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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: Wed Aug 14 14:00:06 2024

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