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Calcium in PDB 4gm4: Crystal Structure of Benzoylformate Decarboxylase Mutant L403I

Enzymatic activity of Crystal Structure of Benzoylformate Decarboxylase Mutant L403I

All present enzymatic activity of Crystal Structure of Benzoylformate Decarboxylase Mutant L403I:
4.1.1.7;

Protein crystallography data

The structure of Crystal Structure of Benzoylformate Decarboxylase Mutant L403I, PDB code: 4gm4 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) 36.04 / 1.28
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 81.146, 95.768, 137.002, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 15.9

Other elements in 4gm4:

The structure of Crystal Structure of Benzoylformate Decarboxylase Mutant L403I also contains other interesting chemical elements:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Benzoylformate Decarboxylase Mutant L403I (pdb code 4gm4). 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 L403I, PDB code: 4gm4:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4gm4

Go back to Calcium Binding Sites List in 4gm4
Calcium binding site 1 out of 2 in the Crystal Structure of Benzoylformate Decarboxylase Mutant L403I


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 L403I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:12.5
occ:1.00
O12 A:TZD605 2.3 14.3 1.0
O A:THR457 2.3 12.9 1.0
O23 A:TZD605 2.4 12.6 1.0
OD1 A:ASP428 2.4 13.5 1.0
O A:HOH766 2.4 14.2 1.0
OD1 A:ASN455 2.4 14.8 1.0
CG A:ASN455 3.3 16.7 1.0
P1 A:TZD605 3.5 12.5 1.0
CG A:ASP428 3.5 12.8 1.0
P2 A:TZD605 3.5 12.8 1.0
C A:THR457 3.5 12.3 1.0
O11 A:TZD605 3.6 12.6 1.0
ND2 A:ASN455 3.7 19.5 1.0
N A:THR457 4.0 13.9 1.0
OD2 A:ASP428 4.0 16.6 1.0
N A:ASP428 4.1 10.4 1.0
O5G A:TZD605 4.2 14.4 1.0
N A:GLY459 4.2 13.1 1.0
N A:GLY429 4.2 10.6 1.0
O A:MET453 4.3 12.3 1.0
CA A:THR457 4.4 13.9 1.0
O21 A:TZD605 4.4 12.6 1.0
N A:ASN455 4.4 13.2 1.0
N A:TYR458 4.5 12.8 1.0
O A:HOH778 4.5 13.3 1.0
CB A:ASN455 4.6 16.6 1.0
N A:GLY456 4.6 15.3 1.0
CA A:TYR458 4.6 12.7 1.0
O13 A:TZD605 4.6 12.7 1.0
O22 A:TZD605 4.7 14.5 1.0
CB A:ASP428 4.7 11.6 1.0
CA A:GLY427 4.7 9.8 1.0
CG2 A:THR457 4.8 15.8 1.0
CA A:ASP428 4.8 11.0 1.0
C A:GLY427 4.8 9.9 1.0
C A:ASN455 4.8 16.2 1.0
CA A:ASN455 4.8 15.0 1.0
C A:TYR458 5.0 13.0 1.0
C A:ASP428 5.0 11.0 1.0

Calcium binding site 2 out of 2 in 4gm4

Go back to Calcium Binding Sites List in 4gm4
Calcium binding site 2 out of 2 in the Crystal Structure of Benzoylformate Decarboxylase Mutant L403I


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 L403I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:17.1
occ:1.00
O A:GLU37 2.4 11.8 1.0
O A:HOH775 2.5 13.0 1.0
O A:HOH984 2.6 26.9 1.0
O A:HOH972 2.6 27.6 1.0
O A:HOH933 2.7 24.1 1.0
O A:HOH1047 2.7 29.5 1.0
O A:HOH998 2.7 32.5 1.0
O A:HOH1186 2.8 41.8 1.0
C A:GLU37 3.5 11.4 1.0
CA A:GLU37 4.3 12.2 1.0
N A:ASP38 4.5 11.0 1.0
CB A:GLU37 4.5 16.3 1.0
CA A:ASP38 4.5 11.3 1.0
O A:HOH801 4.7 18.0 1.0

Reference:

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
Page generated: Sat Dec 12 04:48:19 2020

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