Calcium in PDB 7ffp: Crystal Structure of Di-Peptidase-E From Xenopus Laevis

Enzymatic activity of Crystal Structure of Di-Peptidase-E From Xenopus Laevis

All present enzymatic activity of Crystal Structure of Di-Peptidase-E From Xenopus Laevis:
3.4.13.21;

Protein crystallography data

The structure of Crystal Structure of Di-Peptidase-E From Xenopus Laevis, PDB code: 7ffp was solved by A.Kumar, R.Singh, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.22 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 82.666, 42.15, 75.68, 90, 118.24, 90
R / Rfree (%) 18.7 / 22.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Di-Peptidase-E From Xenopus Laevis (pdb code 7ffp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Di-Peptidase-E From Xenopus Laevis, PDB code: 7ffp:

Calcium binding site 1 out of 1 in 7ffp

Go back to Calcium Binding Sites List in 7ffp
Calcium binding site 1 out of 1 in the Crystal Structure of Di-Peptidase-E From Xenopus Laevis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Di-Peptidase-E From Xenopus Laevis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:34.2
occ:1.00
O A:HOH526 2.9 29.7 1.0
O A:HOH456 3.0 23.7 1.0
O A:HOH469 3.1 42.5 1.0
OG A:SER124 3.1 13.4 1.0
N A:GLY91 3.3 12.5 1.0
CB A:SER14 3.4 24.8 1.0
CA A:GLY91 3.4 11.8 1.0
OG A:SER14 3.6 21.8 1.0
CB A:SER124 3.6 14.2 1.0
O A:HOH564 3.9 23.9 0.3
N A:SER14 4.0 16.7 1.0
O A:SER124 4.0 12.6 1.0
O A:HOH564 4.1 24.9 0.7
CA A:SER14 4.2 16.3 1.0
CB A:SER125 4.2 11.7 1.0
C A:GLY91 4.3 12.9 1.0
C A:SER124 4.3 13.3 1.0
OH A:TYR53 4.3 17.7 1.0
C A:GLY90 4.5 11.3 1.0
CA A:SER124 4.6 11.5 1.0
O A:GLY91 4.7 10.7 1.0
O A:ASP301 4.8 22.7 1.0
C A:ASN13 4.9 13.6 1.0
OXT A:ASP301 4.9 20.5 1.0
N A:SER125 4.9 11.2 1.0
CA A:GLY90 4.9 12.6 1.0
CE1 A:TYR21 5.0 18.5 1.0

Reference:

A.Kumar, R.Singh, B.Ghosh, R.D.Makde. Crystal Structure of Aspartyl Dipeptidase From Xenopus Laevis Revealed Ligand Binding Induced Loop Ordering and Catalytic Triad Assembly. Proteins 2021.
ISSN: ESSN 1097-0134
PubMed: 34431561
DOI: 10.1002/PROT.26220
Page generated: Fri Sep 24 12:14:09 2021

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