug 22 14:38:43 2025

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