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Calcium in PDB 1yno: High Resolution Structure of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate

Enzymatic activity of High Resolution Structure of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate

All present enzymatic activity of High Resolution Structure of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate:
4.1.1.7;

Protein crystallography data

The structure of High Resolution Structure of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate, PDB code: 1yno was solved by A.K.Bera, M.S.Hasson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.22
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 80.951, 95.460, 136.701, 90.00, 90.00, 90.00
R / Rfree (%) 12.4 / 15.5

Other elements in 1yno:

The structure of High Resolution Structure of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the High Resolution Structure of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate (pdb code 1yno). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the High Resolution Structure of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate, PDB code: 1yno:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1yno

Go back to Calcium Binding Sites List in 1yno
Calcium binding site 1 out of 3 in the High Resolution Structure of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of High Resolution Structure of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca532

b:11.8
occ:1.00
 O12 A:TZD530 2.2 11.2 1.0
O A:THR457 2.3 11.6 1.0
OD1 A:ASN455 2.3 12.9 1.0
OD1 A:ASP428 2.3 12.8 1.0
O21 A:TZD530 2.3 10.9 1.0
O A:HOH1002 2.3 13.1 1.0
CG A:ASN455 3.2 16.2 1.0
CG A:ASP428 3.4 10.1 1.0
P1 A:TZD530 3.5 11.0 1.0
C A:THR457 3.5 12.0 1.0
P2 A:TZD530 3.5 9.0 0.8
ND2 A:ASN455 3.6 22.3 1.0
O11 A:TZD530 3.6 10.4 1.0
N A:THR457 4.0 12.6 1.0
OD2 A:ASP428 4.0 16.3 1.0
N A:ASP428 4.1 9.6 1.0
N A:GLY459 4.2 11.9 1.0
O5G A:TZD530 4.2 12.5 1.0
N A:GLY429 4.3 9.4 1.0
O A:MET453 4.3 11.3 1.0
O22 A:TZD530 4.3 12.1 1.0
CA A:THR457 4.3 12.1 1.0
N A:ASN455 4.4 12.0 1.0
N A:TYR458 4.5 11.7 1.0
O A:HOH602 4.5 12.3 1.0
CB A:ASN455 4.5 17.7 1.0
CB A:ASP428 4.6 9.8 1.0
O13 A:TZD530 4.6 10.8 1.0
CA A:TYR458 4.6 10.3 1.0
N A:GLY456 4.6 13.3 1.0
O23 A:TZD530 4.6 12.3 1.0
CG2 A:THR457 4.7 15.6 1.0
CA A:GLY427 4.8 9.9 1.0
CA A:ASP428 4.8 9.0 1.0
C A:ASN455 4.8 12.9 1.0
CA A:ASN455 4.8 13.9 1.0
C A:GLY427 4.8 9.3 1.0
C A:TYR458 5.0 11.7 1.0

Calcium binding site 2 out of 3 in 1yno

Go back to Calcium Binding Sites List in 1yno
Calcium binding site 2 out of 3 in the High Resolution Structure of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of High Resolution Structure of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca533

b:20.1
occ:1.00
 OD1 A:ASP364 2.4 20.2 1.0
O A:HOH1090 2.4 14.0 1.0
O A:HOH683 2.5 26.4 1.0
O A:HOH886 2.6 33.1 1.0
O A:HOH1059 2.8 40.1 1.0
CG A:ASP364 3.4 17.7 1.0
OD2 A:ASP364 3.8 20.6 1.0
O A:ASP360 4.5 11.8 1.0
O A:HOH1051 4.6 46.0 1.0
O A:HOH973 4.6 38.6 1.0
O A:HOH889 4.6 37.4 1.0
ND2 A:ASN363 4.7 16.3 1.0
O A:HOH579 4.7 13.4 1.0
CB A:ASP364 4.8 18.1 1.0

Calcium binding site 3 out of 3 in 1yno

Go back to Calcium Binding Sites List in 1yno
Calcium binding site 3 out of 3 in the High Resolution Structure of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of High Resolution Structure of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca534

b:15.2
occ:0.95
 O A:ALA416 2.3 11.5 1.0
O A:HOH623 2.4 16.8 1.0
O A:HOH841 2.5 18.1 1.0
O A:HOH816 2.5 19.8 1.0
O A:HOH861 2.5 22.9 1.0
C A:ALA416 3.4 10.7 1.0
CA A:ALA416 4.0 10.3 1.0
O A:HOH759 4.1 25.1 1.0
CD A:PRO418 4.4 12.6 1.0
N A:GLU417 4.5 10.0 1.0
O A:HOH677 4.6 17.9 1.0
CB A:ALA416 4.7 10.3 1.0
OG A:SER61 4.7 9.4 0.6
O A:LEU415 4.8 11.1 1.0
O A:HOH760 4.8 35.0 1.0
CA A:GLU417 4.9 10.7 1.0
O A:HOH909 4.9 22.8 1.0

Reference:

A.K.Bera, N.L.Anderson, M.S.Hasson. High Resolution Structure of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate; To Be Published.
Page generated: Fri Jul 12 08:07:56 2024

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