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Zinc in PDB 6r58: Crystal Structure of Ppep-1(E143A/Y178F/E184A) in Complex with Substrate Peptide Ac-Evnapvp-CONH2

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

All present enzymatic activity of Crystal Structure of Ppep-1(E143A/Y178F/E184A) in Complex with Substrate Peptide Ac-Evnapvp-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-Evnapvp-CONH2, PDB code: 6r58 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) 46.13 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.995, 73.322, 237.348, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 21.4

Other elements in 6r58:

The structure of Crystal Structure of Ppep-1(E143A/Y178F/E184A) in Complex with Substrate Peptide Ac-Evnapvp-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 Ppep-1(E143A/Y178F/E184A) in Complex with Substrate Peptide Ac-Evnapvp-CONH2 (pdb code 6r58). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Ppep-1(E143A/Y178F/E184A) in Complex with Substrate Peptide Ac-Evnapvp-CONH2, PDB code: 6r58:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6r58

Go back to Zinc Binding Sites List in 6r58
Zinc binding site 1 out of 3 in the Crystal Structure of Ppep-1(E143A/Y178F/E184A) in Complex with Substrate Peptide Ac-Evnapvp-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-Evnapvp-CONH2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:12.3
occ:0.13
 OE1 A:GLU185 2.0 33.1 1.0
NE2 A:HIS142 2.1 24.3 1.0
NE2 A:HIS146 2.1 25.3 1.0
O E:ALA4 2.5 30.2 1.0
CD A:GLU185 2.8 32.9 1.0
OE2 A:GLU185 2.9 34.8 1.0
CD2 A:HIS146 2.9 24.6 1.0
CD2 A:HIS142 2.9 23.3 1.0
HD2 A:HIS146 3.0 29.6 1.0
HD2 A:HIS142 3.0 28.0 1.0
CE1 A:HIS146 3.1 25.9 1.0
CE1 A:HIS142 3.1 24.4 1.0
HA E:PRO5 3.1 34.7 1.0
HE1 A:HIS146 3.4 31.1 1.0
HE1 A:HIS142 3.4 29.3 1.0
HB3 E:ASN3 3.4 34.6 1.0
C E:ALA4 3.6 29.2 1.0
O E:HOH104 3.9 39.4 1.0
CA E:PRO5 3.9 28.9 1.0
HA A:GLU185 4.0 32.8 1.0
CG A:HIS146 4.1 24.1 1.0
CG A:HIS142 4.1 22.5 1.0
ND1 A:HIS146 4.1 25.5 1.0
N E:PRO5 4.2 28.8 1.0
ND1 A:HIS142 4.2 23.9 1.0
HB2 E:ASN3 4.2 34.6 1.0
CG A:GLU185 4.2 31.4 1.0
CB E:ASN3 4.2 28.8 1.0
HB3 A:ALA188 4.3 22.4 1.0
C E:PRO5 4.3 29.1 1.0
HE2 A:PHE178 4.4 38.4 1.0
C E:ASN3 4.5 26.5 1.0
HZ A:PHE178 4.5 40.7 1.0
N E:ALA4 4.6 27.9 1.0
HB3 A:GLU185 4.6 35.2 1.0
O E:ASN3 4.6 25.0 1.0
H E:VAL6 4.6 35.4 1.0
N E:VAL6 4.7 29.5 1.0
HG3 A:GLU185 4.7 37.7 1.0
HB1 A:ALA188 4.7 22.4 1.0
CA E:ALA4 4.7 28.0 1.0
HG2 A:GLU185 4.7 37.7 1.0
CB A:GLU185 4.8 29.4 1.0
CB A:ALA188 4.8 18.7 1.0
HB2 A:ALA188 4.8 22.4 1.0
H E:ALA4 4.8 33.5 1.0
O E:PRO5 4.8 28.8 1.0
CA A:GLU185 4.8 27.3 1.0
HD1 A:HIS146 4.9 30.6 1.0
HG22 E:VAL6 5.0 38.9 1.0
HG23 E:VAL6 5.0 38.9 1.0
HD1 A:HIS142 5.0 28.6 1.0

Zinc binding site 2 out of 3 in 6r58

Go back to Zinc Binding Sites List in 6r58
Zinc binding site 2 out of 3 in the Crystal Structure of Ppep-1(E143A/Y178F/E184A) in Complex with Substrate Peptide Ac-Evnapvp-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 Ppep-1(E143A/Y178F/E184A) in Complex with Substrate Peptide Ac-Evnapvp-CONH2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn300

b:15.3
occ:0.34
 OE1 C:GLU185 2.0 34.4 1.0
NE2 C:HIS146 2.0 32.1 1.0
NE2 C:HIS142 2.0 27.4 1.0
O I:ALA4 2.5 58.2 1.0
CD C:GLU185 2.8 32.7 1.0
CD2 C:HIS146 2.9 30.0 1.0
OE2 C:GLU185 2.9 34.0 1.0
CD2 C:HIS142 3.0 24.1 1.0
CE1 C:HIS146 3.1 32.3 1.0
HD2 C:HIS146 3.1 36.0 1.0
CE1 C:HIS142 3.1 26.0 1.0
HD2 C:HIS142 3.1 28.9 1.0
HA I:PRO5 3.1 70.9 1.0
HE1 C:HIS146 3.3 38.8 1.0
HE1 C:HIS142 3.3 31.2 1.0
HB3 I:ASN3 3.5 75.4 1.0
C I:ALA4 3.6 58.6 1.0
CA I:PRO5 3.9 59.1 1.0
HA C:GLU185 3.9 32.7 1.0
CG C:HIS146 4.1 29.4 1.0
ND1 C:HIS146 4.1 31.5 1.0
CG C:HIS142 4.1 23.9 1.0
N I:PRO5 4.1 58.7 1.0
ND1 C:HIS142 4.2 25.0 1.0
HB3 C:ALA188 4.2 26.1 1.0
CG C:GLU185 4.2 31.8 1.0
HB2 I:ASN3 4.2 75.4 1.0
HE2 C:PHE178 4.3 44.0 1.0
CB I:ASN3 4.3 62.8 1.0
HZ C:PHE178 4.3 45.1 1.0
C I:PRO5 4.3 59.9 1.0
HB3 C:GLU185 4.4 35.8 1.0
C I:ASN3 4.5 61.0 1.0
N I:ALA4 4.6 61.4 1.0
O I:ASN3 4.6 59.3 1.0
H I:VAL6 4.6 67.7 1.0
HB1 C:ALA188 4.7 26.1 1.0
N I:VAL6 4.7 56.4 1.0
CB C:GLU185 4.7 29.8 1.0
HG3 C:GLU185 4.7 38.2 1.0
CA C:GLU185 4.7 27.2 1.0
CA I:ALA4 4.7 59.8 1.0
HG2 C:GLU185 4.7 38.2 1.0
CB C:ALA188 4.7 21.8 1.0
O I:PRO5 4.8 64.1 1.0
HB2 C:ALA188 4.8 26.1 1.0
H I:ALA4 4.9 73.7 1.0
HD1 C:HIS146 4.9 37.8 1.0
HD1 C:HIS142 4.9 30.0 1.0
CE2 C:PHE178 5.0 36.6 1.0
CZ C:PHE178 5.0 37.6 1.0
HG22 I:VAL6 5.0 67.9 1.0

Zinc binding site 3 out of 3 in 6r58

Go back to Zinc Binding Sites List in 6r58
Zinc binding site 3 out of 3 in the Crystal Structure of Ppep-1(E143A/Y178F/E184A) in Complex with Substrate Peptide Ac-Evnapvp-CONH2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Ppep-1(E143A/Y178F/E184A) in Complex with Substrate Peptide Ac-Evnapvp-CONH2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:11.7
occ:0.06
 OE1 D:GLU185 2.0 33.9 1.0
NE2 D:HIS142 2.0 25.9 1.0
NE2 D:HIS146 2.1 24.5 1.0
O G:ALA4 2.8 27.9 1.0
CD2 D:HIS146 2.8 23.4 1.0
CD D:GLU185 2.9 33.7 1.0
HD2 D:HIS146 2.9 28.1 1.0
CD2 D:HIS142 2.9 25.3 1.0
HD2 D:HIS142 3.1 30.4 1.0
CE1 D:HIS142 3.1 26.3 1.0
OE2 D:GLU185 3.1 34.6 1.0
CE1 D:HIS146 3.2 24.6 1.0
HA G:PRO5 3.3 39.4 1.0
HE1 D:HIS142 3.3 31.6 1.0
HE1 D:HIS146 3.5 29.5 1.0
HB3 G:ASN3 3.5 33.7 1.0
C G:ALA4 3.8 28.4 1.0
O G:HOH102 3.8 30.5 1.0
HA D:GLU185 3.9 33.6 1.0
CG D:HIS146 4.0 23.5 1.0
CA G:PRO5 4.1 32.9 1.0
HB3 D:ALA188 4.1 25.7 1.0
CG D:HIS142 4.1 25.1 1.0
ND1 D:HIS142 4.1 26.1 1.0
ND1 D:HIS146 4.1 24.5 1.0
HB2 G:ASN3 4.2 33.7 1.0
HZ D:PHE178 4.2 51.0 1.0
HE2 D:PHE178 4.3 49.9 1.0
CB G:ASN3 4.3 28.1 1.0
CG D:GLU185 4.3 33.2 1.0
N G:PRO5 4.4 30.9 1.0
HB3 D:GLU185 4.4 37.1 1.0
C G:PRO5 4.4 32.0 1.0
HB1 D:ALA188 4.5 25.7 1.0
HB2 D:ALA188 4.5 25.7 1.0
CB D:ALA188 4.6 21.4 1.0
C G:ASN3 4.6 25.8 1.0
H G:VAL6 4.7 34.0 1.0
CB D:GLU185 4.7 30.9 1.0
HG3 D:GLU185 4.7 39.9 1.0
CA D:GLU185 4.7 28.0 1.0
O G:ASN3 4.7 24.0 1.0
N G:ALA4 4.7 27.4 1.0
N G:VAL6 4.8 28.4 1.0
HG2 D:GLU185 4.9 39.9 1.0
HD1 D:HIS142 4.9 31.4 1.0
CA G:ALA4 4.9 26.6 1.0
CZ D:PHE178 4.9 42.5 1.0
CE2 D:PHE178 4.9 41.6 1.0
O G:PRO5 5.0 33.4 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 06:01:55 2024

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