Calcium in PDB 4jd5: Crystal Structure of Benzoylformate Decarboxylase Mutant L403E

All present enzymatic activity of Crystal Structure of Benzoylformate Decarboxylase Mutant L403E:
4.1.1.7;

The structure of Crystal Structure of Benzoylformate Decarboxylase Mutant L403E, PDB code: 4jd5 was solved by W.R.P.Novak, F.H.Andrews, A.R.Tom, P.R.Gunderman, M.J.Mcleish, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.36 / 1.33
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	81.550, 95.790, 137.150, 90.00, 90.00, 90.00
R / Rfree (%)	13.4 / 15.2

The structure of Crystal Structure of Benzoylformate Decarboxylase Mutant L403E also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Benzoylformate Decarboxylase Mutant L403E (pdb code 4jd5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Benzoylformate Decarboxylase Mutant L403E, PDB code: 4jd5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Benzoylformate Decarboxylase Mutant L403E


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 L403E within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:9.3 occ:1.00 O12 A:TZD601 2.3 11.0 1.0 O A:THR457 2.4 10.0 1.0 OD1 A:ASN455 2.4 11.5 1.0 O22 A:TZD601 2.4 9.5 1.0 O A:HOH726 2.4 10.6 1.0 OD1 A:ASP428 2.4 11.0 1.0 CG A:ASN455 3.3 13.0 1.0 P1 A:TZD601 3.4 9.3 1.0 CG A:ASP428 3.5 11.2 1.0 P2 A:TZD601 3.5 9.4 1.0 C A:THR457 3.6 10.0 1.0 O11 A:TZD601 3.6 9.3 1.0 ND2 A:ASN455 3.6 16.1 1.0 OD2 A:ASP428 4.0 15.4 1.0 N A:THR457 4.0 10.6 1.0 O5G A:TZD601 4.1 10.8 1.0 N A:ASP428 4.1 8.1 1.0 N A:GLY459 4.2 10.3 1.0 N A:GLY429 4.3 8.6 1.0 O A:MET453 4.3 11.4 1.0 O23 A:TZD601 4.4 9.7 1.0 N A:ASN455 4.4 10.0 1.0 CA A:THR457 4.4 10.6 1.0 O A:HOH730 4.5 11.1 1.0 N A:TYR458 4.5 9.6 1.0 CB A:ASN455 4.6 13.8 1.0 N A:GLY456 4.6 11.9 1.0 CA A:TYR458 4.6 9.3 1.0 O13 A:TZD601 4.7 11.5 1.0 O21 A:TZD601 4.7 10.6 1.0 CB A:ASP428 4.7 9.8 1.0 CA A:ASN455 4.8 11.5 1.0 CA A:GLY427 4.8 8.7 1.0 C A:ASN455 4.8 13.1 1.0 CG2 A:THR457 4.8 13.9 1.0 CA A:ASP428 4.8 9.3 1.0 C A:GLY427 4.9 7.5 1.0 C A:TYR458 5.0 10.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Benzoylformate Decarboxylase Mutant L403E


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 L403E within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:16.6 occ:1.00 O A:GLU37 2.4 10.7 1.0 O A:HOH870 2.6 22.2 1.0 O A:HOH902 2.7 26.1 1.0 O A:HOH1138 2.8 35.6 1.0 O A:HOH991 2.9 35.0 1.0 O A:HOH1145 2.9 43.2 1.0 C A:GLU37 3.5 9.9 1.0 CA A:GLU37 4.3 10.7 1.0 CB A:GLU37 4.5 15.2 1.0 N A:ASP38 4.5 10.1 1.0 CA A:ASP38 4.6 10.1 1.0 O A:HOH786 4.7 15.9 1.0 O A:HOH1040 4.8 31.3 1.0

F.H.Andrews, A.R.Tom, P.R.Gunderman, W.R.Novak, M.J.Mcleish. A Bulky Hydrophobic Residue Is Not Required to Maintain the V-Conformation of Enzyme-Bound Thiamin Diphosphate. Biochemistry V. 52 3028 2013.
ISSN: ISSN 0006-2960
PubMed: 23607689
DOI: 10.1021/BI400368J