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Calcium in PDB 2bu3: Acyl-Enzyme Intermediate Between ALR0975 and Glutathione at pH 3.4

Enzymatic activity of Acyl-Enzyme Intermediate Between ALR0975 and Glutathione at pH 3.4

All present enzymatic activity of Acyl-Enzyme Intermediate Between ALR0975 and Glutathione at pH 3.4:
2.3.2.15;

Protein crystallography data

The structure of Acyl-Enzyme Intermediate Between ALR0975 and Glutathione at pH 3.4, PDB code: 2bu3 was solved by D.Vivares, P.Arnoux, D.Pignol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.59 / 1.4
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.253, 58.259, 72.561, 90.00, 108.87, 90.00
R / Rfree (%) 17.4 / 18.8

Other elements in 2bu3:

The structure of Acyl-Enzyme Intermediate Between ALR0975 and Glutathione at pH 3.4 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Acyl-Enzyme Intermediate Between ALR0975 and Glutathione at pH 3.4 (pdb code 2bu3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Acyl-Enzyme Intermediate Between ALR0975 and Glutathione at pH 3.4, PDB code: 2bu3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2bu3

Go back to Calcium Binding Sites List in 2bu3
Calcium binding site 1 out of 2 in the Acyl-Enzyme Intermediate Between ALR0975 and Glutathione at pH 3.4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Acyl-Enzyme Intermediate Between ALR0975 and Glutathione at pH 3.4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1242

b:11.5
occ:1.00
O A:ASN165 2.3 4.4 1.0
O A:ASN159 2.3 5.0 1.0
OD1 A:ASN165 2.4 6.9 1.0
OD2 A:ASP53 2.4 6.5 1.0
O A:GLN162 2.4 6.5 1.0
OD1 A:ASN159 2.4 6.2 1.0
C A:ASN165 3.1 4.8 1.0
CG A:ASP53 3.1 5.8 1.0
OD1 A:ASP53 3.2 6.2 1.0
C A:ASN159 3.2 5.1 1.0
CG A:ASN159 3.3 6.6 1.0
CG A:ASN165 3.5 6.5 1.0
C A:GLN162 3.5 6.2 1.0
N A:PHE166 3.9 3.7 1.0
ND2 A:ASN159 3.9 7.9 1.0
CA A:ASN165 4.0 5.4 1.0
CA A:ASN159 4.0 5.5 1.0
CB A:GLN162 4.0 7.0 1.0
N A:LEU160 4.1 5.2 1.0
CA A:GLN162 4.1 7.3 1.0
N A:GLN162 4.1 6.6 1.0
CA A:PHE166 4.1 3.7 1.0
N A:ASN165 4.1 5.3 1.0
CA A:LEU160 4.1 5.3 1.0
CB A:ASN159 4.2 5.5 1.0
CB A:ASN165 4.2 5.8 1.0
ND2 A:ASN165 4.5 9.8 1.0
C A:LEU160 4.5 5.9 1.0
CB A:ASP53 4.6 5.3 1.0
N A:ASP163 4.6 6.0 1.0
O A:HOH2144 4.7 6.1 1.0
CD1 A:PHE166 4.7 4.8 1.0
O A:LEU160 4.8 6.0 1.0
CA A:ASP163 4.9 6.2 1.0
C A:ASP163 4.9 6.3 1.0
CG A:PHE166 5.0 3.9 1.0
N A:LYS161 5.0 5.8 1.0

Calcium binding site 2 out of 2 in 2bu3

Go back to Calcium Binding Sites List in 2bu3
Calcium binding site 2 out of 2 in the Acyl-Enzyme Intermediate Between ALR0975 and Glutathione at pH 3.4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Acyl-Enzyme Intermediate Between ALR0975 and Glutathione at pH 3.4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1242

b:22.0
occ:1.00
O B:GLN162 2.4 8.1 1.0
OD1 B:ASP53 2.6 13.7 1.0
O B:ASN159 2.6 6.1 1.0
O B:ASN165 2.7 9.6 1.0
N B:ASN165 3.1 8.9 1.0
OD2 B:ASP53 3.2 11.3 1.0
C B:ASN165 3.2 8.2 1.0
CG B:ASP53 3.2 10.8 1.0
CA B:ASN165 3.4 9.0 1.0
C B:GLN162 3.5 7.3 1.0
CB B:ASN165 3.6 10.1 1.0
C B:ASN159 3.7 6.1 1.0
N B:GLY164 4.1 8.3 1.0
N B:GLN162 4.2 6.8 1.0
N B:PHE166 4.2 5.8 1.0
CA B:LEU160 4.2 5.8 1.0
CA B:GLN162 4.3 7.3 1.0
C B:GLY164 4.3 8.9 1.0
C B:ASP163 4.3 7.7 1.0
N B:LEU160 4.4 5.9 1.0
CG B:GLU52 4.5 8.4 1.0
O B:HOH2156 4.5 17.5 1.0
C B:LEU160 4.5 5.7 1.0
N B:ASP163 4.5 7.2 1.0
CB B:GLN162 4.5 7.8 1.0
CB B:GLU52 4.6 7.0 1.0
CA B:GLY164 4.6 9.0 1.0
CB B:ASP53 4.7 7.4 1.0
CA B:ASP163 4.7 7.5 1.0
CA B:PHE166 4.7 4.8 1.0
O B:ASP163 4.8 7.0 1.0
O B:LEU160 4.8 5.8 1.0
CA B:ASN159 4.8 6.7 1.0
CG B:ASN165 4.9 12.4 1.0
N B:LYS161 4.9 5.3 1.0
C B:LYS161 5.0 6.1 1.0

Reference:

D.Vivares, P.Arnoux, D.Pignol. A Papain-Like Enzyme at Work: Native and Acyl- Enzyme Intermediate Structures in Phytochelatin Synthesis. Proc.Natl.Acad.Sci.Usa V. 102 18848 2005.
ISSN: ISSN 0027-8424
PubMed: 16339904
DOI: 10.1073/PNAS.0505833102
Page generated: Sat Dec 12 03:32:52 2020

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