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Nickel 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:

Zinc (Zn) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total only one binding site of Nickel was 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:

Nickel binding site 1 out of 1 in 6r4z

Go back to Nickel Binding Sites List in 6r4z
Nickel binding site 1 out of 1 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 Nickel with other atoms in the Ni 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:Ni302

b:14.3
occ:0.48
 N A:SER24 1.9 29.7 1.0
N A:HIS25 2.0 27.6 1.0
ND1 A:HIS25 2.0 25.6 1.0
N A:GLY23 2.1 30.5 1.0
C A:GLY23 2.8 30.9 1.0
C A:SER24 2.8 30.4 1.0
H A:MET26 2.8 32.2 1.0
CA A:SER24 2.9 29.8 1.0
CG A:HIS25 2.9 26.8 1.0
CA A:GLY23 2.9 30.3 1.0
CE1 A:HIS25 3.0 25.9 1.0
CA A:HIS25 3.0 27.5 1.0
HB3 A:HIS25 3.2 33.0 1.0
CB A:HIS25 3.2 27.5 1.0
HE1 A:HIS25 3.2 31.1 1.0
N A:MET26 3.5 26.9 1.0
HA2 A:GLY23 3.5 36.4 1.0
HG A:SER24 3.6 35.6 1.0
HA A:SER24 3.6 35.8 1.0
HA3 A:GLY23 3.6 36.4 1.0
C A:HIS25 3.7 28.3 1.0
OG A:SER24 3.8 29.7 1.0
O A:HOH649 3.8 38.9 1.0
HA A:HIS25 3.8 33.0 1.0
CB A:SER24 3.9 29.4 1.0
O A:GLY23 4.0 31.0 1.0
O A:HOH603 4.0 33.2 1.0
O A:SER24 4.0 31.9 1.0
CD2 A:HIS25 4.1 26.8 1.0
NE2 A:HIS25 4.1 25.9 1.0
O A:HOH646 4.2 30.0 1.0
HB2 A:HIS25 4.2 33.0 1.0
HB3 A:SER24 4.4 35.3 1.0
HB3 A:MET26 4.6 29.7 1.0
HB2 A:SER24 4.6 35.3 1.0
O A:HOH650 4.6 30.0 1.0
CA A:MET26 4.7 25.2 1.0
O A:MET26 4.8 26.5 1.0
HB2 A:MET26 4.8 29.7 1.0
O A:HIS25 4.9 30.2 1.0
HE2 A:HIS25 4.9 31.1 1.0
CB A:MET26 4.9 24.8 1.0
HD2 A:HIS25 4.9 32.2 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: Thu Oct 10 08:49:28 2024

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