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Magnesium in PDB 5dei: Benzoylformate Decarboxylase From Pseudomonas Putida

Enzymatic activity of Benzoylformate Decarboxylase From Pseudomonas Putida

All present enzymatic activity of Benzoylformate Decarboxylase From Pseudomonas Putida:
4.1.1.7;

Protein crystallography data

The structure of Benzoylformate Decarboxylase From Pseudomonas Putida, PDB code: 5dei 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) 27.41 / 1.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.166, 92.451, 93.715, 63.59, 72.42, 72.88
R / Rfree (%) 13.6 / 14.8

Other elements in 5dei:

The structure of Benzoylformate Decarboxylase From Pseudomonas Putida also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Benzoylformate Decarboxylase From Pseudomonas Putida (pdb code 5dei). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Benzoylformate Decarboxylase From Pseudomonas Putida, PDB code: 5dei:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5dei

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Magnesium binding site 1 out of 8 in the 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 Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:10.8
occ:1.00
O C:ARG121 2.5 13.2 1.0
O A:ARG121 2.5 12.8 1.0
O C:LEU119 2.6 11.2 1.0
O A:LEU119 2.6 11.8 1.0
O C:ASN118 2.7 12.1 1.0
O A:ASN118 2.8 12.6 1.0
O C:HOH1050 3.2 19.3 1.0
C C:LEU119 3.3 11.5 1.0
C A:LEU119 3.4 11.8 1.0
HA A:LEU119 3.4 14.0 1.0
HA C:LEU119 3.4 13.8 1.0
HE1 C:MET80 3.6 13.0 0.4
HE1 A:MET80 3.6 17.4 0.5
H C:ARG121 3.6 13.8 1.0
H A:ARG121 3.6 14.1 1.0
C C:ARG121 3.7 12.8 1.0
C A:ARG121 3.7 12.7 1.0
HB2 A:ARG121 3.8 15.2 1.0
HB2 C:ARG121 3.8 15.8 1.0
N C:ARG121 3.8 11.5 1.0
C C:ASN118 3.8 11.5 1.0
N A:ARG121 3.8 11.8 1.0
CA C:LEU119 3.8 11.5 1.0
CA A:LEU119 3.8 11.7 1.0
C A:ASN118 3.8 11.7 1.0
HD12 C:LEU119 4.2 16.2 1.0
CA C:ARG121 4.2 12.0 1.0
CA A:ARG121 4.2 11.9 1.0
HD12 A:LEU119 4.2 15.9 1.0
N C:PRO120 4.3 12.1 1.0
N A:PRO120 4.3 11.7 1.0
C C:PRO120 4.3 11.7 1.0
HE2 C:MET80 4.3 25.1 0.6
C A:PRO120 4.3 12.4 1.0
N C:LEU119 4.3 11.6 1.0
N A:LEU119 4.3 11.1 1.0
HE2 A:MET80 4.3 24.9 0.5
CE C:MET80 4.5 10.8 0.4
CB A:ARG121 4.5 12.7 1.0
CB C:ARG121 4.5 13.2 1.0
CE A:MET80 4.5 14.5 0.5
HE3 C:MET80 4.6 13.0 0.4
HD3 C:PRO122 4.6 15.8 1.0
HD3 A:PRO122 4.6 17.1 1.0
HA A:PRO120 4.6 12.8 1.0
HB3 A:ASN118 4.6 16.1 1.0
CA A:PRO120 4.6 10.7 1.0
HB3 C:ASN118 4.6 15.1 1.0
HE3 A:MET80 4.6 17.4 0.5
CA C:PRO120 4.7 11.0 1.0
HA C:PRO120 4.7 13.2 1.0
HE1 A:MET80 4.7 24.9 0.5
HE1 C:MET80 4.7 25.1 0.6
N C:PRO122 4.8 12.4 1.0
N A:PRO122 4.8 11.8 1.0
CE C:MET80 5.0 20.9 0.6

Magnesium binding site 2 out of 8 in 5dei

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Magnesium binding site 2 out of 8 in the 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 Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:16.7
occ:1.00
H A:LYS497 2.5 18.5 1.0
HG2 A:LYS497 2.9 32.3 1.0
HA A:LEU496 3.0 17.8 1.0
O A:HOH1241 3.1 40.7 1.0
O A:HOH1002 3.1 37.6 1.0
O A:HOH931 3.1 22.6 1.0
N A:LYS497 3.3 15.4 1.0
HB3 A:LEU496 3.5 18.4 1.0
HD22 A:LEU496 3.5 20.1 1.0
CA A:LEU496 3.8 14.8 1.0
CG A:LYS497 3.8 26.9 1.0
C A:LEU496 4.0 15.0 1.0
CB A:LEU496 4.1 15.3 1.0
HD23 A:LEU496 4.1 20.1 1.0
O A:LYS497 4.1 17.6 1.0
HG3 A:LYS497 4.1 32.3 1.0
HE2 A:LYS497 4.1 41.8 1.0
HG A:SER507 4.2 17.7 0.5
CD2 A:LEU496 4.2 16.8 1.0
HH11 A:ARG485 4.3 22.7 1.0
CA A:LYS497 4.3 17.8 1.0
HB3 A:LYS497 4.4 29.6 1.0
CB A:LYS497 4.4 24.7 1.0
OG A:SER507 4.4 14.8 0.5
C A:LYS497 4.6 17.0 1.0
CG A:LEU496 4.7 15.2 1.0
HH12 A:ARG485 4.8 22.7 1.0
NH1 A:ARG485 4.8 18.9 1.0
O A:ALA495 4.8 18.3 1.0
CD A:LYS497 4.9 28.3 1.0
HB2 A:LEU496 4.9 18.4 1.0
CE A:LYS497 4.9 34.8 1.0
HD13 A:LEU496 5.0 20.1 1.0
HD21 A:LEU496 5.0 20.1 1.0

Magnesium binding site 3 out of 8 in 5dei

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Magnesium binding site 3 out of 8 in the 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 Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:18.7
occ:1.00
H D:ASP188 2.4 20.3 1.0
HE A:ARG185 2.4 30.4 1.0
HH21 A:ARG185 3.0 36.9 1.0
O A:HOH871 3.0 24.7 1.0
HB2 D:ASN187 3.2 20.6 1.0
HA D:ASN187 3.2 18.1 1.0
N D:ASP188 3.2 16.9 1.0
NE A:ARG185 3.2 25.3 1.0
HG2 A:ARG185 3.3 23.6 1.0
HB2 D:ASP188 3.4 22.4 1.0
O D:HOH1059 3.4 28.6 1.0
CG D:ASP188 3.7 28.9 1.0
NH2 A:ARG185 3.7 30.7 1.0
CA D:ASN187 3.8 15.1 1.0
OD2 D:ASP188 3.8 26.9 1.0
CB D:ASP188 3.9 18.6 1.0
CB D:ASN187 3.9 17.2 1.0
CZ A:ARG185 4.0 25.6 1.0
HB2 A:ALA325 4.0 22.9 1.0
C D:ASN187 4.0 16.6 1.0
CG A:ARG185 4.0 19.6 1.0
OD1 D:ASP188 4.1 29.7 1.0
HG3 A:ARG185 4.1 23.6 1.0
CA D:ASP188 4.2 16.4 1.0
CD A:ARG185 4.2 26.1 1.0
HB3 D:ASN187 4.3 20.6 1.0
HH12 D:ARG185 4.4 22.1 1.0
O A:HOH937 4.5 42.0 1.0
HH22 A:ARG185 4.5 36.9 1.0
H D:GLN189 4.7 22.2 1.0
HA D:ASP188 4.7 19.7 1.0
O D:HOH1221 4.8 38.9 1.0
HB3 D:ASP188 4.8 22.4 1.0
HB1 A:ALA321 4.8 19.4 1.0
HD3 A:ARG185 4.8 31.3 1.0
NH1 D:ARG185 4.9 18.4 1.0
HD2 A:ARG185 4.9 31.3 1.0
CB A:ALA325 4.9 19.1 1.0
HH11 D:ARG185 5.0 22.1 1.0

Magnesium binding site 4 out of 8 in 5dei

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Magnesium binding site 4 out of 8 in the 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 Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:10.3
occ:1.00
O D:ARG121 2.6 12.6 1.0
O B:ARG121 2.6 12.8 1.0
O B:LEU119 2.6 12.0 1.0
O D:LEU119 2.6 12.4 1.0
O D:ASN118 2.7 12.0 1.0
O B:ASN118 2.8 12.2 1.0
O B:HOH1065 3.2 19.8 1.0
C B:LEU119 3.3 10.6 1.0
C D:LEU119 3.3 11.0 1.0
HA D:LEU119 3.4 13.4 1.0
HA B:LEU119 3.4 13.8 1.0
HE1 B:MET80 3.5 15.4 0.5
H B:ARG121 3.6 14.2 1.0
H D:ARG121 3.6 14.7 1.0
HE1 D:MET80 3.6 12.3 0.4
C D:ARG121 3.7 12.0 1.0
C B:ARG121 3.7 12.4 1.0
HB2 D:ARG121 3.8 16.5 1.0
HB2 B:ARG121 3.8 16.1 1.0
N B:ARG121 3.8 11.8 1.0
C D:ASN118 3.8 11.1 1.0
N D:ARG121 3.8 12.2 1.0
CA D:LEU119 3.8 11.2 1.0
CA B:LEU119 3.8 11.5 1.0
C B:ASN118 3.8 11.9 1.0
CA D:ARG121 4.2 12.2 1.0
CA B:ARG121 4.2 12.8 1.0
HD12 D:LEU119 4.2 17.3 1.0
HD12 B:LEU119 4.2 16.9 1.0
N B:PRO120 4.3 12.0 1.0
N D:PRO120 4.3 12.0 1.0
N D:LEU119 4.3 11.0 1.0
C D:PRO120 4.3 13.8 1.0
N B:LEU119 4.3 11.8 1.0
HE2 D:MET80 4.3 25.0 0.6
HE2 B:MET80 4.3 23.1 0.5
C B:PRO120 4.3 11.9 1.0
CE B:MET80 4.4 12.8 0.5
CB D:ARG121 4.5 13.8 1.0
CB B:ARG121 4.5 13.4 1.0
CE D:MET80 4.5 10.2 0.4
HE3 B:MET80 4.6 15.4 0.5
HB3 D:ASN118 4.6 17.2 1.0
HB3 B:ASN118 4.6 16.2 1.0
HD3 B:PRO122 4.6 17.6 1.0
HA B:PRO120 4.6 13.6 1.0
CA D:PRO120 4.6 11.4 1.0
HA D:PRO120 4.6 13.7 1.0
CA B:PRO120 4.7 11.3 1.0
HE1 D:MET80 4.7 25.0 0.6
HE3 D:MET80 4.7 12.3 0.4
HD3 D:PRO122 4.7 14.5 1.0
HE1 B:MET80 4.7 23.1 0.5
N B:PRO122 4.8 11.9 1.0
N D:PRO122 4.8 12.2 1.0
CE D:MET80 5.0 20.8 0.6
CE B:MET80 5.0 19.3 0.5
HD2 B:PRO122 5.0 17.6 1.0
HE2 B:MET80 5.0 15.4 0.5

Magnesium binding site 5 out of 8 in 5dei

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Magnesium binding site 5 out of 8 in the 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 Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:18.8
occ:1.00
HE B:ARG185 2.3 28.3 1.0
H C:ASP188 2.4 20.0 1.0
HH21 B:ARG185 2.9 35.9 1.0
O B:HOH956 3.1 23.6 1.0
HB2 C:ASN187 3.1 23.9 1.0
NE B:ARG185 3.1 23.6 1.0
HA C:ASN187 3.2 20.2 1.0
N C:ASP188 3.2 16.6 1.0
HB2 C:ASP188 3.3 23.4 1.0
HG2 B:ARG185 3.3 24.3 1.0
O C:HOH1112 3.4 26.4 1.0
NH2 B:ARG185 3.6 29.9 1.0
CG C:ASP188 3.7 29.1 1.0
CA C:ASN187 3.8 16.8 1.0
CZ B:ARG185 3.8 24.2 1.0
CB C:ASP188 3.8 19.5 1.0
CB C:ASN187 3.9 19.9 1.0
OD2 C:ASP188 3.9 31.3 1.0
OD1 C:ASP188 4.0 31.6 1.0
HB2 B:ALA325 4.0 24.1 1.0
C C:ASN187 4.0 16.1 1.0
CG B:ARG185 4.0 20.3 1.0
HG3 B:ARG185 4.1 24.3 1.0
CA C:ASP188 4.2 16.8 1.0
CD B:ARG185 4.2 23.2 1.0
HB3 C:ASN187 4.3 23.9 1.0
O B:HOH957 4.3 39.5 1.0
HH22 B:ARG185 4.3 35.9 1.0
HH12 C:ARG185 4.4 25.4 1.0
H C:GLN189 4.7 21.2 1.0
HA C:ASP188 4.7 20.2 1.0
HB3 C:ASP188 4.8 23.4 1.0
HD3 B:ARG185 4.8 27.9 1.0
HD2 B:ARG185 4.8 27.9 1.0
HB1 B:ALA321 4.8 20.9 1.0
NH1 C:ARG185 4.9 21.1 1.0
CB B:ALA325 4.9 20.1 1.0
O B:HOH1280 4.9 37.9 1.0
HH11 C:ARG185 5.0 25.4 1.0

Magnesium binding site 6 out of 8 in 5dei

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Magnesium binding site 6 out of 8 in the 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 Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg605

b:17.2
occ:1.00
H B:LYS497 2.5 19.9 1.0
HA B:LEU496 3.1 18.0 1.0
O B:HOH970 3.1 21.0 1.0
O B:HOH1042 3.1 37.2 1.0
O B:HOH1233 3.3 41.1 1.0
N B:LYS497 3.3 16.6 1.0
HG2 B:LYS497 3.4 34.4 1.0
HB3 B:LEU496 3.4 18.5 1.0
HD22 B:LEU496 3.6 19.8 1.0
CA B:LEU496 3.8 15.0 1.0
HB3 B:LYS497 4.0 29.0 1.0
C B:LEU496 4.0 14.0 1.0
CB B:LEU496 4.0 15.4 1.0
HD23 B:LEU496 4.1 19.8 1.0
HE2 B:LYS497 4.1 34.6 1.0
O B:LYS497 4.1 17.9 1.0
HH11 B:ARG485 4.2 25.6 1.0
CD2 B:LEU496 4.2 16.5 1.0
CG B:LYS497 4.2 28.6 1.0
CA B:LYS497 4.3 15.9 1.0
HG B:SER507 4.3 22.8 0.5
CB B:LYS497 4.4 24.1 1.0
OG B:SER507 4.5 19.0 0.5
O B:HOH1189 4.7 39.5 1.0
C B:LYS497 4.7 15.8 1.0
HH12 B:ARG485 4.7 25.6 1.0
NH1 B:ARG485 4.7 21.3 1.0
CG B:LEU496 4.8 13.4 1.0
HB2 B:LEU496 4.8 18.5 1.0
O B:ALA495 4.9 18.5 1.0
CE B:LYS497 4.9 28.9 1.0
HG3 B:LYS497 4.9 34.4 1.0
HD3 B:LYS497 4.9 33.8 1.0
CD B:LYS497 5.0 28.2 1.0
HD13 B:LEU496 5.0 19.2 1.0

Magnesium binding site 7 out of 8 in 5dei

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Magnesium binding site 7 out of 8 in the 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 7 of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg606

b:19.1
occ:1.00
HG3 B:GLN494 3.2 20.2 1.0
HB2 B:GLN494 3.3 17.3 1.0
OE1 B:GLN494 3.4 20.3 1.0
CG B:GLN494 3.8 16.9 1.0
CB B:GLN494 4.0 14.4 1.0
CD B:GLN494 4.0 15.3 1.0
HA B:GLN494 4.2 17.7 1.0
CA B:GLN494 4.6 14.7 1.0
HG2 B:GLN494 4.7 20.2 1.0
HB3 B:GLN494 4.8 17.3 1.0
O B:HOH1029 5.0 32.8 1.0

Magnesium binding site 8 out of 8 in 5dei

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Magnesium binding site 8 out of 8 in the 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 8 of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:16.4
occ:1.00
H D:LYS497 2.5 19.7 1.0
HG2 D:LYS497 3.0 30.9 1.0
HA D:LEU496 3.1 17.5 1.0
O D:HOH824 3.1 21.2 1.0
O D:HOH1042 3.2 37.8 1.0
N D:LYS497 3.3 16.4 1.0
HB3 D:LEU496 3.4 18.1 1.0
HD22 D:LEU496 3.6 22.2 1.0
CA D:LEU496 3.8 14.6 1.0
CG D:LYS497 3.9 25.8 1.0
C D:LEU496 4.1 13.6 1.0
CB D:LEU496 4.1 15.1 1.0
HD23 D:LEU496 4.1 22.2 1.0
O D:LYS497 4.1 18.9 1.0
HH11 D:ARG485 4.2 25.0 1.0
CD2 D:LEU496 4.3 18.5 1.0
HB3 D:LYS497 4.3 31.3 1.0
CA D:LYS497 4.3 17.5 1.0
HE2 D:LYS497 4.3 40.9 1.0
HG3 D:LYS497 4.3 30.9 1.0
CB D:LYS497 4.4 26.1 1.0
HG D:SER507 4.5 22.7 0.5
C D:LYS497 4.7 15.1 1.0
OG D:SER507 4.7 18.9 0.5
NH1 D:ARG485 4.7 20.9 1.0
HH12 D:ARG485 4.8 25.0 1.0
CG D:LEU496 4.8 14.3 1.0
O D:ALA495 4.8 19.1 1.0
HB2 D:LEU496 4.8 18.1 1.0
CD D:LYS497 4.9 28.4 1.0
HD3 D:LYS497 4.9 34.1 1.0
HD3 D:ARG485 4.9 19.9 1.0

Reference:

A.K.Bera, M.S.Hasson. Benzoylformate Decarboxylase From Pseudomonas Putida To Be Published.
Page generated: Mon Dec 14 20:11:10 2020

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