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Calcium in PDB 1q6z: High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamin Thiazolone Diphosphate

Enzymatic activity of High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamin Thiazolone Diphosphate

All present enzymatic activity of High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamin Thiazolone Diphosphate:
4.1.1.7;

Protein crystallography data

The structure of High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamin Thiazolone Diphosphate, PDB code: 1q6z 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 / 1.00
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 81.371, 95.600, 136.881, 90.00, 90.00, 90.00
R / Rfree (%) 12.2 / 14

Other elements in 1q6z:

The structure of High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamin 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 E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamin Thiazolone Diphosphate (pdb code 1q6z). 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 E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamin Thiazolone Diphosphate, PDB code: 1q6z:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1q6z

Go back to Calcium Binding Sites List in 1q6z
Calcium binding site 1 out of 3 in the High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamin 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 E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamin Thiazolone Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca532

b:7.6
occ:0.67
 O12 A:TZD530 2.1 7.4 1.0
OD1 A:ASN455 2.1 9.1 0.9
OD1 A:ASP428 2.1 9.8 1.0
O A:THR457 2.1 8.4 1.0
O21 A:TZD530 2.1 7.9 1.0
CG A:ASN455 3.0 9.6 1.0
P1 A:TZD530 3.3 7.1 1.0
CG A:ASP428 3.3 8.4 1.0
C A:THR457 3.3 8.0 1.0
ND2 A:ASN455 3.3 10.8 1.0
P2 A:TZD530 3.4 7.6 1.0
O11 A:TZD530 3.5 7.0 1.0
OD2 A:ASP428 3.9 11.4 1.0
N A:THR457 3.9 9.3 1.0
N A:ASP428 4.0 7.0 1.0
O5G A:TZD530 4.0 7.3 1.0
N A:GLY459 4.1 8.0 1.0
N A:GLY429 4.2 6.9 1.0
CA A:THR457 4.2 8.5 1.0
O A:MET453 4.2 9.1 1.0
O22 A:TZD530 4.2 8.0 1.0
N A:TYR458 4.3 7.8 1.0
CB A:ASN455 4.3 10.3 1.0
O A:HOH542 4.4 8.8 1.0
N A:ASN455 4.4 8.9 1.0
CB A:ASP428 4.4 8.0 1.0
O13 A:TZD530 4.5 7.3 1.0
CA A:TYR458 4.5 7.5 1.0
O23 A:TZD530 4.5 8.0 1.0
CG2 A:THR457 4.5 11.4 1.0
CA A:ASP428 4.7 7.5 1.0
CA A:GLY427 4.7 7.3 1.0
CA A:ASN455 4.7 9.9 1.0
N A:GLY456 4.7 9.0 1.0
C A:GLY427 4.8 6.9 1.0
C A:ASN455 4.8 9.9 1.0
C A:TYR458 4.9 7.6 1.0
C A:ASP428 4.9 6.9 1.0
CA A:GLY459 5.0 9.0 1.0

Calcium binding site 2 out of 3 in 1q6z

Go back to Calcium Binding Sites List in 1q6z
Calcium binding site 2 out of 3 in the High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamin 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 E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamin Thiazolone Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca533

b:12.1
occ:0.73
 OD1 A:ASP364 2.5 23.6 1.0
O A:HOH692 2.5 13.0 1.0
O A:HOH845 2.5 27.9 0.9
CG A:ASP364 3.2 20.4 1.0
OD2 A:ASP364 3.4 25.3 1.0
O A:ASP360 4.5 10.0 1.0
CB A:ASP364 4.7 15.7 1.0
O A:HOH710 4.8 16.1 0.6
O A:HOH682 4.8 11.2 0.9
ND2 A:ASN363 4.8 13.8 1.0
O A:HOH695 4.8 17.2 0.8

Calcium binding site 3 out of 3 in 1q6z

Go back to Calcium Binding Sites List in 1q6z
Calcium binding site 3 out of 3 in the High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamin 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 E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamin Thiazolone Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca534

b:8.8
occ:0.66
 O A:ALA416 2.3 9.2 1.0
O A:HOH713 2.4 13.3 0.9
O A:HOH702 2.5 12.3 0.8
O A:HOH977 2.5 20.1 0.9
O A:HOH997 2.6 18.6 0.9
C A:ALA416 3.4 8.8 1.0
CA A:ALA416 4.0 8.2 1.0
O A:HOH846 4.3 23.7 1.0
CD A:PRO418 4.5 11.1 1.0
N A:GLU417 4.5 8.3 1.0
O A:HOH703 4.6 13.9 0.7
O A:HOH727 4.6 12.1 0.7
CB A:ALA416 4.7 8.8 1.0
O A:LEU415 4.7 9.0 1.0
O A:HOH910 4.7 30.5 1.0
OG A:SER61 4.8 8.2 0.5
O A:HOH1097 4.9 18.5 0.8
CA A:GLU417 4.9 8.3 1.0

Reference:

A.K.Bera, N.L.Anderson, M.S.Hasson. High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with Thiamin Thiazolone Diphosphate To Be Published.
Page generated: Mon Jul 7 22:46:56 2025

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