Calcium in PDB 4mq5: Crystal Structure of Benzoylformate Decarboxylase Mutant A306F

All present enzymatic activity of Crystal Structure of Benzoylformate Decarboxylase Mutant A306F:
4.1.1.7;

The structure of Crystal Structure of Benzoylformate Decarboxylase Mutant A306F, PDB code: 4mq5 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)	26.44 / 1.50
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	81.629, 95.540, 137.590, 90.00, 90.00, 90.00
R / Rfree (%)	12 / 14.7

The structure of Crystal Structure of Benzoylformate Decarboxylase Mutant A306F also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Benzoylformate Decarboxylase Mutant A306F (pdb code 4mq5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Benzoylformate Decarboxylase Mutant A306F, PDB code: 4mq5:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Benzoylformate Decarboxylase Mutant A306F


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 Benzoylformate Decarboxylase Mutant A306F within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:11.6 occ:1.00 O A:THR457 2.3 12.8 1.0 OD1 A:ASN455 2.3 14.6 1.0 O2A A:TPP603 2.3 11.3 1.0 OD1 A:ASP428 2.3 12.8 1.0 O3B A:TPP603 2.3 11.2 1.0 O A:HOH716 2.4 12.7 1.0 CG A:ASN455 3.3 15.2 1.0 CG A:ASP428 3.4 13.7 1.0 PA A:TPP603 3.5 11.2 1.0 C A:THR457 3.5 11.9 1.0 PB A:TPP603 3.5 11.4 1.0 O3A A:TPP603 3.7 11.2 1.0 ND2 A:ASN455 3.7 18.5 1.0 OD2 A:ASP428 4.0 15.8 1.0 N A:THR457 4.0 12.9 1.0 N A:ASP428 4.1 9.8 1.0 O7 A:TPP603 4.2 11.0 1.0 N A:GLY459 4.2 11.9 1.0 O A:MET453 4.3 12.3 1.0 N A:GLY429 4.3 10.3 1.0 N A:ASN455 4.3 12.9 1.0 CA A:THR457 4.3 13.2 1.0 O2B A:TPP603 4.4 12.2 1.0 N A:TYR458 4.5 11.9 1.0 O A:HOH736 4.5 11.8 1.0 CB A:ASN455 4.6 15.3 1.0 N A:GLY456 4.6 13.3 1.0 CA A:TYR458 4.6 11.7 1.0 CG2 A:THR457 4.7 15.5 1.0 CB A:ASP428 4.7 11.0 1.0 O1B A:TPP603 4.7 12.2 1.0 O1A A:TPP603 4.7 11.7 1.0 CA A:ASN455 4.7 14.0 1.0 C A:ASN455 4.8 14.4 1.0 CA A:ASP428 4.8 10.8 1.0 CA A:GLY427 4.8 10.2 1.0 C A:GLY427 4.9 9.9 1.0 C A:TYR458 5.0 12.3 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Benzoylformate Decarboxylase Mutant A306F


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 Benzoylformate Decarboxylase Mutant A306F within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:28.1 occ:1.00 O A:HOH791 2.4 17.5 1.0 OD1 A:ASP364 2.4 20.9 1.0 O A:HOH1029 2.6 27.1 1.0 O A:HOH997 2.8 28.6 1.0 O A:HOH968 3.0 25.1 1.0 CG A:ASP364 3.4 21.1 1.0 OD2 A:ASP364 3.8 22.9 1.0 O A:ASP360 4.6 13.1 1.0 O A:HOH1282 4.6 33.3 1.0 ND2 A:ASN363 4.7 15.4 1.0 CB A:ASP364 4.8 18.4 1.0 O A:HOH738 4.8 14.7 1.0 O A:HOH1235 4.9 32.4 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Benzoylformate Decarboxylase Mutant A306F


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 Benzoylformate Decarboxylase Mutant A306F within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca606 b:15.4 occ:0.50 O A:ARG120 2.5 10.8 1.0 O A:LEU118 2.5 9.7 1.0 O A:ASN117 2.7 10.7 1.0 O A:HOH754 3.3 13.6 0.5 C A:LEU118 3.3 9.4 1.0 C A:ARG120 3.6 9.7 1.0 C A:ASN117 3.8 9.9 1.0 CA A:LEU118 3.8 8.7 1.0 N A:ARG120 3.8 9.5 1.0 CA A:ARG120 4.2 9.6 1.0 N A:PRO119 4.3 9.1 1.0 N A:LEU118 4.3 8.6 1.0 C A:PRO119 4.3 9.4 1.0 CE A:MET79 4.4 10.8 0.5 CB A:ARG120 4.6 10.6 1.0 CA A:PRO119 4.6 9.9 1.0 N A:PRO121 4.7 9.4 1.0 CD A:PRO121 4.9 10.9 1.0 O A:PRO119 5.0 10.2 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