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Zinc in PDB 6r4z: Crystal Structure of Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnppvp-CONH2)

Enzymatic activity of Crystal Structure of Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnppvp-CONH2)

All present enzymatic activity of Crystal Structure of Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnppvp-CONH2):
3.4.24.89;

Protein crystallography data

The structure of Crystal Structure of Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnppvp-CONH2), PDB code: 6r4z was solved by C.Pichlo, U.Baumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.92 / 1.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 37.039, 42.806, 119.048, 90.00, 92.41, 90.00
R / Rfree (%) 13.3 / 15.1

Other elements in 6r4z:

The structure of Crystal Structure of Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnppvp-CONH2) also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnppvp-CONH2) (pdb code 6r4z). 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 Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnppvp-CONH2), PDB code: 6r4z:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6r4z

Go back to Zinc Binding Sites List in 6r4z
Zinc binding site 1 out of 2 in the Crystal Structure of Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnppvp-CONH2)


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 Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnppvp-CONH2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:8.4
occ:1.00
 OXT E:PRO4 1.9 11.2 1.0
OE1 A:GLU185 1.9 8.7 1.0
NE2 A:HIS142 2.0 8.3 1.0
NE2 A:HIS146 2.0 8.2 1.0
CD A:GLU185 2.7 9.1 1.0
OE2 A:GLU185 2.9 10.1 1.0
C E:PRO4 2.9 9.4 1.0
CE1 A:HIS142 3.0 9.1 1.0
CD2 A:HIS142 3.0 8.7 1.0
CE1 A:HIS146 3.0 8.3 1.0
CD2 A:HIS146 3.0 8.2 1.0
HE1 A:HIS146 3.2 10.0 1.0
HD2 A:HIS142 3.2 10.4 1.0
HE1 A:HIS142 3.2 10.9 1.0
HD2 A:HIS146 3.2 9.8 1.0
O E:PRO4 3.3 10.6 1.0
HB3 E:ASN3 3.5 10.2 1.0
HZ A:PHE178 3.7 16.4 1.0
HA A:GLU185 3.7 10.3 1.0
HB3 A:ALA188 3.8 9.8 1.0
O E:HOH105 4.0 10.2 1.0
HB2 E:ASN3 4.0 10.2 1.0
HE2 A:PHE178 4.1 15.7 1.0
ND1 A:HIS142 4.1 8.5 1.0
ND1 A:HIS146 4.1 8.4 1.0
CG A:HIS142 4.1 8.2 1.0
CG A:HIS146 4.2 7.4 1.0
CG A:GLU185 4.2 9.4 1.0
CB E:ASN3 4.2 8.5 1.0
O E:HOH104 4.3 10.4 1.0
CA E:PRO4 4.3 9.0 1.0
HB1 A:ALA188 4.3 9.8 1.0
CZ A:PHE178 4.4 13.7 1.0
CB A:ALA188 4.4 8.2 1.0
N E:PRO4 4.4 9.0 1.0
HB3 A:GLU185 4.4 11.2 1.0
HD2 E:PRO4 4.5 10.9 1.0
HB2 A:ALA188 4.5 9.8 1.0
C E:ASN3 4.5 8.1 1.0
CE2 A:PHE178 4.6 13.1 1.0
CA A:GLU185 4.6 8.6 1.0
HG3 A:GLU185 4.6 11.2 1.0
HG2 E:PRO4 4.6 12.2 1.0
CB A:GLU185 4.6 9.3 1.0
O E:ASN3 4.7 8.4 1.0
HG2 A:GLU185 4.7 11.2 1.0
HZ1 A:LYS101 4.7 14.5 1.0
HA E:PRO4 4.8 10.8 1.0
HD1 A:HIS142 4.9 10.2 1.0
CD E:PRO4 4.9 9.1 1.0
HD1 A:HIS146 4.9 10.0 1.0

Zinc binding site 2 out of 2 in 6r4z

Go back to Zinc Binding Sites List in 6r4z
Zinc binding site 2 out of 2 in the Crystal Structure of Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnppvp-CONH2)


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 Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnppvp-CONH2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn300

b:9.3
occ:1.00
 OXT D:PRO4 1.9 12.8 1.0
OE1 B:GLU185 1.9 10.0 1.0
NE2 B:HIS142 2.0 8.8 1.0
NE2 B:HIS146 2.0 8.9 1.0
CD B:GLU185 2.7 9.8 1.0
OE2 B:GLU185 2.9 10.4 1.0
C D:PRO4 2.9 10.8 1.0
CD2 B:HIS142 3.0 9.6 1.0
CE1 B:HIS146 3.0 9.3 1.0
CE1 B:HIS142 3.0 9.4 1.0
CD2 B:HIS146 3.0 9.2 1.0
HD2 B:HIS142 3.2 11.5 1.0
HE1 B:HIS146 3.2 11.2 1.0
HE1 B:HIS142 3.2 11.2 1.0
HD2 B:HIS146 3.2 11.0 1.0
O D:PRO4 3.3 12.9 1.0
HB3 D:ASN3 3.4 11.5 1.0
HA B:GLU185 3.7 11.1 1.0
HZ B:PHE178 3.8 18.8 1.0
HB3 B:ALA188 3.9 10.8 1.0
O D:HOH109 3.9 11.2 1.0
HB2 D:ASN3 4.0 11.5 1.0
HE2 B:PHE178 4.1 18.2 1.0
ND1 B:HIS142 4.1 9.4 1.0
ND1 B:HIS146 4.1 9.2 1.0
CG B:HIS142 4.1 9.4 1.0
CG B:HIS146 4.2 8.4 1.0
CB D:ASN3 4.2 9.6 1.0
CG B:GLU185 4.2 10.1 1.0
O D:HOH107 4.2 12.2 1.0
CA D:PRO4 4.3 10.8 1.0
N D:PRO4 4.4 10.2 1.0
HB1 B:ALA188 4.4 10.8 1.0
HB3 B:GLU185 4.5 11.4 1.0
CB B:ALA188 4.5 9.0 1.0
C D:ASN3 4.5 9.6 1.0
HD2 D:PRO4 4.5 12.9 1.0
CZ B:PHE178 4.5 15.7 1.0
HB2 B:ALA188 4.6 10.8 1.0
CA B:GLU185 4.6 9.3 1.0
O D:ASN3 4.6 9.6 1.0
HG3 B:GLU185 4.6 12.1 1.0
CB B:GLU185 4.6 9.5 1.0
CE2 B:PHE178 4.7 15.2 1.0
HG2 D:PRO4 4.7 14.0 1.0
HG2 B:GLU185 4.7 12.1 1.0
HZ1 B:LYS101 4.7 14.4 1.0
HA D:PRO4 4.8 12.9 1.0
HD1 B:HIS142 4.9 11.3 1.0
HD1 B:HIS146 4.9 11.1 1.0
CD D:PRO4 4.9 10.7 1.0
CA D:ASN3 5.0 9.4 1.0

Reference:

C.Pichlo, L.Juetten, F.Wojtalla, M.Schacherl, D.Diaz, U.Baumann. Molecular Determinants of the Mechanism and Substrate Specificity Ofclostridium Difficileproline-Proline Endopeptidase-1. J.Biol.Chem. V. 294 11525 2019.
ISSN: ESSN 1083-351X
PubMed: 31182482
DOI: 10.1074/JBC.RA119.009029
Page generated: Tue Oct 29 06:00:35 2024

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