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Calcium in PDB 2zal: Crystal Structure of E. Coli Isoaspartyl Aminopeptidase/L-Asparaginase in Complex with L-Aspartate

Enzymatic activity of Crystal Structure of E. Coli Isoaspartyl Aminopeptidase/L-Asparaginase in Complex with L-Aspartate

All present enzymatic activity of Crystal Structure of E. Coli Isoaspartyl Aminopeptidase/L-Asparaginase in Complex with L-Aspartate:
3.4.19.5; 3.5.1.1;

Protein crystallography data

The structure of Crystal Structure of E. Coli Isoaspartyl Aminopeptidase/L-Asparaginase in Complex with L-Aspartate, PDB code: 2zal was solved by K.Michalska, K.Brzezinski, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.890, 77.280, 147.530, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 18.8

Other elements in 2zal:

The structure of Crystal Structure of E. Coli Isoaspartyl Aminopeptidase/L-Asparaginase in Complex with L-Aspartate also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of E. Coli Isoaspartyl Aminopeptidase/L-Asparaginase in Complex with L-Aspartate (pdb code 2zal). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of E. Coli Isoaspartyl Aminopeptidase/L-Asparaginase in Complex with L-Aspartate, PDB code: 2zal:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2zal

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Calcium binding site 1 out of 5 in the Crystal Structure of E. Coli Isoaspartyl Aminopeptidase/L-Asparaginase in Complex with L-Aspartate


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 E. Coli Isoaspartyl Aminopeptidase/L-Asparaginase in Complex with L-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca804

b:20.9
occ:1.00
 O A:ASP503 2.4 26.3 1.0
O A:HOH886 2.4 24.4 1.0
OE2 A:GLU137 2.4 17.0 1.0
OE1 A:GLU137 2.5 14.0 1.0
CD A:GLU137 2.8 16.1 1.0
C A:ASP503 3.4 25.9 1.0
OXT A:ASP503 3.9 24.1 1.0
CG A:GLU137 4.3 14.9 1.0
CA A:ASP503 4.7 25.4 1.0
CB A:ASP503 5.0 25.6 1.0

Calcium binding site 2 out of 5 in 2zal

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Calcium binding site 2 out of 5 in the Crystal Structure of E. Coli Isoaspartyl Aminopeptidase/L-Asparaginase in Complex with L-Aspartate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of E. Coli Isoaspartyl Aminopeptidase/L-Asparaginase in Complex with L-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:22.8
occ:1.00
 O B:HOH845 2.3 23.5 1.0
OD1 B:ASP502 2.3 19.5 1.0
O B:HOH846 2.4 22.5 1.0
OD2 B:ASP504 2.4 24.3 1.0
O B:ASP502 2.5 23.8 1.0
N B:ASP502 2.5 23.3 1.0
O B:ASP504 2.5 25.3 1.0
N B:ASP504 2.5 25.7 1.0
C B:ASP504 3.3 25.9 1.0
C B:ASP502 3.4 24.6 1.0
CA B:ASP504 3.4 26.2 1.0
CA B:ASP502 3.4 24.7 1.0
CG B:ASP504 3.5 25.9 1.0
CG B:ASP502 3.5 25.8 1.0
O B:GLY253 4.0 8.6 1.0
CA B:CA805 4.0 22.4 1.0
CB B:ASP502 4.0 23.8 1.0
CB B:ASP504 4.0 26.8 1.0
C B:GLY253 4.2 8.7 1.0
CA B:GLY253 4.3 9.4 1.0
OXT B:ASP504 4.4 25.5 1.0
OD1 B:ASP504 4.5 24.7 1.0
OD2 B:ASP502 4.5 20.9 1.0
O B:MET249 4.5 12.2 1.0
OXT B:ASP502 4.6 24.9 1.0
O B:LEU254 4.7 8.4 1.0
N B:LEU254 5.0 8.6 1.0

Calcium binding site 3 out of 5 in 2zal

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Calcium binding site 3 out of 5 in the Crystal Structure of E. Coli Isoaspartyl Aminopeptidase/L-Asparaginase in Complex with L-Aspartate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of E. Coli Isoaspartyl Aminopeptidase/L-Asparaginase in Complex with L-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:25.4
occ:1.00
 OD2 B:ASP188 2.3 15.9 1.0
O B:HOH848 2.4 23.7 1.0
O B:HOH847 2.4 20.2 1.0
O A:HOH817 2.5 20.9 1.0
CG B:ASP188 3.4 14.0 1.0
CB B:ASP188 4.0 12.9 1.0
O A:GLY46 4.1 12.1 1.0
OD1 B:ASP188 4.3 14.9 1.0
OD2 B:ASP186 4.4 11.3 1.0
CA A:SER48 4.4 10.6 1.0
CB A:SER48 4.6 9.8 1.0
N A:SER48 4.7 10.3 1.0
O A:HOH857 4.8 33.5 1.0
CG B:ASP186 4.8 11.9 1.0
O A:GLU47 4.8 11.8 1.0
O A:HOH838 4.8 26.7 1.0
C A:GLU47 4.9 11.3 1.0
ND2 B:ASN190 4.9 16.7 1.0
OD1 B:ASP186 4.9 9.7 1.0

Calcium binding site 4 out of 5 in 2zal

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Calcium binding site 4 out of 5 in the Crystal Structure of E. Coli Isoaspartyl Aminopeptidase/L-Asparaginase in Complex with L-Aspartate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of E. Coli Isoaspartyl Aminopeptidase/L-Asparaginase in Complex with L-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca805

b:22.4
occ:1.00
 O B:GLY253 2.3 8.6 1.0
O B:HOH814 2.4 20.8 1.0
OD1 B:ASP502 2.4 19.5 1.0
OD2 B:ASP502 2.6 20.9 1.0
O B:ASP504 2.6 25.3 1.0
CG B:ASP502 2.9 25.8 1.0
C B:GLY253 3.5 8.7 1.0
C B:ASP504 3.5 25.9 1.0
OXT B:ASP504 3.6 25.5 1.0
CA B:CA802 4.0 22.8 1.0
CA B:GLY253 4.3 9.4 1.0
CB B:ASP502 4.4 23.8 1.0
OD2 B:ASP504 4.4 24.3 1.0
N B:LEU254 4.4 8.6 1.0
CA B:LEU254 4.5 8.3 1.0
O B:HOH845 4.5 23.5 1.0
C B:LEU254 4.6 8.4 1.0
N B:SER255 4.6 8.5 1.0
OE1 B:GLU258 4.7 9.6 1.0
CA B:ASP504 4.9 26.2 1.0
N B:ASP502 5.0 23.3 1.0

Calcium binding site 5 out of 5 in 2zal

Go back to Calcium Binding Sites List in 2zal
Calcium binding site 5 out of 5 in the Crystal Structure of E. Coli Isoaspartyl Aminopeptidase/L-Asparaginase in Complex with L-Aspartate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of E. Coli Isoaspartyl Aminopeptidase/L-Asparaginase in Complex with L-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca806

b:21.4
occ:1.00
 OD1 B:ASP188 2.3 14.9 1.0
CG B:ASP188 3.5 14.0 1.0
OD2 B:ASP188 4.1 15.9 1.0
CB B:ASP188 4.6 12.9 1.0
CA B:ASP188 4.7 11.7 1.0

Reference:

K.Michalska, K.Brzezinski, M.Jaskolski. Crystal Structure of Isoaspartyl Aminopeptidase in Complex with L-Aspartate J.Biol.Chem. V. 280 28484 2005.
ISSN: ISSN 0021-9258
PubMed: 15946951
DOI: 10.1074/JBC.M504501200
Page generated: Fri Jul 12 19:57:12 2024

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