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Zinc in PDB 3m6p: Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin

Enzymatic activity of Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin, PDB code: 3m6p was solved by S.Fieulaine, T.Meinnel, C.Giglione, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.560, 56.470, 145.950, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 26.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin (pdb code 3m6p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin, PDB code: 3m6p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 3m6p

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Zinc binding site 1 out of 9 in the Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn195

b:17.2
occ:1.00
 O4 A:BB2194 2.1 11.2 1.0
SG A:CYS91 2.2 15.4 1.0
NE2 A:HIS137 2.2 17.7 1.0
NE2 A:HIS133 2.3 13.1 1.0
O2 A:BB2194 2.4 16.7 1.0
C3 A:BB2194 2.9 16.1 1.0
N1 A:BB2194 3.0 13.5 1.0
CD2 A:HIS133 3.0 12.2 1.0
CD2 A:HIS137 3.1 13.4 1.0
NE2 A:GLN48 3.1 11.0 1.0
CE1 A:HIS137 3.4 14.9 1.0
CE1 A:HIS133 3.4 14.8 1.0
CB A:CYS91 3.4 18.0 1.0
O A:HOH255 3.8 12.9 1.0
CD A:GLN48 3.8 16.7 1.0
OE1 A:GLN48 3.9 13.0 1.0
CA A:CYS91 3.9 16.5 1.0
C5 A:BB2194 4.2 7.5 1.0
N A:LEU92 4.3 14.8 1.0
CG A:HIS133 4.3 18.6 1.0
CG A:HIS137 4.3 14.7 1.0
ND1 A:HIS137 4.4 16.5 1.0
ND1 A:HIS133 4.4 14.2 1.0
C6 A:BB2194 4.5 15.2 1.0
C A:CYS91 4.5 15.5 1.0
O A:HOH334 4.7 20.0 1.0
OE1 A:GLU134 4.8 19.6 1.0
C7 A:BB2194 4.8 12.6 1.0
N A:SER93 4.9 13.2 1.0
O A:GLY90 5.0 17.3 1.0
OE2 A:GLU134 5.0 21.4 1.0

Zinc binding site 2 out of 9 in 3m6p

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Zinc binding site 2 out of 9 in the Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn196

b:44.5
occ:1.00
 OE2 A:GLU63 2.2 21.7 1.0
NZ B:LYS38 2.7 27.8 1.0
CD A:GLU63 3.1 19.8 1.0
O A:HOH439 3.1 35.3 1.0
O A:HOH318 3.2 43.4 1.0
OE1 A:GLU63 3.2 17.9 1.0
CE B:LYS38 3.7 26.3 1.0
OD1 A:ASP40 4.3 32.5 1.0
O B:HOH440 4.4 26.1 1.0
O A:GLY62 4.4 19.8 1.0
CG A:GLU63 4.4 12.2 1.0
CG A:ASP40 4.6 29.2 1.0
CB A:ASP40 4.7 25.1 1.0
O A:HOH374 4.7 30.2 1.0
CD B:LYS38 4.9 25.5 1.0
O A:HOH406 4.9 21.4 1.0

Zinc binding site 3 out of 9 in 3m6p

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Zinc binding site 3 out of 9 in the Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn197

b:18.1
occ:1.00
 OE1 A:GLU179 1.9 23.0 1.0
OE2 A:GLU160 1.9 17.8 1.0
CD A:GLU160 2.8 18.7 1.0
CD A:GLU179 3.0 30.9 1.0
OE1 A:GLU160 3.1 24.2 1.0
OE2 A:GLU179 3.8 33.9 1.0
CG A:GLU179 3.9 32.2 1.0
CG A:GLU160 4.2 15.4 1.0
NH1 A:ARG177 4.3 33.6 1.0
CB A:GLU179 4.3 31.6 1.0
O A:HOH414 4.4 20.9 1.0
OE2 A:GLU157 4.9 23.6 1.0

Zinc binding site 4 out of 9 in 3m6p

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Zinc binding site 4 out of 9 in the Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn198

b:19.3
occ:1.00
 OE1 B:GLU69 1.9 7.9 1.0
OD1 A:ASP34 2.0 13.7 1.0
OD2 A:ASP30 2.4 30.4 1.0
OD1 A:ASP30 2.7 29.1 1.0
CD B:GLU69 2.8 15.5 1.0
CG A:ASP30 2.8 23.4 1.0
CG A:ASP34 3.0 15.1 1.0
OE2 B:GLU69 3.0 12.9 1.0
ZN A:ZN199 3.1 20.5 1.0
OD2 A:ASP34 3.2 18.4 1.0
CE1 B:TYR37 3.7 14.1 1.0
O A:HOH257 3.7 12.5 1.0
CG B:GLU69 4.2 18.6 1.0
O A:ASP30 4.2 14.5 1.0
OH B:TYR37 4.2 17.2 1.0
CB A:ASP30 4.3 18.8 1.0
CB A:ASP34 4.3 12.6 1.0
CZ B:TYR37 4.4 16.5 1.0
C A:ASP30 4.6 16.2 1.0
CD1 B:TYR37 4.6 13.2 1.0
CB B:PHE33 4.8 16.0 1.0
OD2 B:ASP34 4.8 15.7 1.0
CA A:ASP30 4.9 18.0 1.0
CG B:PHE33 5.0 12.3 1.0
O B:HOH428 5.0 27.4 1.0

Zinc binding site 5 out of 9 in 3m6p

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Zinc binding site 5 out of 9 in the Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn199

b:20.5
occ:1.00
 OD2 A:ASP34 2.0 18.4 1.0
OD2 B:ASP34 2.0 15.7 1.0
CG A:ASP34 3.0 15.1 1.0
CG B:ASP34 3.1 14.7 1.0
ZN A:ZN198 3.1 19.3 1.0
ZN B:ZN198 3.2 19.3 1.0
OD1 A:ASP34 3.4 13.7 1.0
OD1 B:ASP34 3.4 13.9 1.0
OD2 A:ASP30 3.5 30.4 1.0
OD1 B:ASP30 3.7 26.3 1.0
CB A:ASP34 4.4 12.6 1.0
CB B:ASP34 4.4 12.3 1.0
O B:ASP30 4.4 13.4 1.0
N B:ASP34 4.5 12.2 1.0
N A:ASP34 4.5 13.1 1.0
CD1 B:TYR37 4.5 13.2 1.0
O A:ASP30 4.5 14.5 1.0
CE1 B:TYR37 4.6 14.1 1.0
CD1 A:TYR37 4.6 9.7 1.0
CA B:ASP34 4.6 14.5 1.0
CB A:PHE33 4.6 14.9 1.0
CG A:ASP30 4.6 23.4 1.0
CB B:PHE33 4.6 16.0 1.0
CE1 A:TYR37 4.6 15.3 1.0
CA A:ASP34 4.6 14.9 1.0
OE1 B:GLU69 4.7 7.9 1.0
OE2 A:GLU69 4.8 10.6 1.0
CG B:ASP30 4.9 21.9 1.0
C A:PHE33 5.0 14.7 1.0

Zinc binding site 6 out of 9 in 3m6p

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Zinc binding site 6 out of 9 in the Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn195

b:16.0
occ:1.00
 O4 B:BB2194 2.0 11.7 1.0
NE2 B:HIS133 2.1 10.0 1.0
NE2 B:HIS137 2.1 16.9 1.0
SG B:CYS91 2.2 15.1 1.0
O2 B:BB2194 2.4 12.8 1.0
C3 B:BB2194 2.9 13.3 1.0
NE2 B:GLN48 2.9 12.6 1.0
CD2 B:HIS133 3.1 9.8 1.0
CD2 B:HIS137 3.1 13.4 1.0
N1 B:BB2194 3.1 10.6 1.0
CE1 B:HIS133 3.2 10.6 1.0
CE1 B:HIS137 3.2 18.1 1.0
CB B:CYS91 3.5 18.0 1.0
O B:HOH213 3.7 11.8 1.0
CD B:GLN48 3.7 17.6 1.0
CA B:CYS91 3.9 17.3 1.0
OE1 B:GLN48 3.9 14.1 1.0
CG B:HIS133 4.2 15.0 1.0
N B:LEU92 4.2 15.1 1.0
CG B:HIS137 4.2 15.7 1.0
C5 B:BB2194 4.2 12.4 1.0
ND1 B:HIS137 4.3 17.9 1.0
ND1 B:HIS133 4.3 12.4 1.0
C6 B:BB2194 4.5 15.3 1.0
C B:CYS91 4.5 16.1 1.0
O B:HOH263 4.8 17.6 1.0
C7 B:BB2194 4.9 15.5 1.0
N B:SER93 4.9 13.9 1.0
O B:GLY90 4.9 17.9 1.0
OE1 B:GLU134 4.9 21.6 1.0
CG B:GLN48 4.9 16.1 1.0
OE2 B:GLU134 5.0 25.5 1.0

Zinc binding site 7 out of 9 in 3m6p

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Zinc binding site 7 out of 9 in the Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn196

b:46.7
occ:1.00
 OE1 B:GLU63 2.1 23.0 1.0
NZ A:LYS38 2.4 26.8 1.0
CD B:GLU63 3.0 23.1 1.0
OE2 B:GLU63 3.2 19.8 1.0
O B:HOH424 3.4 42.1 1.0
CE A:LYS38 3.5 26.7 1.0
O B:GLY62 4.2 21.3 1.0
O B:HOH362 4.2 25.4 1.0
O A:HOH256 4.4 17.1 1.0
CG B:GLU63 4.4 14.0 1.0
OD1 B:ASP40 4.5 30.4 1.0
CB B:ASP40 4.6 25.1 1.0
CG B:ASP40 4.7 29.4 1.0
CD A:LYS38 4.8 21.9 1.0
O B:HOH214 5.0 26.1 1.0

Zinc binding site 8 out of 9 in 3m6p

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Zinc binding site 8 out of 9 in the Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn197

b:18.5
occ:1.00
 OE1 B:GLU179 1.9 23.4 1.0
OE2 B:GLU160 1.9 20.7 1.0
CD B:GLU160 2.8 21.0 1.0
CD B:GLU179 3.0 29.5 1.0
OE1 B:GLU160 3.0 21.3 1.0
OE2 B:GLU179 3.8 30.9 1.0
NH2 B:ARG177 3.8 26.3 1.0
CG B:GLU179 4.1 30.9 1.0
CG B:GLU160 4.2 16.6 1.0
CB B:GLU179 4.3 29.0 1.0
OE1 B:GLU157 4.6 23.9 1.0
O B:HOH271 4.6 24.3 1.0

Zinc binding site 9 out of 9 in 3m6p

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Zinc binding site 9 out of 9 in the Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn198

b:19.3
occ:1.00
 OE2 A:GLU69 1.9 10.6 1.0
OD1 B:ASP34 2.0 13.9 1.0
OD1 B:ASP30 2.0 26.3 1.0
CD A:GLU69 2.7 16.0 1.0
OE1 A:GLU69 2.9 15.9 1.0
CG B:ASP30 2.9 21.9 1.0
CG B:ASP34 2.9 14.7 1.0
OD2 B:ASP30 3.1 27.9 1.0
OD2 B:ASP34 3.2 15.7 1.0
ZN A:ZN199 3.2 20.5 1.0
CE1 A:TYR37 3.7 15.3 1.0
O B:HOH319 3.8 16.6 1.0
O B:ASP30 4.1 13.4 1.0
CG A:GLU69 4.1 19.4 1.0
OH A:TYR37 4.2 16.8 1.0
CB B:ASP30 4.3 19.4 1.0
CB B:ASP34 4.3 12.3 1.0
CZ A:TYR37 4.3 15.6 1.0
C B:ASP30 4.6 16.1 1.0
CD1 A:TYR37 4.6 9.7 1.0
CB A:PHE33 4.7 14.9 1.0
OD2 A:ASP34 4.8 18.4 1.0
CA B:ASP30 4.9 18.1 1.0
CG A:PHE33 4.9 15.3 1.0
O A:HOH326 5.0 21.7 1.0

Reference:

S.Fieulaine, A.Boularot, I.Artaud, M.Desmadril, F.Dardel, T.Meinnel, C.Giglione. Trapping Conformational States Along Ligand-Binding Dynamics of Peptide Deformylase: the Impact of Induced Fit on Enzyme Catalysis Plos Biol. V. 9 01066 2011.
ISSN: ISSN 1544-9173
PubMed: 21629676
DOI: 10.1371/JOURNAL.PBIO.1001066
Page generated: Wed Dec 16 04:34:27 2020

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