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Zinc in PDB 3pn4: Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Actinonin (Crystallized in Peg-550-Mme)

Enzymatic activity of Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Actinonin (Crystallized in Peg-550-Mme)

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Actinonin (Crystallized in Peg-550-Mme):
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Actinonin (Crystallized in Peg-550-Mme), PDB code: 3pn4 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) 40.00 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 56.570, 56.570, 146.110, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Actinonin (Crystallized in Peg-550-Mme) (pdb code 3pn4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Actinonin (Crystallized in Peg-550-Mme), PDB code: 3pn4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 3pn4

Go back to Zinc Binding Sites List in 3pn4
Zinc binding site 1 out of 5 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Actinonin (Crystallized in Peg-550-Mme)


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 Petide Deformylase 1B (ATPDF1B) in Complex with Actinonin (Crystallized in Peg-550-Mme) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:15.4
occ:1.00
 NE2 A:HIS133 2.1 5.8 1.0
NE2 A:HIS137 2.2 5.8 1.0
O4 A:BB2501 2.2 16.1 1.0
SG A:CYS91 2.3 2.8 1.0
O2 A:BB2501 2.4 16.7 1.0
C3 A:BB2501 2.9 16.7 1.0
CD2 A:HIS133 3.0 4.6 1.0
N1 A:BB2501 3.0 14.4 1.0
CD2 A:HIS137 3.1 4.6 1.0
CE1 A:HIS133 3.2 5.4 1.0
CE1 A:HIS137 3.2 4.6 1.0
NE2 A:GLN48 3.2 5.7 1.0
CB A:CYS91 3.3 3.8 1.0
O A:HOH1006 3.7 17.0 1.0
CA A:CYS91 3.8 3.5 1.0
CD A:GLN48 3.8 4.9 1.0
OE1 A:GLN48 3.9 5.8 1.0
CG A:HIS133 4.2 5.2 1.0
ND1 A:HIS133 4.2 7.2 1.0
C5 A:BB2501 4.2 16.2 1.0
N A:LEU92 4.2 2.8 1.0
CG A:HIS137 4.3 6.2 1.0
ND1 A:HIS137 4.3 4.9 1.0
C A:CYS91 4.4 3.7 1.0
C6 A:BB2501 4.5 15.8 1.0
O A:HOH1017 4.6 15.8 1.0
N A:SER93 4.9 2.5 1.0
O A:GLY90 4.9 4.9 1.0
C7 A:BB2501 4.9 14.4 1.0

Zinc binding site 2 out of 5 in 3pn4

Go back to Zinc Binding Sites List in 3pn4
Zinc binding site 2 out of 5 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Actinonin (Crystallized in Peg-550-Mme)


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 Petide Deformylase 1B (ATPDF1B) in Complex with Actinonin (Crystallized in Peg-550-Mme) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:27.8
occ:1.00
 O A:HOH1212 1.9 16.7 1.0
O A:HOH1075 2.0 23.1 1.0
OD2 A:ASP40 2.1 26.2 1.0
O A:HOH1213 2.1 15.3 1.0
O A:HOH1172 2.3 26.0 1.0
O A:HOH1226 2.6 30.4 1.0
O A:HOH1171 3.0 6.3 1.0
CG A:ASP40 3.1 20.3 1.0
OD1 A:ASP40 3.4 27.3 1.0
O A:HOH1225 3.6 34.1 1.0
OE2 A:GLU63 3.7 23.6 1.0
OE1 A:GLU63 3.9 16.5 1.0
CD A:GLU63 4.2 17.9 1.0
O A:HOH1214 4.3 23.7 1.0
CB A:ASP40 4.3 11.4 1.0
O A:HOH1120 4.7 21.8 1.0

Zinc binding site 3 out of 5 in 3pn4

Go back to Zinc Binding Sites List in 3pn4
Zinc binding site 3 out of 5 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Actinonin (Crystallized in Peg-550-Mme)


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 Petide Deformylase 1B (ATPDF1B) in Complex with Actinonin (Crystallized in Peg-550-Mme) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:6.5
occ:1.00
 OE1 A:GLU179 1.6 23.4 1.0
OE2 A:GLU160 1.9 11.9 1.0
O A:HOH1244 2.0 6.3 1.0
CD A:GLU160 2.7 11.3 1.0
CD A:GLU179 2.7 23.3 1.0
OE1 A:GLU160 2.9 9.7 1.0
CG A:GLU179 3.3 26.2 1.0
O A:HOH1173 3.6 17.9 1.0
OE2 A:GLU179 3.8 28.6 1.0
CG A:GLU160 4.1 9.5 1.0
O A:HOH1013 4.4 19.2 1.0
CB A:GLU179 4.4 25.4 1.0
OE2 A:GLU157 4.5 11.8 1.0
NH2 A:ARG177 4.6 37.7 1.0

Zinc binding site 4 out of 5 in 3pn4

Go back to Zinc Binding Sites List in 3pn4
Zinc binding site 4 out of 5 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Actinonin (Crystallized in Peg-550-Mme)


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 Petide Deformylase 1B (ATPDF1B) in Complex with Actinonin (Crystallized in Peg-550-Mme) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1004

b:11.6
occ:1.00
 N A:MET1 1.9 8.7 1.0
O A:MET1 2.2 9.6 1.0
C A:MET1 2.9 9.3 1.0
CA A:MET1 3.0 10.5 1.0
N A:GLU2 4.1 9.6 1.0
CB A:MET1 4.2 8.9 1.0
O A:HOH1174 4.7 29.3 1.0
CA A:GLU2 4.8 9.8 1.0
CB A:GLU2 5.0 11.5 1.0

Zinc binding site 5 out of 5 in 3pn4

Go back to Zinc Binding Sites List in 3pn4
Zinc binding site 5 out of 5 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Actinonin (Crystallized in Peg-550-Mme)


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 Petide Deformylase 1B (ATPDF1B) in Complex with Actinonin (Crystallized in Peg-550-Mme) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1005

b:10.4
occ:1.00
 OD2 A:ASP34 2.0 4.9 1.0
OD2 A:ASP30 2.2 18.2 1.0
OD1 A:ASP30 2.5 17.6 1.0
CG A:ASP30 2.7 13.7 1.0
CG A:ASP34 3.0 6.0 1.0
OD1 A:ASP34 3.3 7.0 1.0
O A:HOH1021 3.7 13.3 1.0
O A:HOH1224 4.0 23.6 1.0
CB A:ASP30 4.1 14.1 1.0
O A:ASP30 4.2 8.6 1.0
CB A:ASP34 4.3 1.9 1.0
C A:ASP30 4.5 10.2 1.0
CA A:ASP30 4.7 11.2 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 E1001 2011.
ISSN: ISSN 1544-9173
PubMed: 21629676
DOI: 10.1371/JOURNAL.PBIO.1001066
Page generated: Wed Aug 20 12:56:09 2025

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