Atomistry » Magnesium » PDB 4k6e-4kft » 4k9n
Atomistry »
  Magnesium »
    PDB 4k6e-4kft »
      4k9n »

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

Go back to Magnesium Binding Sites List in 4k9n
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

Go back to Magnesium Binding Sites List in 4k9n
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

Go back to Magnesium Binding Sites List in 4k9n
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

Go back to Magnesium Binding Sites List in 4k9n
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

Go back to Magnesium Binding Sites List in 4k9n
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

Go back to Magnesium Binding Sites List in 4k9n
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: Sat Aug 17 03:30:15 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy