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Zinc in PDB 3o3j: Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 6B

Enzymatic activity of Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 6B

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 6B:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 6B, PDB code: 3o3j 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) 28.75 / 3.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.500, 57.500, 144.840, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 28.5

Other elements in 3o3j:

The structure of Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 6B also contains other interesting chemical elements:

Bromine (Br) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 6B (pdb code 3o3j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 6B, PDB code: 3o3j:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3o3j

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


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 Inhibitor 6B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:53.3
occ:1.00
 NE2 A:HIS133 1.9 31.7 1.0
O14 A:BB4300 2.0 53.6 1.0
NE2 A:HIS137 2.0 37.5 1.0
SG A:CYS91 2.2 29.7 1.0
N1 A:BB4300 2.8 60.4 1.0
CE1 A:HIS133 2.9 39.6 1.0
CD2 A:HIS137 2.9 38.0 1.0
CD2 A:HIS133 3.0 37.0 1.0
CB A:CYS91 3.1 30.1 1.0
CE1 A:HIS137 3.1 37.1 1.0
O2 A:BB4300 3.2 66.2 1.0
C13 A:BB4300 3.4 66.6 1.0
NE2 A:GLN48 3.6 32.8 1.0
CA A:CYS91 3.6 30.0 1.0
ND1 A:HIS133 4.0 43.5 1.0
CD A:GLN48 4.1 28.9 1.0
CG A:HIS137 4.1 37.1 1.0
N A:LEU92 4.1 25.9 1.0
CG A:HIS133 4.1 40.6 1.0
OE1 A:GLN48 4.2 29.7 1.0
ND1 A:HIS137 4.2 35.6 1.0
C A:CYS91 4.3 29.4 1.0
OE1 A:GLU134 4.5 27.8 1.0
O A:GLY90 4.7 37.7 1.0
N A:SER93 4.8 23.4 1.0
OG A:SER93 4.9 21.9 1.0
C12 A:BB4300 4.9 63.0 1.0
OE2 A:GLU134 4.9 37.1 1.0
N A:CYS91 4.9 34.4 1.0
CD A:GLU134 4.9 40.5 1.0

Zinc binding site 2 out of 6 in 3o3j

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Zinc binding site 2 out of 6 in the Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 6B


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 Inhibitor 6B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:67.3
occ:1.00
 OD1 A:ASP40 2.0 52.9 1.0
OE1 A:GLU63 2.0 44.6 1.0
CD A:GLU63 2.7 40.4 1.0
OE2 A:GLU63 2.8 32.7 1.0
CG A:ASP40 2.9 38.7 1.0
OD2 A:ASP40 3.0 46.4 1.0
O A:HOH220 3.3 40.6 1.0
O A:HOH247 3.9 48.7 1.0
O A:HOH248 4.0 71.3 1.0
CG A:GLU63 4.1 39.0 1.0
O A:GLY62 4.3 30.9 1.0
CB A:ASP40 4.4 32.6 1.0
O A:ASP40 4.8 30.1 1.0

Zinc binding site 3 out of 6 in 3o3j

Go back to Zinc Binding Sites List in 3o3j
Zinc binding site 3 out of 6 in the Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 6B


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 Inhibitor 6B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:53.8
occ:1.00
 OE2 A:GLU160 1.4 0.1 1.0
OE1 A:GLU179 1.8 0.4 1.0
CD A:GLU160 2.5 94.3 1.0
CD A:GLU179 2.8 0.6 1.0
OE1 A:GLU160 2.9 0.9 1.0
CG A:GLU179 3.4 0.1 1.0
OE2 A:GLU179 3.8 0.5 1.0
CG A:GLU160 3.8 80.6 1.0
NH1 A:ARG177 4.3 0.5 1.0
OE1 A:GLU157 4.5 89.3 1.0
CB A:GLU179 4.9 0.5 1.0
CB A:GLU160 4.9 80.3 1.0

Zinc binding site 4 out of 6 in 3o3j

Go back to Zinc Binding Sites List in 3o3j
Zinc binding site 4 out of 6 in the Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 6B


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 Inhibitor 6B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:76.2
occ:1.00
 N A:MET1 2.2 58.0 1.0
O A:MET1 2.4 59.6 1.0
C A:MET1 3.1 53.1 1.0
CA A:MET1 3.2 54.4 1.0
N A:GLU2 4.2 50.5 1.0
CB A:MET1 4.4 47.6 1.0
CB A:GLU2 4.5 57.0 1.0
CA A:GLU2 4.9 50.6 1.0

Zinc binding site 5 out of 6 in 3o3j

Go back to Zinc Binding Sites List in 3o3j
Zinc binding site 5 out of 6 in the Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 6B


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 Inhibitor 6B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:0.4
occ:1.00
 OD1 A:ASP19 2.7 0.0 1.0
CG A:ASP19 3.5 0.2 1.0
OD2 A:ASP19 3.6 0.8 1.0
O A:HOH233 3.9 44.1 1.0
N A:ASP19 4.3 0.8 1.0
O A:ARG17 4.9 93.8 1.0
CB A:ASP19 5.0 1.0 1.0

Zinc binding site 6 out of 6 in 3o3j

Go back to Zinc Binding Sites List in 3o3j
Zinc binding site 6 out of 6 in the Crystal Structure of Arabidopsis Thaliana Peptide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 6B


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 Inhibitor 6B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn206

b:54.0
occ:1.00
 OD1 A:ASP30 2.3 13.9 1.0
OD1 A:ASP34 2.3 14.9 1.0
CG A:ASP34 2.7 28.4 1.0
OD2 A:ASP34 2.8 25.4 1.0
CG A:ASP30 2.9 37.7 1.0
OD2 A:ASP30 3.0 45.3 1.0
CB A:ASP34 4.2 24.9 1.0
CB A:ASP30 4.2 36.5 1.0
CA A:ASP30 4.6 33.6 1.0
O A:ASP30 4.8 22.7 1.0
C A:ASP30 4.9 27.6 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: Sat Oct 26 10:43:55 2024

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