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Calcium in PDB 4k9o: Crystal Structure of the PHE397ALA Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida

Enzymatic activity of Crystal Structure of the PHE397ALA Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida

All present enzymatic activity of Crystal Structure of the PHE397ALA Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida:
4.1.1.7;

Protein crystallography data

The structure of Crystal Structure of the PHE397ALA Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida, PDB code: 4k9o was solved by H.R.Brodkin, M.J.Mcleish, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.49 / 1.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.183, 161.218, 175.204, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 19.2

Other elements in 4k9o:

The structure of Crystal Structure of the PHE397ALA Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the PHE397ALA Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida (pdb code 4k9o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the PHE397ALA Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida, PDB code: 4k9o:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4k9o

Go back to Calcium Binding Sites List in 4k9o
Calcium binding site 1 out of 4 in the Crystal Structure of the PHE397ALA Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida


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 the PHE397ALA Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:26.6
occ:0.85
 O A:THR457 2.1 30.4 1.0
O1B A:TPP602 2.1 33.5 0.8
O2A A:TPP602 2.1 31.1 1.0
OD1 A:ASP428 2.2 34.5 1.0
OD1 A:ASN455 2.2 32.2 1.0
O A:HOH735 2.4 29.6 1.0
CG A:ASN455 3.1 32.9 1.0
C A:THR457 3.3 30.6 1.0
PA A:TPP602 3.4 32.1 1.0
CG A:ASP428 3.4 29.4 1.0
ND2 A:ASN455 3.4 33.2 1.0
PB A:TPP602 3.4 30.8 1.0
O3A A:TPP602 3.6 28.2 0.8
OD2 A:ASP428 3.9 36.5 1.0
N A:THR457 4.0 32.1 1.0
N A:GLY459 4.1 33.2 1.0
O7 A:TPP602 4.1 32.6 0.8
N A:ASP428 4.2 26.0 1.0
CA A:THR457 4.2 31.1 1.0
N A:TYR458 4.3 30.7 1.0
N A:GLY429 4.3 25.8 1.0
O A:MET453 4.3 29.0 1.0
O2B A:TPP602 4.4 26.6 0.8
O3B A:TPP602 4.4 31.9 1.0
CA A:TYR458 4.4 30.0 1.0
N A:ASN455 4.5 28.8 1.0
CB A:ASN455 4.5 27.4 1.0
O A:HOH745 4.6 30.9 1.0
CG2 A:THR457 4.6 37.3 1.0
CB A:ASP428 4.6 27.6 1.0
O1A A:TPP602 4.6 31.2 1.0
N A:GLY456 4.7 34.8 1.0
CA A:GLY427 4.8 30.4 1.0
C A:TYR458 4.8 34.8 1.0
CA A:ASP428 4.8 26.2 1.0
CA A:ASN455 4.9 29.7 1.0
C A:GLY427 4.9 26.0 1.0
C A:ASN455 4.9 33.4 1.0
CA A:GLY459 4.9 35.9 1.0

Calcium binding site 2 out of 4 in 4k9o

Go back to Calcium Binding Sites List in 4k9o
Calcium binding site 2 out of 4 in the Crystal Structure of the PHE397ALA Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida


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 the PHE397ALA Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:30.6
occ:0.85
 O2A B:TPP603 2.0 34.8 0.8
O1B B:TPP603 2.1 32.0 0.8
O B:HOH765 2.1 33.4 1.0
OD1 B:ASP428 2.3 40.4 1.0
O B:THR457 2.3 41.1 1.0
OD1 B:ASN455 2.3 38.5 1.0
CG B:ASN455 3.1 41.5 1.0
ND2 B:ASN455 3.2 45.2 1.0
PA B:TPP603 3.4 34.2 1.0
CG B:ASP428 3.4 40.6 1.0
PB B:TPP603 3.5 36.2 1.0
C B:THR457 3.5 40.2 1.0
O3A B:TPP603 3.7 33.5 1.0
OD2 B:ASP428 3.9 43.2 1.0
N B:GLY459 4.0 39.4 1.0
N B:ASP428 4.1 28.6 1.0
N B:THR457 4.1 41.0 1.0
O7 B:TPP603 4.1 36.8 1.0
O B:MET453 4.1 34.4 1.0
O B:HOH881 4.3 36.8 1.0
N B:GLY429 4.3 29.3 1.0
CA B:THR457 4.4 40.0 1.0
O2B B:TPP603 4.4 33.8 0.8
N B:ASN455 4.4 33.2 1.0
CB B:ASN455 4.4 36.0 1.0
O3B B:TPP603 4.5 36.3 1.0
N B:TYR458 4.5 36.9 1.0
O1A B:TPP603 4.6 33.0 0.8
CA B:TYR458 4.6 38.6 1.0
CA B:GLY427 4.6 32.1 1.0
CB B:ASP428 4.6 33.0 1.0
C B:GLY427 4.7 33.7 1.0
N B:GLY456 4.8 40.0 1.0
CA B:ASP428 4.8 34.8 1.0
C B:TYR458 4.8 39.2 1.0
CA B:ASN455 4.8 39.0 1.0
CA B:GLY459 4.9 41.5 1.0
CG2 B:THR457 4.9 46.1 1.0
C B:ASN455 5.0 39.5 1.0

Calcium binding site 3 out of 4 in 4k9o

Go back to Calcium Binding Sites List in 4k9o
Calcium binding site 3 out of 4 in the Crystal Structure of the PHE397ALA Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida


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 the PHE397ALA Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:27.3
occ:0.80
 O2A C:TPP602 2.0 34.5 0.8
O1B C:TPP602 2.1 29.9 0.8
OD1 C:ASP428 2.1 34.8 1.0
O C:THR457 2.2 36.0 1.0
O C:HOH766 2.2 31.7 1.0
OD1 C:ASN455 2.4 35.3 1.0
CG C:ASP428 3.3 35.0 1.0
CG C:ASN455 3.3 36.7 1.0
C C:THR457 3.4 40.5 1.0
PA C:TPP602 3.4 32.7 0.8
PB C:TPP602 3.5 31.4 0.8
ND2 C:ASN455 3.6 38.2 1.0
O3A C:TPP602 3.8 28.3 0.8
OD2 C:ASP428 3.8 39.5 1.0
N C:ASP428 4.0 28.9 1.0
N C:THR457 4.0 39.7 1.0
N C:GLY459 4.1 31.2 0.7
N C:GLY429 4.2 25.8 1.0
O7 C:TPP602 4.2 39.5 0.8
CA C:THR457 4.3 39.1 1.0
O2B C:TPP602 4.3 30.2 0.8
O C:MET453 4.3 31.2 1.0
N C:TYR458 4.3 38.7 1.0
O C:HOH782 4.4 31.2 1.0
N C:ASN455 4.5 34.1 1.0
CA C:TYR458 4.5 40.0 1.0
CB C:ASP428 4.5 28.0 1.0
O3B C:TPP602 4.5 29.0 0.8
O1A C:TPP602 4.5 29.2 0.8
CB C:ASN455 4.6 34.1 1.0
CG2 C:THR457 4.6 37.3 1.0
CA C:GLY427 4.7 26.4 1.0
CA C:ASP428 4.7 26.6 1.0
C C:GLY427 4.8 27.6 1.0
N C:GLY456 4.8 37.3 1.0
CA C:ASN455 4.9 31.3 1.0
C C:TYR458 4.9 36.4 1.0
C C:ASN455 4.9 37.6 1.0
C C:ASP428 4.9 28.4 1.0
CA C:GLY459 4.9 34.9 1.0

Calcium binding site 4 out of 4 in 4k9o

Go back to Calcium Binding Sites List in 4k9o
Calcium binding site 4 out of 4 in the Crystal Structure of the PHE397ALA Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the PHE397ALA Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:41.6
occ:1.00
 OD1 D:ASN455 2.1 42.8 1.0
O D:THR457 2.2 40.3 1.0
O1B D:TPP602 2.2 37.1 0.8
O2A D:TPP602 2.3 35.5 0.8
OD1 D:ASP428 2.4 39.6 1.0
O D:HOH716 2.4 32.8 1.0
CG D:ASN455 2.9 45.2 1.0
ND2 D:ASN455 3.2 50.5 1.0
C D:THR457 3.4 43.7 1.0
CG D:ASP428 3.4 37.9 1.0
PA D:TPP602 3.5 41.5 1.0
PB D:TPP602 3.5 39.4 1.0
O3A D:TPP602 3.6 37.6 1.0
OD2 D:ASP428 3.9 43.4 1.0
N D:THR457 3.9 46.8 1.0
N D:GLY459 4.2 40.2 1.0
N D:ASP428 4.2 32.6 1.0
O7 D:TPP602 4.2 45.0 1.0
CA D:THR457 4.2 40.1 1.0
N D:GLY429 4.3 37.2 1.0
O D:MET453 4.3 35.3 1.0
CB D:ASN455 4.3 46.3 1.0
O D:HOH981 4.3 42.5 1.0
N D:ASN455 4.3 34.6 1.0
N D:TYR458 4.4 42.0 1.0
O2B D:TPP602 4.4 46.2 1.0
O3B D:TPP602 4.5 38.4 1.0
CA D:TYR458 4.6 40.3 1.0
N D:GLY456 4.6 39.3 1.0
CG2 D:THR457 4.7 41.0 1.0
CA D:ASN455 4.7 42.9 1.0
CB D:ASP428 4.7 31.1 1.0
C D:ASN455 4.7 43.6 1.0
CA D:GLY427 4.7 33.1 1.0
O1A D:TPP602 4.8 36.8 1.0
C D:GLY427 4.8 36.0 1.0
CA D:ASP428 4.9 36.5 1.0
C D:TYR458 4.9 40.1 1.0

Reference:

H.R.Brodkin, F.H.Andrews, A.C.Milne, G.A.Petsko, D.Ringe, M.J.Mcleish. Crystal Structure of the PHE397ALA Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida To Be Published.
Page generated: Sun Jul 14 09:00:52 2024

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