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Nickel 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:

Zinc (Zn) 3 atoms

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of Ppep-1(E143A/Y178F/E184A) in Complex with Substrate Peptide Ac-Evnapvp-CONH2, PDB code: 6r58:

Nickel binding site 1 out of 1 in 6r58

Go back to Nickel Binding Sites List in 6r58
Nickel binding site 1 out of 1 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 Nickel with other atoms in the Ni 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
D:Ni302

b:62.8
occ:0.85
 N D:GLY23 2.0 89.3 1.0
ND1 D:HIS25 2.0 70.0 1.0
N D:SER24 2.0 95.9 1.0
N D:HIS25 2.0 82.3 1.0
C D:GLY23 2.7 89.7 1.0
C D:SER24 2.8 82.9 1.0
H D:MET26 2.8 82.3 1.0
CA D:GLY23 2.8 84.3 1.0
CA D:SER24 2.9 89.9 1.0
CG D:HIS25 3.0 59.8 1.0
CE1 D:HIS25 3.0 59.7 1.0
CA D:HIS25 3.0 61.8 1.0
HE1 D:HIS25 3.2 71.6 1.0
CB D:HIS25 3.3 57.3 1.0
HB3 D:HIS25 3.3 68.7 1.0
HA D:SER24 3.4 0.9 1.0
HA3 D:GLY23 3.4 0.1 1.0
HB2 D:GLN198 3.4 57.5 1.0
N D:MET26 3.5 68.6 1.0
HA2 D:GLY23 3.5 0.1 1.0
C D:HIS25 3.7 59.6 1.0
HA D:HIS25 3.8 74.1 1.0
O D:GLY23 3.8 94.4 1.0
O D:SER24 4.0 85.9 1.0
NE2 D:HIS25 4.1 57.1 1.0
CD2 D:HIS25 4.1 57.9 1.0
CB D:SER24 4.2 94.3 1.0
HB3 D:SER24 4.2 0.1 1.0
H D:GLN198 4.2 44.8 1.0
OE1 D:GLN198 4.2 56.2 1.0
HB2 D:HIS25 4.2 68.7 1.0
CB D:GLN198 4.4 47.9 1.0
O D:MET26 4.5 71.4 1.0
N D:GLN198 4.5 37.4 1.0
HB2 D:SER24 4.5 0.1 1.0
HA D:GLN198 4.5 48.7 1.0
O D:HOH480 4.5 43.9 1.0
HA D:ASN197 4.6 37.9 1.0
HB2 D:MET26 4.6 87.2 1.0
CA D:MET26 4.7 72.1 1.0
CA D:GLN198 4.7 40.6 1.0
HE2 D:HIS25 4.9 68.5 1.0
HG2 D:MET26 4.9 88.0 1.0
O D:HIS25 4.9 52.0 1.0
O D:HOH457 4.9 45.0 1.0
HB3 D:GLN198 4.9 57.5 1.0
HD2 D:HIS25 4.9 69.5 1.0
CD D:GLN198 5.0 55.3 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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