Atomistry » Magnesium » PDB 2uxj-2v7y » 2v3w
Atomistry »
  Magnesium »
    PDB 2uxj-2v7y »
      2v3w »

Magnesium in PDB 2v3w: Crystal Structure of the Benzoylformate Decarboxylase Variant L461A From Pseudomonas Putida

Enzymatic activity of Crystal Structure of the Benzoylformate Decarboxylase Variant L461A From Pseudomonas Putida

All present enzymatic activity of Crystal Structure of the Benzoylformate Decarboxylase Variant L461A From Pseudomonas Putida:
4.1.1.7;

Protein crystallography data

The structure of Crystal Structure of the Benzoylformate Decarboxylase Variant L461A From Pseudomonas Putida, PDB code: 2v3w was solved by D.Gocke, L.Walter, K.Gauchenova, G.Kolter, M.Knoll, C.L.Berthold, G.Schneider, J.Pleiss, M.Mueller, M.Pohl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.704, 139.938, 169.054, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 22.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Benzoylformate Decarboxylase Variant L461A From Pseudomonas Putida (pdb code 2v3w). 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 Benzoylformate Decarboxylase Variant L461A From Pseudomonas Putida, PDB code: 2v3w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2v3w

Go back to Magnesium Binding Sites List in 2v3w
Magnesium binding site 1 out of 6 in the Crystal Structure of the Benzoylformate Decarboxylase Variant L461A 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 Benzoylformate Decarboxylase Variant L461A From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1528

b:18.6
occ:1.00
 O2A A:TPP1531 2.0 24.1 1.0
O A:HOH2226 2.1 19.0 1.0
O A:THR457 2.1 23.7 1.0
O1B A:TPP1531 2.1 23.6 1.0
OD1 A:ASN455 2.3 24.3 1.0
OD1 A:ASP428 2.4 25.0 1.0
PA A:TPP1531 3.1 21.1 1.0
CG A:ASN455 3.1 25.5 1.0
PB A:TPP1531 3.2 21.5 1.0
O3A A:TPP1531 3.3 24.4 1.0
C A:THR457 3.3 25.0 1.0
ND2 A:ASN455 3.4 26.6 1.0
CG A:ASP428 3.6 23.3 1.0
O7 A:TPP1531 3.8 24.0 1.0
N A:GLY459 4.0 24.7 1.0
N A:THR457 4.0 25.5 1.0
OD2 A:ASP428 4.1 25.6 1.0
O2B A:TPP1531 4.1 21.8 1.0
N A:ASP428 4.2 21.8 1.0
N A:GLY429 4.2 22.8 1.0
N A:TYR458 4.3 24.5 1.0
O A:MET453 4.3 24.0 1.0
CA A:THR457 4.3 24.8 1.0
O3B A:TPP1531 4.3 20.5 1.0
O1A A:TPP1531 4.3 22.6 1.0
CA A:TYR458 4.4 24.7 1.0
O A:HOH2190 4.4 20.6 1.0
CB A:ASN455 4.5 25.4 1.0
N A:ASN455 4.5 24.9 1.0
CG2 A:THR457 4.6 25.1 1.0
C A:TYR458 4.7 24.7 1.0
CA A:GLY427 4.7 21.3 1.0
CB A:ASP428 4.7 22.6 1.0
N A:GLY456 4.8 24.8 1.0
C A:GLY427 4.8 21.0 1.0
CA A:ASP428 4.8 22.1 1.0
CA A:ASN455 4.9 24.9 1.0
CA A:GLY459 4.9 24.7 1.0
C A:ASN455 4.9 24.5 1.0

Magnesium binding site 2 out of 6 in 2v3w

Go back to Magnesium Binding Sites List in 2v3w
Magnesium binding site 2 out of 6 in the Crystal Structure of the Benzoylformate Decarboxylase Variant L461A 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 Benzoylformate Decarboxylase Variant L461A From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1529

b:18.0
occ:1.00
 O C:LEU118 2.4 17.8 1.0
O A:LEU118 2.4 19.2 1.0
O C:ARG120 2.4 20.6 1.0
O A:ARG120 2.4 20.0 1.0
O A:ASN117 2.5 20.1 1.0
O C:ASN117 2.6 19.7 1.0
C C:LEU118 3.2 20.1 1.0
C A:LEU118 3.2 19.1 1.0
O C:HOH2062 3.2 23.1 1.0
CA C:LEU118 3.6 20.1 1.0
C C:ARG120 3.6 20.7 1.0
C A:ARG120 3.6 19.8 1.0
C A:ASN117 3.6 19.1 1.0
CA A:LEU118 3.7 19.0 1.0
C C:ASN117 3.7 19.4 1.0
N A:ARG120 4.0 19.8 1.0
N C:ARG120 4.0 21.0 1.0
N C:LEU118 4.1 20.2 1.0
N A:LEU118 4.1 19.0 1.0
N A:PRO119 4.2 18.9 1.0
N C:PRO119 4.2 20.3 1.0
C A:PRO119 4.3 20.0 1.0
CA A:ARG120 4.3 20.3 1.0
CA C:ARG120 4.3 20.9 1.0
C C:PRO119 4.3 20.9 1.0
CE A:MET79 4.5 19.3 0.5
CA A:PRO119 4.6 19.3 1.0
CB C:ARG120 4.6 21.2 1.0
N C:PRO121 4.6 21.1 1.0
CB A:ARG120 4.6 20.6 1.0
N A:PRO121 4.7 19.9 1.0
CA C:PRO119 4.7 20.7 1.0
CD C:PRO121 4.8 21.4 1.0
O A:PRO119 4.8 19.8 1.0
CD A:PRO121 4.9 19.3 1.0
CA A:ASN117 4.9 19.5 1.0
O C:PRO119 4.9 20.6 1.0
CD1 C:LEU118 4.9 19.7 1.0
CB C:LEU118 5.0 20.8 1.0

Magnesium binding site 3 out of 6 in 2v3w

Go back to Magnesium Binding Sites List in 2v3w
Magnesium binding site 3 out of 6 in the Crystal Structure of the Benzoylformate Decarboxylase Variant L461A 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 Benzoylformate Decarboxylase Variant L461A From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1528

b:23.8
occ:1.00
 O2A B:TPP1531 2.0 24.6 1.0
O B:THR457 2.0 26.2 1.0
O1B B:TPP1531 2.0 23.7 1.0
O B:HOH2214 2.1 33.6 1.0
OD1 B:ASN455 2.2 25.6 1.0
OD1 B:ASP428 2.3 29.1 1.0
PA B:TPP1531 3.1 23.1 1.0
CG B:ASN455 3.2 25.7 1.0
C B:THR457 3.2 26.6 1.0
PB B:TPP1531 3.2 25.0 1.0
O3A B:TPP1531 3.4 23.0 1.0
CG B:ASP428 3.4 27.0 1.0
ND2 B:ASN455 3.5 23.6 1.0
O7 B:TPP1531 3.8 25.5 1.0
N B:THR457 3.9 26.1 1.0
OD2 B:ASP428 4.0 29.0 1.0
N B:GLY459 4.1 26.7 1.0
N B:ASP428 4.1 24.7 1.0
CA B:THR457 4.1 25.9 1.0
N B:TYR458 4.1 26.5 1.0
N B:GLY429 4.2 24.5 1.0
O3B B:TPP1531 4.2 23.2 1.0
O2B B:TPP1531 4.2 20.8 1.0
O1A B:TPP1531 4.3 24.9 1.0
CA B:TYR458 4.3 26.0 1.0
O B:MET453 4.5 28.0 1.0
O B:HOH2176 4.5 19.1 1.0
CB B:ASN455 4.5 26.2 1.0
N B:ASN455 4.5 26.6 1.0
CG2 B:THR457 4.6 24.7 1.0
CB B:ASP428 4.6 25.9 1.0
CA B:ASP428 4.7 25.5 1.0
CA B:GLY427 4.8 25.2 1.0
C B:TYR458 4.8 26.7 1.0
C B:GLY427 4.8 25.3 1.0
CA B:ASN455 4.9 26.5 1.0
N B:GLY456 4.9 26.1 1.0
C B:ASN455 4.9 26.3 1.0
C B:ASP428 5.0 24.8 1.0
CA B:GLY429 5.0 23.8 1.0

Magnesium binding site 4 out of 6 in 2v3w

Go back to Magnesium Binding Sites List in 2v3w
Magnesium binding site 4 out of 6 in the Crystal Structure of the Benzoylformate Decarboxylase Variant L461A 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 Benzoylformate Decarboxylase Variant L461A From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1529

b:20.3
occ:1.00
 O D:ARG120 2.4 19.7 1.0
O B:LEU118 2.4 18.3 1.0
O D:LEU118 2.4 19.4 1.0
O B:ARG120 2.6 21.1 1.0
O B:ASN117 2.6 18.9 1.0
O D:ASN117 2.7 18.8 1.0
C B:LEU118 3.1 19.3 1.0
C D:LEU118 3.2 18.6 1.0
O D:HOH2049 3.4 18.3 1.0
CA B:LEU118 3.5 19.1 1.0
C D:ARG120 3.5 19.9 1.0
C B:ASN117 3.6 19.8 1.0
C B:ARG120 3.7 21.6 1.0
CA D:LEU118 3.8 18.7 1.0
N D:ARG120 3.8 19.5 1.0
C D:ASN117 3.8 18.6 1.0
N B:LEU118 4.0 20.0 1.0
N B:ARG120 4.0 20.6 1.0
CA D:ARG120 4.1 20.2 1.0
N B:PRO119 4.2 19.1 1.0
C D:PRO119 4.2 19.2 1.0
N D:PRO119 4.2 18.8 1.0
N D:LEU118 4.2 18.8 1.0
CE D:MET79 4.3 19.3 0.5
CA B:ARG120 4.3 21.4 1.0
C B:PRO119 4.5 19.9 1.0
CB D:ARG120 4.5 20.1 1.0
CE B:MET79 4.6 19.0 0.5
CA D:PRO119 4.6 19.2 1.0
N D:PRO121 4.6 20.8 1.0
CB B:ARG120 4.7 21.5 1.0
CA B:PRO119 4.7 19.4 1.0
CD D:PRO121 4.8 20.4 1.0
CB B:LEU118 4.8 19.7 1.0
N B:PRO121 4.8 22.0 1.0
O D:PRO119 4.9 19.8 1.0
CA B:ASN117 4.9 20.6 1.0
CD1 B:LEU118 4.9 20.7 1.0

Magnesium binding site 5 out of 6 in 2v3w

Go back to Magnesium Binding Sites List in 2v3w
Magnesium binding site 5 out of 6 in the Crystal Structure of the Benzoylformate Decarboxylase Variant L461A 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 Benzoylformate Decarboxylase Variant L461A From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1528

b:20.5
occ:1.00
 O2A C:TPP1530 2.0 24.7 1.0
O C:HOH2206 2.0 16.0 1.0
OD1 C:ASP428 2.0 26.5 1.0
OD1 C:ASN455 2.0 26.7 1.0
O1B C:TPP1530 2.3 24.3 1.0
O C:THR457 2.3 19.9 1.0
CG C:ASN455 3.1 25.9 1.0
CG C:ASP428 3.2 23.9 1.0
PA C:TPP1530 3.2 22.4 1.0
PB C:TPP1530 3.4 21.1 1.0
ND2 C:ASN455 3.5 26.1 1.0
C C:THR457 3.5 21.9 1.0
O3A C:TPP1530 3.5 23.9 1.0
OD2 C:ASP428 3.8 25.3 1.0
N C:ASP428 3.9 22.2 1.0
N C:THR457 4.0 23.1 1.0
O7 C:TPP1530 4.0 23.2 1.0
O C:MET453 4.1 24.5 1.0
N C:GLY429 4.1 22.2 1.0
O2B C:TPP1530 4.3 22.1 1.0
O C:HOH2247 4.3 23.0 1.0
N C:GLY459 4.3 22.0 1.0
N C:ASN455 4.3 24.1 1.0
CA C:THR457 4.4 22.5 1.0
O1A C:TPP1530 4.4 19.9 1.0
CB C:ASN455 4.4 25.1 1.0
CB C:ASP428 4.4 22.6 1.0
N C:TYR458 4.5 22.0 1.0
O3B C:TPP1530 4.5 22.6 1.0
CA C:ASP428 4.5 22.5 1.0
CA C:GLY427 4.6 22.2 1.0
C C:GLY427 4.6 21.7 1.0
CA C:TYR458 4.7 22.2 1.0
N C:GLY456 4.7 24.1 1.0
CA C:ASN455 4.7 24.7 1.0
C C:ASN455 4.8 24.5 1.0
C C:ASP428 4.9 22.4 1.0
CG2 C:THR457 4.9 22.9 1.0

Magnesium binding site 6 out of 6 in 2v3w

Go back to Magnesium Binding Sites List in 2v3w
Magnesium binding site 6 out of 6 in the Crystal Structure of the Benzoylformate Decarboxylase Variant L461A 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 Benzoylformate Decarboxylase Variant L461A From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1528

b:19.5
occ:1.00
 O2A D:TPP1530 1.9 25.0 1.0
O D:HOH2192 2.0 14.4 1.0
OD1 D:ASN455 2.0 28.5 1.0
O1B D:TPP1530 2.1 26.6 1.0
OD1 D:ASP428 2.2 22.1 1.0
O D:THR457 2.4 26.5 1.0
CG D:ASN455 3.0 28.2 1.0
PA D:TPP1530 3.1 26.0 1.0
PB D:TPP1530 3.3 26.9 1.0
O3A D:TPP1530 3.4 25.7 1.0
ND2 D:ASN455 3.4 25.6 1.0
CG D:ASP428 3.5 25.6 1.0
C D:THR457 3.6 27.1 1.0
N D:ASP428 3.9 24.0 1.0
O7 D:TPP1530 4.0 27.1 1.0
OD2 D:ASP428 4.1 26.5 1.0
O D:MET453 4.1 26.3 1.0
O2B D:TPP1530 4.2 26.3 1.0
N D:GLY429 4.2 25.1 1.0
N D:THR457 4.2 27.0 1.0
N D:GLY459 4.2 27.9 1.0
O1A D:TPP1530 4.2 25.9 1.0
N D:ASN455 4.3 27.5 1.0
O D:HOH2158 4.4 23.9 1.0
O3B D:TPP1530 4.4 29.6 1.0
CB D:ASN455 4.4 27.3 1.0
CA D:THR457 4.5 27.2 1.0
CA D:GLY427 4.5 23.1 1.0
N D:TYR458 4.5 27.6 1.0
CB D:ASP428 4.6 24.9 1.0
C D:GLY427 4.6 23.5 1.0
CA D:TYR458 4.7 27.2 1.0
CA D:ASP428 4.7 24.7 1.0
CA D:ASN455 4.7 27.4 1.0
CG2 D:THR457 4.8 25.4 1.0
N D:GLY456 4.8 27.3 1.0
C D:ASN455 4.9 27.2 1.0
C D:ASP428 4.9 24.9 1.0

Reference:

D.Gocke, L.Walter, K.Gauchenova, G.Kolter, M.Knoll, C.L.Berthold, G.Schneider, J.Pleiss, M.Muller, M.Pohl. Rational Protein Design of Thdp-Dependent Enzymes-Engineering Stereoselectivity. Chembiochem V. 9 406 2008.
ISSN: ISSN 1439-4227
PubMed: 18224647
DOI: 10.1002/CBIC.200700598
Page generated: Wed Aug 14 04:57:45 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy