Calcium in PDB 4mpr: Benzoylformate Decarboxylase: Is the Tetramer Vital For Activity?

All present enzymatic activity of Benzoylformate Decarboxylase: Is the Tetramer Vital For Activity?:
4.1.1.7;

The structure of Benzoylformate Decarboxylase: Is the Tetramer Vital For Activity?, PDB code: 4mpr was solved by F.H.Andrews, M.J.Mcleish, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.99 / 1.40
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	80.976, 95.971, 137.349, 90.00, 90.00, 90.00
R / Rfree (%)	12.4 / 15

The structure of Benzoylformate Decarboxylase: Is the Tetramer Vital For Activity? also contains other interesting chemical elements:

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

The binding sites of Calcium atom in the Benzoylformate Decarboxylase: Is the Tetramer Vital For Activity? (pdb code 4mpr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Benzoylformate Decarboxylase: Is the Tetramer Vital For Activity?, PDB code: 4mpr:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Benzoylformate Decarboxylase: Is the Tetramer Vital For Activity?


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Benzoylformate Decarboxylase: Is the Tetramer Vital For Activity? within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:10.7 occ:1.00 O2A A:TPP602 2.2 12.1 1.0 OD1 A:ASP428 2.3 12.3 1.0 O A:THR457 2.3 10.7 1.0 O3B A:TPP602 2.3 10.4 1.0 OD1 A:ASN455 2.3 12.3 1.0 O A:HOH726 2.4 14.2 1.0 CG A:ASN455 3.3 13.6 1.0 CG A:ASP428 3.4 12.1 1.0 PA A:TPP602 3.4 10.6 1.0 PB A:TPP602 3.5 10.6 1.0 C A:THR457 3.5 11.0 1.0 O3A A:TPP602 3.6 9.9 1.0 ND2 A:ASN455 3.6 15.5 1.0 OD2 A:ASP428 4.0 14.9 1.0 N A:THR457 4.0 12.1 1.0 N A:ASP428 4.1 8.6 1.0 N A:GLY459 4.2 11.5 1.0 O7 A:TPP602 4.2 11.8 1.0 N A:GLY429 4.2 9.5 1.0 O A:MET453 4.3 11.8 1.0 O2B A:TPP602 4.4 11.4 1.0 CA A:THR457 4.4 12.3 1.0 N A:ASN455 4.4 11.4 1.0 N A:TYR458 4.5 10.2 1.0 O A:HOH746 4.5 11.8 1.0 CB A:ASN455 4.6 13.5 1.0 CA A:TYR458 4.6 9.9 1.0 O1A A:TPP602 4.6 10.6 1.0 CB A:ASP428 4.6 9.6 1.0 O1B A:TPP602 4.7 11.6 1.0 N A:GLY456 4.7 12.1 1.0 CA A:GLY427 4.7 8.5 1.0 CA A:ASP428 4.7 9.1 1.0 C A:GLY427 4.8 8.2 1.0 CA A:ASN455 4.8 12.3 1.0 CG2 A:THR457 4.8 12.6 1.0 C A:ASN455 4.8 13.4 1.0 C A:TYR458 4.9 11.1 1.0 C A:ASP428 5.0 9.1 1.0

Calcium binding site 2 out of 3 in the Benzoylformate Decarboxylase: Is the Tetramer Vital For Activity?


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Benzoylformate Decarboxylase: Is the Tetramer Vital For Activity? within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:15.5 occ:1.00 O A:HOH886 2.3 25.4 1.0 OD1 A:ASP364 2.4 15.5 1.0 O A:HOH1269 2.5 29.0 1.0 O A:HOH780 2.5 13.9 1.0 O A:HOH853 2.5 19.1 1.0 O A:HOH1232 2.5 22.6 1.0 O A:HOH936 2.6 25.1 1.0 CG A:ASP364 3.5 14.8 1.0 OD2 A:ASP364 3.8 16.7 1.0 O A:ASP360 4.6 12.0 1.0 ND2 A:ASN363 4.7 14.2 1.0 O A:HOH1118 4.7 36.1 1.0 CB A:ASP364 4.8 13.6 1.0 O A:HOH764 4.8 13.4 1.0

Calcium binding site 3 out of 3 in the Benzoylformate Decarboxylase: Is the Tetramer Vital For Activity?


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Benzoylformate Decarboxylase: Is the Tetramer Vital For Activity? within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca606 b:11.9 occ:0.50 O A:ARG120 2.5 9.1 1.0 O A:LEU118 2.6 7.9 1.0 O A:ASN117 2.7 8.7 1.0 O A:HOH759 3.2 13.0 0.5 C A:LEU118 3.3 7.2 1.0 C A:ARG120 3.7 8.2 1.0 C A:ASN117 3.8 8.0 1.0 CA A:LEU118 3.8 7.0 1.0 N A:ARG120 3.9 7.6 1.0 CA A:ARG120 4.2 8.4 1.0 N A:PRO119 4.3 8.3 1.0 N A:LEU118 4.3 7.5 1.0 C A:PRO119 4.3 8.0 1.0 CE A:MET79 4.4 9.6 0.6 CB A:ARG120 4.6 8.5 1.0 CA A:PRO119 4.7 8.6 1.0 N A:PRO121 4.8 7.8 1.0 CD A:PRO121 4.9 9.1 1.0

F.H.Andrews, M.P.Rogers, L.N.Paul, M.J.Mcleish. Perturbation of the Monomer-Monomer Interfaces of the Benzoylformate Decarboxylase Tetramer. Biochemistry V. 53 4358 2014.
ISSN: ISSN 0006-2960
PubMed: 24956165
DOI: 10.1021/BI500081R