Atomistry » Magnesium » PDB 3fzn-3g8c » 3fzn
Atomistry »
  Magnesium »
    PDB 3fzn-3g8c »
      3fzn »

Magnesium in PDB 3fzn: Intermediate Analogue in Benzoylformate Decarboxylase

Enzymatic activity of Intermediate Analogue in Benzoylformate Decarboxylase

All present enzymatic activity of Intermediate Analogue in Benzoylformate Decarboxylase:
4.1.1.7;

Protein crystallography data

The structure of Intermediate Analogue in Benzoylformate Decarboxylase, PDB code: 3fzn was solved by M.Bruning, M.Berheide, D.Meyer, R.Golbik, H.Bartunik, A.Liese, K.Tittmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 1.62
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 71.510, 93.344, 94.525, 63.46, 72.82, 73.21
R / Rfree (%) 17 / 20.3

Other elements in 3fzn:

The structure of Intermediate Analogue in Benzoylformate Decarboxylase also contains other interesting chemical elements:

Chlorine (Cl) 11 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Intermediate Analogue in Benzoylformate Decarboxylase (pdb code 3fzn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Intermediate Analogue in Benzoylformate Decarboxylase, PDB code: 3fzn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3fzn

Go back to Magnesium Binding Sites List in 3fzn
Magnesium binding site 1 out of 4 in the Intermediate Analogue in Benzoylformate Decarboxylase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Intermediate Analogue in Benzoylformate Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:13.6
occ:1.00
 O1A A:D7K601 2.1 11.3 1.0
OD1 A:ASN455 2.1 16.5 1.0
OD1 A:ASP428 2.1 16.3 1.0
O A:HOH545 2.2 14.3 1.0
O A:THR457 2.2 14.4 1.0
O2B A:D7K601 2.3 14.6 1.0
CG A:ASN455 3.0 15.2 1.0
PA A:D7K601 3.3 13.6 1.0
CG A:ASP428 3.3 21.1 1.0
ND2 A:ASN455 3.4 18.7 1.0
C A:THR457 3.4 14.3 1.0
PB A:D7K601 3.4 14.9 1.0
O3A A:D7K601 3.6 11.7 1.0
OD2 A:ASP428 3.9 19.1 1.0
N A:THR457 4.0 15.5 1.0
O01 A:D7K601 4.1 12.3 1.0
N A:ASP428 4.1 13.8 1.0
N A:GLY459 4.1 13.7 1.0
N A:GLY429 4.3 13.2 1.0
CA A:THR457 4.3 13.5 1.0
O A:MET453 4.3 14.3 1.0
O3B A:D7K601 4.4 13.7 1.0
N A:TYR458 4.4 11.6 1.0
CB A:ASN455 4.4 12.8 1.0
O2A A:D7K601 4.5 13.3 1.0
N A:ASN455 4.5 13.3 1.0
O A:HOH1986 4.5 13.7 1.0
CA A:TYR458 4.5 11.1 1.0
CB A:ASP428 4.6 14.2 1.0
O1B A:D7K601 4.6 14.8 1.0
CG2 A:THR457 4.6 15.7 1.0
CA A:ASP428 4.7 16.0 1.0
N A:GLY456 4.7 16.8 1.0
CA A:ASN455 4.8 12.1 1.0
CA A:GLY427 4.8 12.7 1.0
C A:GLY427 4.8 12.3 1.0
C A:ASN455 4.9 15.1 1.0
C A:TYR458 4.9 16.8 1.0
C A:ASP428 5.0 18.4 1.0

Magnesium binding site 2 out of 4 in 3fzn

Go back to Magnesium Binding Sites List in 3fzn
Magnesium binding site 2 out of 4 in the Intermediate Analogue in Benzoylformate Decarboxylase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Intermediate Analogue in Benzoylformate Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg606

b:13.9
occ:1.00
 O1A B:D7K602 2.1 12.9 1.0
O2B B:D7K602 2.1 15.1 1.0
O B:HOH655 2.2 13.2 1.0
OD1 B:ASN455 2.2 14.4 1.0
OD1 B:ASP428 2.2 15.0 1.0
O B:THR457 2.2 12.4 1.0
CG B:ASN455 3.0 17.4 1.0
PA B:D7K602 3.3 13.7 1.0
PB B:D7K602 3.3 14.2 1.0
ND2 B:ASN455 3.3 17.3 1.0
CG B:ASP428 3.4 19.7 1.0
C B:THR457 3.4 12.7 1.0
O3A B:D7K602 3.4 10.4 1.0
N B:THR457 4.0 14.8 1.0
OD2 B:ASP428 4.0 20.0 1.0
N B:ASP428 4.1 13.4 1.0
O01 B:D7K602 4.1 13.5 1.0
N B:GLY459 4.2 12.1 1.0
O3B B:D7K602 4.3 12.2 1.0
CA B:THR457 4.3 13.8 1.0
N B:GLY429 4.3 12.3 1.0
O B:MET453 4.3 14.5 1.0
N B:TYR458 4.4 11.4 1.0
O1B B:D7K602 4.4 12.9 1.0
CB B:ASN455 4.4 13.7 1.0
O B:HOH849 4.4 14.8 1.0
O2A B:D7K602 4.4 13.9 1.0
N B:ASN455 4.5 13.9 1.0
CA B:TYR458 4.6 12.9 1.0
CG2 B:THR457 4.6 12.2 1.0
CB B:ASP428 4.6 15.5 1.0
N B:GLY456 4.7 13.7 1.0
CA B:ASP428 4.7 13.4 1.0
CA B:ASN455 4.8 12.7 1.0
CA B:GLY427 4.8 14.5 1.0
C B:ASN455 4.8 18.2 1.0
C B:GLY427 4.9 11.8 1.0
C B:TYR458 4.9 12.3 1.0

Magnesium binding site 3 out of 4 in 3fzn

Go back to Magnesium Binding Sites List in 3fzn
Magnesium binding site 3 out of 4 in the Intermediate Analogue in Benzoylformate Decarboxylase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Intermediate Analogue in Benzoylformate Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg607

b:13.6
occ:1.00
 O1A C:D7K604 2.1 12.7 1.0
OD1 C:ASP428 2.1 14.7 1.0
O2B C:D7K604 2.1 16.1 1.0
O C:THR457 2.2 14.5 1.0
OD1 C:ASN455 2.2 13.3 1.0
O C:HOH539 2.2 13.5 1.0
CG C:ASN455 3.1 17.7 1.0
PA C:D7K604 3.3 13.7 1.0
CG C:ASP428 3.3 20.8 1.0
ND2 C:ASN455 3.4 17.2 1.0
PB C:D7K604 3.4 15.1 1.0
C C:THR457 3.4 15.7 1.0
O3A C:D7K604 3.5 12.3 1.0
OD2 C:ASP428 3.9 20.8 1.0
N C:THR457 4.0 14.1 1.0
N C:ASP428 4.0 13.9 1.0
O01 C:D7K604 4.1 14.7 1.0
N C:GLY459 4.1 13.2 1.0
N C:GLY429 4.2 15.0 1.0
CA C:THR457 4.3 14.7 1.0
O3B C:D7K604 4.3 12.3 1.0
O C:MET453 4.4 15.6 1.0
N C:TYR458 4.4 12.9 1.0
CB C:ASN455 4.4 16.6 1.0
O2A C:D7K604 4.4 12.8 1.0
N C:ASN455 4.4 13.0 1.0
O1B C:D7K604 4.5 15.0 1.0
O C:HOH1979 4.5 15.6 1.0
CA C:TYR458 4.5 14.4 1.0
CB C:ASP428 4.6 12.7 1.0
CG2 C:THR457 4.6 15.0 1.0
CA C:ASP428 4.7 15.9 1.0
N C:GLY456 4.7 15.4 1.0
CA C:ASN455 4.7 13.6 1.0
C C:GLY427 4.8 13.9 1.0
CA C:GLY427 4.9 15.1 1.0
C C:ASN455 4.9 18.2 1.0
C C:TYR458 4.9 13.4 1.0
C C:ASP428 5.0 16.2 1.0

Magnesium binding site 4 out of 4 in 3fzn

Go back to Magnesium Binding Sites List in 3fzn
Magnesium binding site 4 out of 4 in the Intermediate Analogue in Benzoylformate Decarboxylase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Intermediate Analogue in Benzoylformate Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg608

b:14.1
occ:1.00
 O1A D:D7K603 2.0 12.6 1.0
OD1 D:ASP428 2.1 14.3 1.0
O2B D:D7K603 2.2 15.2 1.0
OD1 D:ASN455 2.2 14.0 1.0
O D:HOH607 2.2 13.2 1.0
O D:THR457 2.2 14.6 1.0
CG D:ASN455 3.1 14.2 1.0
PA D:D7K603 3.3 14.5 1.0
CG D:ASP428 3.3 19.9 1.0
ND2 D:ASN455 3.3 18.3 1.0
PB D:D7K603 3.4 15.3 1.0
C D:THR457 3.4 15.6 1.0
O3A D:D7K603 3.5 14.9 1.0
OD2 D:ASP428 3.9 17.4 1.0
N D:THR457 4.0 16.4 1.0
N D:ASP428 4.1 15.3 1.0
O01 D:D7K603 4.1 14.1 1.0
N D:GLY459 4.1 15.7 1.0
N D:GLY429 4.2 14.6 1.0
O3B D:D7K603 4.3 14.5 1.0
CA D:THR457 4.3 14.1 1.0
O D:MET453 4.4 15.1 1.0
N D:TYR458 4.4 12.7 1.0
O2A D:D7K603 4.4 14.5 1.0
CB D:ASN455 4.4 14.5 1.0
O D:HOH689 4.5 14.9 1.0
O1B D:D7K603 4.5 16.8 1.0
N D:ASN455 4.5 12.8 1.0
CB D:ASP428 4.5 14.2 1.0
CA D:TYR458 4.5 14.1 1.0
CA D:ASP428 4.7 16.9 1.0
CG2 D:THR457 4.7 14.5 1.0
N D:GLY456 4.8 15.1 1.0
CA D:ASN455 4.8 13.4 1.0
C D:GLY427 4.8 11.5 1.0
CA D:GLY427 4.9 14.6 1.0
C D:TYR458 4.9 16.3 1.0
C D:ASN455 4.9 16.9 1.0
C D:ASP428 4.9 15.5 1.0

Reference:

M.Bruning, M.Berheide, D.Meyer, R.Golbik, H.Bartunik, A.Liese, K.Tittmann. Structural and Kinetic Studies on Native Intermediates and An Intermediate Analogue in Benzoylformate Decarboxylase Reveal A Least Motion Mechanism with An Unprecedented Short-Lived Predecarboxylation Intermediate. Biochemistry V. 48 3258 2009.
ISSN: ISSN 0006-2960
PubMed: 19182954
DOI: 10.1021/BI801957D
Page generated: Sun Aug 10 21:08:33 2025

Last articles

Mg in 6TR4
Mg in 6TR3
Mg in 6TMF
Mg in 6TQO
Mg in 6TQN
Mg in 6TQF
Mg in 6TQE
Mg in 6TQB
Mg in 6TQA
Mg in 6TPS
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy