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Chlorine 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:

Magnesium (Mg) 4 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Chlorine atom in the Intermediate Analogue in Benzoylformate Decarboxylase (pdb code 3fzn). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 11 binding sites of Chlorine where determined in the Intermediate Analogue in Benzoylformate Decarboxylase, PDB code: 3fzn:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 11 in 3fzn

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Chlorine binding site 1 out of 11 in the Intermediate Analogue in Benzoylformate Decarboxylase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Intermediate Analogue in Benzoylformate Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl704

b:22.8
occ:1.00
 O D:HOH1094 3.1 23.4 1.0
NE D:ARG184 3.3 27.7 1.0
N A:ASP187 3.3 20.9 1.0
O A:HOH1276 3.5 25.2 1.0
NH2 D:ARG184 3.6 30.1 1.0
CA A:ASN186 3.8 17.8 1.0
CG A:ASP187 3.8 25.5 1.0
OD2 A:ASP187 3.8 32.7 1.0
CB A:ASN186 3.9 15.6 1.0
CZ D:ARG184 3.9 29.9 1.0
CB A:ASP187 4.0 22.0 1.0
C A:ASN186 4.0 15.2 1.0
CG D:ARG184 4.1 21.1 1.0
CA A:ASP187 4.3 18.2 1.0
OD1 A:ASP187 4.3 25.7 1.0
CD D:ARG184 4.3 28.1 1.0
O D:HOH2247 4.5 40.1 1.0
O D:HOH2909 4.8 29.4 1.0
O A:HOH2390 4.9 50.1 1.0
NH1 A:ARG184 4.9 23.0 1.0

Chlorine binding site 2 out of 11 in 3fzn

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Chlorine binding site 2 out of 11 in the Intermediate Analogue in Benzoylformate Decarboxylase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Intermediate Analogue in Benzoylformate Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl705

b:23.4
occ:1.00
 O A:HOH1080 3.2 26.2 1.0
NE A:ARG184 3.2 20.5 1.0
N D:ASP187 3.3 18.9 1.0
O D:HOH966 3.4 31.5 1.0
NH2 A:ARG184 3.7 26.1 1.0
CG D:ASP187 3.7 26.0 1.0
CB D:ASP187 3.8 19.7 1.0
CZ A:ARG184 3.9 28.7 1.0
CA D:ASN186 3.9 17.9 1.0
CB D:ASN186 4.0 17.5 1.0
OD2 D:ASP187 4.0 31.4 1.0
C D:ASN186 4.1 15.6 1.0
CG A:ARG184 4.1 24.2 1.0
OD1 D:ASP187 4.1 27.6 1.0
CA D:ASP187 4.2 18.6 1.0
CD A:ARG184 4.3 26.5 1.0
O A:HOH2167 4.6 44.2 1.0
O A:HOH2798 4.8 32.6 1.0
CB A:ALA324 4.9 16.5 1.0
NH1 D:ARG184 4.9 22.2 1.0

Chlorine binding site 3 out of 11 in 3fzn

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Chlorine binding site 3 out of 11 in the Intermediate Analogue in Benzoylformate Decarboxylase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Intermediate Analogue in Benzoylformate Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl709

b:12.2
occ:1.00
 O A:LEU118 2.7 15.3 1.0
O B:ARG120 2.7 14.8 1.0
O A:ARG120 2.7 13.5 1.0
O B:LEU118 2.7 12.1 1.0
O A:ASN117 2.8 11.7 1.0
O B:ASN117 2.8 12.3 1.0
O B:HOH732 3.2 20.7 1.0
C A:LEU118 3.4 11.0 1.0
C B:LEU118 3.4 11.9 1.0
C B:ARG120 3.8 11.8 1.0
C A:ARG120 3.8 13.1 1.0
N B:ARG120 3.9 13.1 1.0
C B:ASN117 3.9 10.0 1.0
C A:ASN117 3.9 8.8 1.0
N A:ARG120 3.9 13.6 1.0
CA A:LEU118 3.9 10.3 1.0
CA B:LEU118 4.0 12.4 1.0
CA B:ARG120 4.3 12.8 1.0
N A:PRO119 4.3 10.3 1.0
CA A:ARG120 4.3 14.9 1.0
N B:PRO119 4.4 11.7 1.0
C B:PRO119 4.4 12.3 1.0
C A:PRO119 4.4 14.5 1.0
N B:LEU118 4.4 10.8 1.0
CE B:MET79 4.4 9.0 0.5
N A:LEU118 4.4 9.5 1.0
CB B:ARG120 4.5 13.1 1.0
CE A:MET79 4.5 8.8 0.5
CB A:ARG120 4.6 14.1 1.0
CA A:PRO119 4.7 11.9 1.0
CA B:PRO119 4.7 13.9 1.0
N B:PRO121 4.9 11.8 1.0
N A:PRO121 5.0 12.6 1.0

Chlorine binding site 4 out of 11 in 3fzn

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Chlorine binding site 4 out of 11 in the Intermediate Analogue in Benzoylformate Decarboxylase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Intermediate Analogue in Benzoylformate Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl710

b:21.5
occ:1.00
 O A:HOH1992 2.7 20.1 1.0
O A:HOH2763 2.8 43.6 1.0
O A:ALA510 2.8 16.2 1.0
O A:HOH2008 2.8 27.2 1.0
O A:ALA513 2.9 23.1 1.0
NE2 A:GLN421 2.9 16.9 1.0
O A:LEU511 3.3 27.1 1.0
O A:HOH2169 3.6 25.5 1.0
C A:LEU511 3.7 22.6 1.0
N A:ALA513 3.8 15.5 1.0
C A:ALA513 3.8 24.0 1.0
CD A:GLN421 3.9 21.4 1.0
C A:ALA510 3.9 15.7 1.0
CA A:LEU511 4.1 18.6 1.0
CA A:ALA513 4.1 17.5 1.0
CB A:ALA513 4.3 19.3 1.0
OE1 A:GLN421 4.3 19.4 1.0
CD1 A:ILE449 4.4 16.8 1.0
O A:PRO447 4.4 14.7 1.0
C A:SER512 4.5 20.3 1.0
N A:SER512 4.5 17.6 1.0
N A:LEU511 4.5 14.6 1.0
O A:HOH1385 4.5 38.7 1.0
CG1 A:ILE449 4.7 14.3 1.0
CB A:PRO447 4.9 17.3 1.0
CA A:SER512 4.9 20.7 0.5
N A:LYS514 4.9 18.4 1.0
O A:HOH985 5.0 26.6 1.0
CA A:SER512 5.0 19.1 0.5
O A:GLY515 5.0 15.5 1.0

Chlorine binding site 5 out of 11 in 3fzn

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Chlorine binding site 5 out of 11 in the Intermediate Analogue in Benzoylformate Decarboxylase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Intermediate Analogue in Benzoylformate Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl701

b:23.1
occ:1.00
 O C:HOH1007 3.2 24.2 1.0
N B:ASP187 3.3 19.0 1.0
NE C:ARG184 3.3 27.5 1.0
O B:HOH1157 3.4 28.2 1.0
CG B:ASP187 3.8 27.6 1.0
CA B:ASN186 3.8 16.7 1.0
NH2 C:ARG184 3.8 27.0 1.0
OD2 B:ASP187 3.9 30.9 1.0
CB B:ASN186 3.9 19.6 1.0
CB B:ASP187 3.9 21.6 1.0
CZ C:ARG184 4.0 28.5 1.0
C B:ASN186 4.1 17.8 1.0
CG C:ARG184 4.2 23.1 1.0
CA B:ASP187 4.2 18.4 1.0
OD1 B:ASP187 4.3 27.6 1.0
CD C:ARG184 4.3 32.5 1.0
O C:HOH1537 4.5 37.7 1.0
O B:HOH2893 4.8 31.1 1.0
O B:HOH1457 4.9 50.6 1.0
NH1 B:ARG184 4.9 22.1 1.0

Chlorine binding site 6 out of 11 in 3fzn

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Chlorine binding site 6 out of 11 in the Intermediate Analogue in Benzoylformate Decarboxylase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Intermediate Analogue in Benzoylformate Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl702

b:23.3
occ:1.00
 O B:HOH1217 3.1 26.3 1.0
N C:ASP187 3.2 17.8 1.0
NE B:ARG184 3.2 22.5 1.0
O C:HOH1699 3.3 24.1 1.0
NH2 B:ARG184 3.7 27.8 1.0
CG C:ASP187 3.7 24.9 1.0
CA C:ASN186 3.8 18.2 1.0
CB C:ASP187 3.8 19.8 1.0
CB C:ASN186 3.9 17.5 1.0
CZ B:ARG184 3.9 25.9 1.0
OD2 C:ASP187 4.0 30.3 1.0
C C:ASN186 4.0 15.5 1.0
OD1 C:ASP187 4.1 25.3 1.0
CG B:ARG184 4.1 18.0 1.0
CA C:ASP187 4.2 19.4 1.0
CD B:ARG184 4.3 21.2 1.0
O B:HOH2300 4.3 41.9 1.0
NH1 C:ARG184 4.8 19.9 1.0
O C:HOH2853 4.9 31.8 1.0

Chlorine binding site 7 out of 11 in 3fzn

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Chlorine binding site 7 out of 11 in the Intermediate Analogue in Benzoylformate Decarboxylase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Intermediate Analogue in Benzoylformate Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl703

b:22.4
occ:1.00
 O B:HOH2859 2.1 14.6 0.5
O B:HOH1990 2.6 23.1 1.0
O B:HOH1774 2.7 35.9 1.0
O B:ALA510 2.7 16.2 1.0
O B:HOH2159 2.9 17.1 0.5
O B:ALA513 3.0 22.6 1.0
NE2 B:GLN421 3.0 16.1 1.0
O B:LEU511 3.3 26.6 1.0
O B:HOH2131 3.5 15.7 0.5
C B:LEU511 3.7 24.7 1.0
N B:ALA513 3.8 15.2 1.0
C B:ALA513 3.8 20.1 1.0
C B:ALA510 3.9 16.7 1.0
CD B:GLN421 4.0 20.1 1.0
CA B:LEU511 4.1 16.1 1.0
CA B:ALA513 4.1 16.1 1.0
CB B:ALA513 4.2 20.0 1.0
OE1 B:GLN421 4.3 18.2 1.0
N B:SER512 4.4 20.5 1.0
C B:SER512 4.4 21.4 1.0
N B:LEU511 4.5 16.1 1.0
O B:PRO447 4.5 15.1 1.0
CD1 B:ILE449 4.5 15.6 1.0
CG1 B:ILE449 4.7 13.6 1.0
O B:HOH1840 4.7 37.4 1.0
CA B:SER512 4.9 21.8 0.5
O B:HOH860 4.9 24.2 1.0
CB B:PRO447 4.9 19.7 1.0
CA B:SER512 4.9 20.4 0.5
O B:GLY515 4.9 15.7 1.0
N B:LYS514 5.0 17.5 1.0

Chlorine binding site 8 out of 11 in 3fzn

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Chlorine binding site 8 out of 11 in the Intermediate Analogue in Benzoylformate Decarboxylase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Intermediate Analogue in Benzoylformate Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl708

b:23.9
occ:0.50
 O B:HOH2838 2.5 19.0 0.5
O B:HOH1504 2.8 36.5 1.0
N B:ALA116 2.9 14.5 1.0
O B:HOH1867 3.1 30.6 1.0
N B:ALA115 3.3 16.1 1.0
CB B:ALA116 3.4 15.7 1.0
C B:ASP114 3.7 16.7 1.0
CA B:ALA116 3.8 15.9 1.0
C B:ALA115 3.9 14.1 1.0
CA B:ALA115 3.9 16.3 1.0
O B:HOH3207 4.0 23.5 0.5
CB B:ALA115 4.1 17.4 1.0
CA B:ASP114 4.2 15.4 1.0
O B:ASP114 4.2 14.6 1.0
CB B:GLU128 4.3 12.8 1.0
O B:HOH2839 4.6 27.6 1.0
O B:HOH1264 4.6 25.3 1.0
O D:HOH2596 4.6 40.1 1.0
OD1 B:ASP114 4.7 30.9 1.0
OE1 B:GLU128 4.8 31.4 1.0
CD B:GLU128 4.8 21.9 1.0
C B:ALA116 4.9 16.8 1.0
N B:ASN117 4.9 13.2 1.0

Chlorine binding site 9 out of 11 in 3fzn

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Chlorine binding site 9 out of 11 in the Intermediate Analogue in Benzoylformate Decarboxylase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Intermediate Analogue in Benzoylformate Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl707

b:21.4
occ:1.00
 O C:HOH2021 2.8 26.2 1.0
O C:HOH839 2.8 23.9 1.0
O C:ALA510 2.8 14.7 1.0
O C:ALA513 2.9 19.8 1.0
NE2 C:GLN421 2.9 15.9 1.0
O C:LEU511 3.2 26.0 1.0
O C:HOH1592 3.5 27.9 1.0
C C:LEU511 3.7 21.7 1.0
C C:ALA513 3.8 19.2 1.0
N C:ALA513 3.8 16.8 1.0
CD C:GLN421 3.9 21.9 1.0
C C:ALA510 4.0 12.9 1.0
CA C:LEU511 4.1 19.4 1.0
CA C:ALA513 4.1 16.3 1.0
CB C:ALA513 4.2 15.9 1.0
OE1 C:GLN421 4.2 18.5 1.0
O C:PRO447 4.4 16.0 1.0
O C:HOH3046 4.4 32.4 1.0
N C:LEU511 4.5 14.5 1.0
N C:SER512 4.5 17.5 1.0
C C:SER512 4.5 20.2 1.0
CD1 C:ILE449 4.5 16.8 1.0
CB C:PRO447 4.8 17.3 1.0
O C:HOH2552 4.8 45.2 1.0
CG1 C:ILE449 4.8 12.5 1.0
O C:HOH1060 4.8 24.5 1.0
O C:GLY515 4.9 15.7 1.0
N C:LYS514 4.9 17.7 1.0
CA C:SER512 5.0 21.9 0.5
CA C:SER512 5.0 21.0 0.5

Chlorine binding site 10 out of 11 in 3fzn

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Chlorine binding site 10 out of 11 in the Intermediate Analogue in Benzoylformate Decarboxylase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Intermediate Analogue in Benzoylformate Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl711

b:12.1
occ:1.00
 O C:ARG120 2.7 15.7 1.0
O D:ARG120 2.7 15.1 1.0
O D:LEU118 2.7 13.7 1.0
O C:LEU118 2.7 14.5 1.0
O C:ASN117 2.8 13.2 1.0
O D:ASN117 2.9 14.3 1.0
O C:HOH667 3.2 22.0 1.0
C C:LEU118 3.5 11.9 1.0
C D:LEU118 3.5 13.3 1.0
C C:ARG120 3.8 13.2 1.0
C D:ARG120 3.8 11.7 1.0
N C:ARG120 3.9 13.9 1.0
C C:ASN117 3.9 10.8 1.0
C D:ASN117 4.0 11.3 1.0
CA C:LEU118 4.0 15.3 1.0
CA D:LEU118 4.0 12.2 1.0
N D:ARG120 4.0 12.5 1.0
CA C:ARG120 4.3 14.0 1.0
CA D:ARG120 4.3 11.0 1.0
N C:PRO119 4.4 11.8 1.0
N D:PRO119 4.4 11.2 1.0
C C:PRO119 4.5 13.4 1.0
C D:PRO119 4.5 10.4 1.0
N C:LEU118 4.5 12.4 1.0
N D:LEU118 4.5 10.8 1.0
CE C:MET79 4.5 7.7 0.5
CE D:MET79 4.5 8.9 0.5
CB D:ARG120 4.6 14.1 1.0
CB C:ARG120 4.6 15.3 1.0
CA C:PRO119 4.7 14.6 1.0
CA D:PRO119 4.8 13.6 1.0
N C:PRO121 4.9 12.1 1.0
N D:PRO121 4.9 12.0 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: Sat Jul 20 19:52:49 2024

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