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Zinc in PDB 6r57: Crystal Structure of Ppep-1(E143A/Y178F/E184A) in Complex with Substrate Peptide Ac-Evnppvp-CONH2

Enzymatic activity of Crystal Structure of Ppep-1(E143A/Y178F/E184A) in Complex with Substrate Peptide Ac-Evnppvp-CONH2

All present enzymatic activity of Crystal Structure of Ppep-1(E143A/Y178F/E184A) in Complex with Substrate Peptide Ac-Evnppvp-CONH2:
3.4.24.89;

Protein crystallography data

The structure of Crystal Structure of Ppep-1(E143A/Y178F/E184A) in Complex with Substrate Peptide Ac-Evnppvp-CONH2, PDB code: 6r57 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) 40.52 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 37.202, 43.005, 121.908, 90.00, 96.71, 90.00
R / Rfree (%) 16 / 18.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ppep-1(E143A/Y178F/E184A) in Complex with Substrate Peptide Ac-Evnppvp-CONH2 (pdb code 6r57). 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 Crystal Structure of Ppep-1(E143A/Y178F/E184A) in Complex with Substrate Peptide Ac-Evnppvp-CONH2, PDB code: 6r57:

Zinc binding site 1 out of 1 in 6r57

Go back to Zinc Binding Sites List in 6r57
Zinc binding site 1 out of 1 in the Crystal Structure of Ppep-1(E143A/Y178F/E184A) in Complex with 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 Ppep-1(E143A/Y178F/E184A) in Complex with Substrate Peptide Ac-Evnppvp-CONH2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:23.9
occ:0.20
 OE1 B:GLU185 1.8 25.9 1.0
O D:PRO14 2.0 26.1 1.0
NE2 B:HIS142 2.1 20.7 1.0
NE2 B:HIS146 2.2 24.5 1.0
CD B:GLU185 2.4 34.9 1.0
OE2 B:GLU185 2.5 30.3 1.0
CE1 B:HIS142 3.0 21.7 1.0
HA D:PRO15 3.0 34.0 1.0
CD2 B:HIS142 3.1 19.6 1.0
CE1 B:HIS146 3.1 28.6 1.0
HE1 B:HIS142 3.2 26.0 1.0
C D:PRO14 3.2 24.4 1.0
CD2 B:HIS146 3.2 26.2 1.0
HE1 B:HIS146 3.3 34.3 1.0
HD2 B:HIS142 3.3 23.6 1.0
HD2 B:HIS146 3.4 31.4 1.0
HB3 D:ASN13 3.5 31.9 1.0
CA D:PRO15 3.7 28.3 1.0
HA B:GLU185 3.7 25.3 1.0
CG B:GLU185 3.9 25.8 1.0
HE2 B:PHE178 3.9 28.0 1.0
N D:PRO15 3.9 24.2 1.0
HZ B:PHE178 4.0 44.9 1.0
C D:PRO15 4.1 25.4 1.0
O D:HOH103 4.1 27.4 1.0
HB3 B:ALA188 4.2 21.6 1.0
ND1 B:HIS142 4.2 23.2 1.0
HD2 D:PRO14 4.2 43.3 1.0
CG B:HIS142 4.2 16.1 1.0
HB3 B:GLU185 4.2 29.9 1.0
N D:PRO14 4.3 26.2 1.0
ND1 B:HIS146 4.3 28.9 1.0
HG2 B:GLU185 4.3 31.0 1.0
HB2 D:ASN13 4.4 31.9 1.0
CB D:ASN13 4.4 26.6 1.0
CA D:PRO14 4.4 25.4 1.0
CG B:HIS146 4.4 21.6 1.0
HG3 B:GLU185 4.4 31.0 1.0
O D:PRO15 4.4 23.6 1.0
CB B:GLU185 4.4 24.9 1.0
C D:ASN13 4.5 26.2 1.0
CA B:GLU185 4.5 21.1 1.0
N D:VAL16 4.6 28.8 1.0
CE2 B:PHE178 4.6 23.3 1.0
HG2 D:PRO14 4.6 42.5 1.0
H D:VAL16 4.6 34.6 1.0
CZ B:PHE178 4.7 37.4 1.0
O D:ASN13 4.7 25.6 1.0
CD D:PRO14 4.7 36.1 1.0
HB1 B:ALA188 4.8 21.6 1.0
CB B:ALA188 4.8 18.0 1.0
HD1 B:HIS142 4.9 27.8 1.0
HB2 B:ALA188 4.9 21.6 1.0
HG23 D:VAL16 4.9 35.6 1.0
HA D:PRO14 5.0 30.5 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 06:01:55 2024

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