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Calcium in PDB 4k9p: Crystal Structure of the HIS281TYR/ALA460ILE Double Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida

Enzymatic activity of Crystal Structure of the HIS281TYR/ALA460ILE Double Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida

All present enzymatic activity of Crystal Structure of the HIS281TYR/ALA460ILE Double Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida:
4.1.1.7;

Protein crystallography data

The structure of Crystal Structure of the HIS281TYR/ALA460ILE Double Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida, PDB code: 4k9p 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) 41.14 / 2.24
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.769, 164.546, 175.881, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.1

Other elements in 4k9p:

The structure of Crystal Structure of the HIS281TYR/ALA460ILE Double 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 HIS281TYR/ALA460ILE Double Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida (pdb code 4k9p). 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 HIS281TYR/ALA460ILE Double Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida, PDB code: 4k9p:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4k9p

Go back to Calcium Binding Sites List in 4k9p
Calcium binding site 1 out of 4 in the Crystal Structure of the HIS281TYR/ALA460ILE Double 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 HIS281TYR/ALA460ILE Double Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:25.6
occ:1.00
 O2A A:TPP602 2.0 22.9 0.7
O1B A:TPP602 2.1 20.7 0.7
OD1 A:ASN455 2.4 22.2 1.0
O A:THR457 2.4 24.4 1.0
O A:HOH703 2.5 23.0 1.0
OD1 A:ASP428 2.6 28.8 1.0
CG A:ASN455 3.1 29.8 1.0
ND2 A:ASN455 3.2 28.1 1.0
PA A:TPP602 3.3 18.5 0.8
PB A:TPP602 3.4 30.4 1.0
C A:THR457 3.6 26.2 1.0
O3A A:TPP602 3.6 23.8 0.8
CG A:ASP428 3.6 28.3 1.0
O7 A:TPP602 4.0 35.5 1.0
N A:GLY459 4.0 26.6 1.0
OD2 A:ASP428 4.0 38.7 1.0
N A:THR457 4.1 25.1 1.0
O2B A:TPP602 4.2 28.5 1.0
O A:MET453 4.2 27.2 1.0
N A:ASP428 4.2 24.0 1.0
CA A:THR457 4.4 28.6 1.0
N A:ASN455 4.5 27.9 1.0
N A:GLY429 4.5 24.9 1.0
CB A:ASN455 4.5 24.1 1.0
N A:TYR458 4.5 24.7 1.0
O3B A:TPP602 4.5 26.0 1.0
O1A A:TPP602 4.6 24.7 1.0
CG2 A:THR457 4.6 25.1 1.0
O A:HOH708 4.6 23.3 1.0
CA A:TYR458 4.6 24.9 1.0
CA A:GLY427 4.7 22.3 1.0
N A:GLY456 4.7 30.3 1.0
CA A:GLY459 4.8 26.5 1.0
CB A:ASP428 4.8 22.6 1.0
C A:GLY427 4.8 21.2 1.0
CA A:ASN455 4.9 26.3 1.0
C A:TYR458 4.9 26.6 1.0
CA A:ASP428 5.0 20.1 1.0
C A:ASN455 5.0 28.0 1.0

Calcium binding site 2 out of 4 in 4k9p

Go back to Calcium Binding Sites List in 4k9p
Calcium binding site 2 out of 4 in the Crystal Structure of the HIS281TYR/ALA460ILE Double 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 HIS281TYR/ALA460ILE Double Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:25.7
occ:1.00
 O1B B:TPP602 2.0 22.4 0.8
O2A B:TPP602 2.2 21.1 0.7
O B:THR457 2.3 25.6 1.0
OD1 B:ASN455 2.3 22.2 1.0
O B:HOH703 2.4 23.8 1.0
OD1 B:ASP428 2.4 24.5 1.0
CG B:ASN455 3.1 26.4 1.0
ND2 B:ASN455 3.4 31.7 1.0
PB B:TPP602 3.4 30.2 1.0
C B:THR457 3.5 24.1 1.0
CG B:ASP428 3.5 23.5 1.0
PA B:TPP602 3.5 19.9 0.8
O3A B:TPP602 3.8 20.0 0.8
OD2 B:ASP428 3.9 29.2 1.0
N B:THR457 4.0 23.5 1.0
N B:GLY459 4.1 25.9 1.0
N B:ASP428 4.2 17.1 1.0
O2B B:TPP602 4.2 29.8 1.0
O7 B:TPP602 4.2 30.6 1.0
O B:MET453 4.2 24.3 1.0
CA B:THR457 4.3 27.7 1.0
N B:ASN455 4.4 23.1 1.0
N B:GLY429 4.4 20.8 1.0
CB B:ASN455 4.4 29.0 1.0
N B:TYR458 4.5 24.3 1.0
O3B B:TPP602 4.5 29.4 1.0
O B:HOH733 4.6 25.6 1.0
CA B:TYR458 4.6 25.7 1.0
CB B:ASP428 4.7 21.0 1.0
O1A B:TPP602 4.7 25.4 1.0
CA B:ASN455 4.8 28.0 1.0
CA B:GLY427 4.8 21.5 1.0
CG2 B:THR457 4.8 32.4 1.0
N B:GLY456 4.8 26.8 1.0
CA B:ASP428 4.8 23.1 1.0
C B:GLY427 4.8 23.4 1.0
C B:ASN455 4.9 25.5 1.0
CA B:GLY459 4.9 26.9 1.0
C B:TYR458 4.9 27.4 1.0

Calcium binding site 3 out of 4 in 4k9p

Go back to Calcium Binding Sites List in 4k9p
Calcium binding site 3 out of 4 in the Crystal Structure of the HIS281TYR/ALA460ILE Double 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 HIS281TYR/ALA460ILE Double Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:31.6
occ:1.00
 O1B C:TPP602 2.0 23.2 0.5
OD1 C:ASN455 2.1 29.3 1.0
O2A C:TPP602 2.2 20.5 0.6
O C:THR457 2.3 30.3 1.0
OD1 C:ASP428 2.3 29.5 0.8
O C:HOH872 2.3 27.3 1.0
CG C:ASN455 3.1 30.4 1.0
CG C:ASP428 3.2 28.1 1.0
ND2 C:ASN455 3.4 31.2 1.0
PB C:TPP602 3.4 30.7 1.0
C C:THR457 3.5 28.8 1.0
PA C:TPP602 3.5 30.8 1.0
OD2 C:ASP428 3.5 36.3 1.0
O3A C:TPP602 3.7 32.8 1.0
N C:THR457 3.9 28.2 1.0
N C:ASP428 4.1 25.8 1.0
N C:GLY459 4.2 33.5 1.0
O2B C:TPP602 4.2 37.0 1.0
O7 C:TPP602 4.2 33.5 1.0
N C:GLY429 4.3 23.4 1.0
CA C:THR457 4.3 33.0 1.0
O C:MET453 4.4 29.1 1.0
N C:ASN455 4.4 25.0 1.0
CB C:ASN455 4.5 31.7 1.0
N C:TYR458 4.5 26.6 1.0
O3B C:TPP602 4.5 35.8 1.0
CB C:ASP428 4.6 23.9 1.0
CA C:TYR458 4.6 28.9 1.0
CG2 C:THR457 4.6 34.2 1.0
N C:GLY456 4.7 30.0 1.0
O1A C:TPP602 4.7 32.4 1.0
CA C:GLY427 4.7 25.1 1.0
O C:HOH709 4.7 25.5 1.0
CA C:ASP428 4.8 24.8 1.0
C C:GLY427 4.8 29.5 1.0
CA C:ASN455 4.8 29.4 1.0
C C:ASN455 4.8 31.6 1.0
C C:TYR458 4.9 29.5 1.0

Calcium binding site 4 out of 4 in 4k9p

Go back to Calcium Binding Sites List in 4k9p
Calcium binding site 4 out of 4 in the Crystal Structure of the HIS281TYR/ALA460ILE Double 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 HIS281TYR/ALA460ILE Double Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:30.8
occ:1.00
 O2A D:TPP602 1.9 24.3 0.8
O1B D:TPP602 2.0 24.7 0.8
O D:THR457 2.2 29.8 1.0
OD1 D:ASP428 2.4 29.7 1.0
OD1 D:ASN455 2.4 25.4 1.0
O D:HOH706 2.5 26.6 1.0
PA D:TPP602 3.3 29.6 1.0
PB D:TPP602 3.4 27.5 1.0
CG D:ASN455 3.4 28.4 1.0
CG D:ASP428 3.4 31.4 1.0
C D:THR457 3.5 27.4 1.0
ND2 D:ASN455 3.8 30.5 1.0
O3A D:TPP602 3.8 27.3 0.8
OD2 D:ASP428 3.8 41.1 1.0
N D:THR457 4.0 26.2 1.0
N D:GLY459 4.1 29.8 1.0
O2B D:TPP602 4.1 28.3 1.0
O7 D:TPP602 4.2 35.9 1.0
N D:ASP428 4.2 19.5 1.0
O D:MET453 4.3 28.0 1.0
CA D:THR457 4.4 27.8 1.0
N D:GLY429 4.4 26.9 1.0
N D:TYR458 4.4 32.5 1.0
N D:ASN455 4.5 25.0 1.0
O1A D:TPP602 4.5 29.0 1.0
O3B D:TPP602 4.5 30.6 1.0
CA D:TYR458 4.5 25.9 1.0
O D:HOH721 4.7 25.9 1.0
CB D:ASP428 4.7 22.2 1.0
CB D:ASN455 4.7 26.8 1.0
N D:GLY456 4.8 25.1 1.0
C D:TYR458 4.8 30.4 1.0
CG2 D:THR457 4.8 30.2 1.0
CA D:GLY427 4.8 27.3 1.0
CA D:ASP428 4.9 23.1 1.0
C D:GLY427 4.9 20.4 1.0
CA D:GLY459 4.9 23.9 1.0
CA D:ASN455 4.9 26.8 1.0
C D:ASN455 5.0 26.8 1.0

Reference:

H.R.Brodkin, F.H.Andrews, A.C.Milne, G.A.Petsko, D.Ringe, M.J.Mcleish. Crystal Structure of the HIS281TYR/ALA460ILE Double Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida To Be Published.
Page generated: Sat Dec 12 04:54:44 2020

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