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Magnesium in PDB 4k9n: Crystal Structure of the ALA460ILE Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida

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

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

Protein crystallography data

The structure of Crystal Structure of the ALA460ILE Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida, PDB code: 4k9n 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) 38.72 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.637, 163.499, 175.502, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the ALA460ILE Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida (pdb code 4k9n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the ALA460ILE Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida, PDB code: 4k9n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4k9n

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Magnesium binding site 1 out of 6 in the Crystal Structure of the ALA460ILE Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the ALA460ILE Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:19.5
occ:1.00
 O13 A:TZD603 2.1 30.0 0.8
O21 A:TZD603 2.2 26.0 0.6
O A:THR457 2.3 25.8 1.0
OD1 A:ASP428 2.3 27.4 1.0
OD1 A:ASN455 2.3 29.4 1.0
O A:HOH733 2.3 27.1 1.0
CG A:ASN455 3.2 31.4 1.0
CG A:ASP428 3.4 25.3 1.0
P1 A:TZD603 3.5 24.7 0.8
C A:THR457 3.5 28.6 1.0
P2 A:TZD603 3.5 20.2 0.6
ND2 A:ASN455 3.6 33.2 1.0
O11 A:TZD603 3.8 20.7 0.7
OD2 A:ASP428 3.9 27.4 1.0
N A:THR457 4.0 28.5 1.0
N A:GLY459 4.1 34.6 1.0
N A:ASP428 4.1 21.5 1.0
O5G A:TZD603 4.2 21.7 0.8
O22 A:TZD603 4.3 28.6 0.8
N A:GLY429 4.3 19.9 1.0
O A:MET453 4.3 22.9 1.0
CA A:THR457 4.3 24.6 1.0
O A:HOH811 4.4 26.3 1.0
N A:TYR458 4.5 26.6 1.0
N A:ASN455 4.5 21.2 1.0
CG2 A:THR457 4.5 27.3 1.0
CB A:ASN455 4.5 28.8 1.0
CA A:TYR458 4.6 25.7 1.0
CB A:ASP428 4.7 22.1 1.0
O12 A:TZD603 4.7 25.1 0.8
O23 A:TZD603 4.7 27.7 0.8
N A:GLY456 4.7 27.0 1.0
CA A:GLY427 4.8 21.2 1.0
CA A:ASP428 4.8 23.3 1.0
CA A:ASN455 4.8 28.9 1.0
C A:ASN455 4.8 33.1 1.0
C A:GLY427 4.8 23.1 1.0
CA A:GLY459 4.9 28.7 1.0
C A:TYR458 4.9 28.9 1.0

Magnesium binding site 2 out of 6 in 4k9n

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Magnesium binding site 2 out of 6 in the Crystal Structure of the ALA460ILE Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the ALA460ILE Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:14.5
occ:1.00
 O A:LEU118 2.5 19.4 1.0
O A:ARG120 2.5 18.3 1.0
O C:ARG120 2.6 18.6 1.0
O C:LEU118 2.6 18.4 1.0
O A:ASN117 2.6 17.7 1.0
O C:ASN117 2.7 17.9 1.0
O C:HOH749 3.0 23.6 1.0
C A:LEU118 3.3 16.3 1.0
C C:LEU118 3.3 16.7 1.0
C A:ARG120 3.7 17.2 1.0
C C:ARG120 3.7 20.2 1.0
C A:ASN117 3.8 17.1 1.0
CA A:LEU118 3.8 15.8 1.0
C C:ASN117 3.8 15.8 1.0
N A:ARG120 3.8 15.5 1.0
CA C:LEU118 3.8 14.3 1.0
N C:ARG120 3.9 16.0 1.0
CA A:ARG120 4.2 16.1 1.0
N A:LEU118 4.3 18.0 1.0
CA C:ARG120 4.3 15.5 1.0
CE C:MET79 4.3 18.4 0.5
N A:PRO119 4.3 16.7 1.0
N C:PRO119 4.3 15.4 1.0
N C:LEU118 4.3 16.3 1.0
C C:PRO119 4.3 17.8 1.0
C A:PRO119 4.3 18.2 1.0
CE A:MET79 4.4 15.9 0.5
CB A:ARG120 4.5 15.4 1.0
CB C:ARG120 4.5 17.2 1.0
CA C:PRO119 4.6 17.7 1.0
CA A:PRO119 4.6 18.4 1.0
N A:PRO121 4.8 15.8 1.0
N C:PRO121 4.8 17.8 1.0

Magnesium binding site 3 out of 6 in 4k9n

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Magnesium binding site 3 out of 6 in the Crystal Structure of the ALA460ILE Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the ALA460ILE Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:23.7
occ:1.00
 O21 B:TZD603 2.2 28.8 0.7
O12 B:TZD603 2.2 31.2 0.8
O B:THR457 2.3 33.6 1.0
OD1 B:ASN455 2.3 28.9 1.0
OD1 B:ASP428 2.3 31.7 1.0
O B:HOH762 2.4 28.9 1.0
CG B:ASN455 3.1 33.3 1.0
ND2 B:ASN455 3.3 34.3 1.0
CG B:ASP428 3.5 32.0 1.0
C B:THR457 3.5 31.7 1.0
P2 B:TZD603 3.5 26.5 0.7
P1 B:TZD603 3.5 26.4 0.8
O11 B:TZD603 3.8 26.2 0.8
OD2 B:ASP428 4.0 34.3 1.0
N B:THR457 4.0 32.5 1.0
N B:GLY459 4.1 34.0 1.0
N B:ASP428 4.1 24.6 1.0
O B:MET453 4.2 27.6 1.0
O22 B:TZD603 4.3 27.4 0.8
O5G B:TZD603 4.3 28.4 0.8
CA B:THR457 4.3 29.4 1.0
N B:GLY429 4.4 29.0 1.0
N B:ASN455 4.4 27.8 1.0
CB B:ASN455 4.4 28.4 1.0
O B:HOH893 4.5 31.2 1.0
N B:TYR458 4.5 31.1 1.0
CA B:TYR458 4.6 30.5 1.0
O23 B:TZD603 4.7 31.2 0.8
CB B:ASP428 4.7 28.1 1.0
N B:GLY456 4.7 30.8 1.0
CG2 B:THR457 4.7 33.7 1.0
O13 B:TZD603 4.7 26.4 0.8
CA B:GLY427 4.8 25.7 1.0
CA B:ASN455 4.8 28.9 1.0
CA B:ASP428 4.8 25.1 1.0
C B:GLY427 4.8 26.8 1.0
CA B:GLY459 4.8 33.2 1.0
C B:TYR458 4.9 32.0 1.0
C B:ASN455 4.9 36.1 1.0

Magnesium binding site 4 out of 6 in 4k9n

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Magnesium binding site 4 out of 6 in the Crystal Structure of the ALA460ILE Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the ALA460ILE Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:15.4
occ:1.00
 O B:ARG120 2.5 19.6 1.0
O D:ARG120 2.5 21.2 1.0
O D:LEU118 2.6 19.1 1.0
O B:LEU118 2.6 20.0 1.0
O B:ASN117 2.7 19.2 1.0
O D:ASN117 2.7 19.1 1.0
O D:HOH712 3.1 23.2 1.0
C B:LEU118 3.3 17.5 1.0
C D:LEU118 3.3 19.8 1.0
C B:ARG120 3.6 17.7 1.0
C D:ARG120 3.7 17.8 1.0
C B:ASN117 3.8 17.3 1.0
C D:ASN117 3.8 19.4 1.0
CA D:LEU118 3.8 17.3 1.0
CA B:LEU118 3.8 20.3 1.0
N B:ARG120 3.8 17.9 1.0
N D:ARG120 3.9 18.2 1.0
CA B:ARG120 4.2 20.8 1.0
CA D:ARG120 4.2 18.2 1.0
N B:PRO119 4.3 19.1 1.0
N D:LEU118 4.3 18.4 1.0
N B:LEU118 4.3 17.8 1.0
C B:PRO119 4.3 18.7 1.0
N D:PRO119 4.3 19.6 1.0
C D:PRO119 4.4 19.9 1.0
CE D:MET79 4.4 20.5 0.5
CE B:MET79 4.5 20.2 0.5
CB B:ARG120 4.5 18.1 1.0
CB D:ARG120 4.5 19.5 1.0
CA B:PRO119 4.6 17.9 1.0
CA D:PRO119 4.7 21.2 1.0
N B:PRO121 4.7 17.6 1.0
N D:PRO121 4.8 17.4 1.0
CD B:PRO121 4.9 19.8 1.0

Magnesium binding site 5 out of 6 in 4k9n

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Magnesium binding site 5 out of 6 in the Crystal Structure of the ALA460ILE Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the ALA460ILE Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:23.4
occ:1.00
 O13 C:TZD602 2.1 30.4 0.8
O21 C:TZD602 2.2 30.8 0.8
O C:THR457 2.2 31.5 1.0
OD1 C:ASP428 2.2 29.7 1.0
OD1 C:ASN455 2.3 34.1 1.0
O C:HOH783 2.4 33.2 1.0
CG C:ASN455 3.2 37.1 1.0
CG C:ASP428 3.4 33.2 1.0
ND2 C:ASN455 3.4 35.3 1.0
P1 C:TZD602 3.4 29.6 0.8
C C:THR457 3.4 33.6 0.9
P2 C:TZD602 3.5 28.9 0.7
O11 C:TZD602 3.8 29.8 0.8
OD2 C:ASP428 3.9 35.9 1.0
N C:GLY459 4.0 31.2 0.9
N C:THR457 4.0 31.4 0.9
N C:ASP428 4.0 25.0 1.0
O5G C:TZD602 4.2 28.6 0.8
N C:GLY429 4.3 25.1 1.0
O C:MET453 4.3 26.4 1.0
O23 C:TZD602 4.3 31.3 0.8
CA C:THR457 4.3 33.7 1.0
O C:HOH794 4.4 34.3 1.0
N C:TYR458 4.4 32.7 1.0
N C:ASN455 4.5 28.5 1.0
CB C:ASN455 4.5 30.1 1.0
CA C:TYR458 4.6 31.4 1.0
CG2 C:THR457 4.6 31.1 1.0
CB C:ASP428 4.6 26.2 1.0
O12 C:TZD602 4.6 30.2 0.8
O22 C:TZD602 4.6 29.9 0.8
CA C:GLY427 4.7 25.1 1.0
CA C:ASP428 4.7 25.9 1.0
N C:GLY456 4.7 37.3 1.0
C C:GLY427 4.7 25.4 1.0
CA C:GLY459 4.8 33.8 1.0
C C:TYR458 4.8 36.3 1.0
CA C:ASN455 4.9 28.1 1.0
C C:ASN455 4.9 35.5 1.0
C C:ASP428 5.0 27.6 1.0

Magnesium binding site 6 out of 6 in 4k9n

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Magnesium binding site 6 out of 6 in the Crystal Structure of the ALA460ILE Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the ALA460ILE Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:28.6
occ:1.00
 O22 D:TZD602 2.1 35.0 0.6
O D:THR457 2.2 35.7 1.0
OD1 D:ASN455 2.2 42.3 1.0
O12 D:TZD602 2.3 35.0 0.7
OD1 D:ASP428 2.3 36.4 1.0
O D:HOH877 2.4 37.1 1.0
CG D:ASN455 3.0 40.7 1.0
ND2 D:ASN455 3.1 42.6 1.0
C D:THR457 3.4 40.3 1.0
CG D:ASP428 3.4 34.2 1.0
P2 D:TZD602 3.5 31.9 0.6
P1 D:TZD602 3.5 32.1 0.7
O11 D:TZD602 3.8 28.5 0.7
N D:THR457 3.9 41.4 1.0
OD2 D:ASP428 3.9 36.0 1.0
N D:GLY459 4.0 39.9 1.0
N D:ASP428 4.1 29.2 1.0
CA D:THR457 4.2 38.3 1.0
N D:GLY429 4.2 31.3 1.0
O5G D:TZD602 4.3 33.8 0.8
O21 D:TZD602 4.3 34.0 0.9
CB D:ASN455 4.4 40.9 1.0
N D:TYR458 4.4 31.0 0.6
O D:MET453 4.4 35.9 1.0
O D:HOH844 4.4 36.4 1.0
N D:ASN455 4.5 35.3 1.0
O23 D:TZD602 4.5 33.5 0.7
CA D:TYR458 4.5 36.7 0.7
CG2 D:THR457 4.6 43.1 1.0
N D:GLY456 4.6 39.2 1.0
CB D:ASP428 4.6 32.3 1.0
O13 D:TZD602 4.8 33.3 0.8
CA D:ASP428 4.8 31.6 1.0
CA D:ASN455 4.8 36.8 1.0
C D:TYR458 4.8 34.1 0.7
CA D:GLY427 4.8 30.0 1.0
C D:ASN455 4.9 42.1 1.0
CA D:GLY459 4.9 41.4 1.0
C D:GLY427 4.9 32.9 1.0

Reference:

H.R.Brodkin, F.H.Andrews, A.C.Milne, G.A.Petsko, D.Ringe, M.J.Mcleish. Crystal Structure of the ALA460ILE Mutant of Benzoylformate Decarboxylase From Pseudomonas Putida To Be Published.
Page generated: Mon Aug 11 17:29:10 2025

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