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Zinc in PDB 3pn2: Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) (Crystallized in Peg-550-Mme)

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

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

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) (Crystallized in Peg-550-Mme), PDB code: 3pn2 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) 30.00 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 56.320, 56.320, 148.440, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 25.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) (Crystallized in Peg-550-Mme) (pdb code 3pn2). 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 Petide Deformylase 1B (ATPDF1B) (Crystallized in Peg-550-Mme), PDB code: 3pn2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3pn2

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Zinc binding site 1 out of 6 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) (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) (Crystallized in Peg-550-Mme) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:42.5
occ:1.00
 O A:HOH1214 1.8 34.7 1.0
NE2 A:HIS133 2.0 30.7 1.0
NE2 A:HIS137 2.2 35.5 1.0
SG A:CYS91 2.2 27.8 1.0
CD2 A:HIS133 2.9 27.9 1.0
CE1 A:HIS133 3.0 29.3 1.0
CE1 A:HIS137 3.1 30.8 1.0
CD2 A:HIS137 3.2 31.1 1.0
CB A:CYS91 3.2 27.2 1.0
O A:HOH1116 3.4 35.8 1.0
NE2 A:GLN48 3.6 35.6 1.0
CA A:CYS91 3.7 26.6 1.0
ZN A:ZN1002 3.7 0.3 1.0
CG A:HIS133 4.1 29.8 1.0
OE1 A:GLU134 4.1 41.2 1.0
ND1 A:HIS133 4.1 30.1 1.0
ND1 A:HIS137 4.2 34.6 1.0
CG A:HIS137 4.3 30.4 1.0
N A:LEU92 4.4 23.5 1.0
O A:HOH1195 4.4 34.8 1.0
C A:CYS91 4.4 25.6 1.0
CD A:GLN48 4.4 38.4 1.0
O A:GLY90 4.7 29.8 1.0
N A:CYS91 5.0 28.2 1.0
N A:SER93 5.0 23.8 1.0

Zinc binding site 2 out of 6 in 3pn2

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Zinc binding site 2 out of 6 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) (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) (Crystallized in Peg-550-Mme) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:0.3
occ:1.00
 O A:HOH1214 2.2 34.7 1.0
OE2 A:GLU134 2.5 40.5 1.0
OE1 A:GLU134 2.5 41.2 1.0
CD A:GLU134 2.8 39.9 1.0
OE1 A:GLN48 2.9 43.8 1.0
CD A:GLN48 3.0 38.4 1.0
O A:HOH1050 3.0 44.9 1.0
NE2 A:GLN48 3.4 35.6 1.0
CG A:GLN48 3.4 39.7 1.0
CD2 A:HIS137 3.6 31.1 1.0
NE2 A:HIS137 3.7 35.5 1.0
ZN A:ZN1001 3.7 42.5 1.0
CD1 A:LEU44 4.1 34.4 1.0
CB A:GLN48 4.3 32.7 1.0
CG A:GLU134 4.3 36.2 1.0
OG A:SER45 4.4 38.4 1.0
O A:GLY43 4.4 31.9 1.0
CA A:LEU44 4.5 32.7 1.0
N A:SER45 4.5 34.8 1.0
CG A:HIS137 4.6 30.4 1.0
CE1 A:HIS137 4.7 30.8 1.0
CD2 A:HIS133 4.7 27.9 1.0
NE2 A:HIS133 4.8 30.7 1.0

Zinc binding site 3 out of 6 in 3pn2

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Zinc binding site 3 out of 6 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) (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) (Crystallized in Peg-550-Mme) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:41.9
occ:1.00
 O A:HOH1060 1.9 35.3 1.0
O A:HOH1059 1.9 44.8 1.0
OD1 A:ASP40 2.0 32.3 1.0
OE1 A:GLU63 2.1 37.5 1.0
OD2 A:ASP40 2.7 31.5 1.0
CG A:ASP40 2.7 31.5 1.0
O A:HOH1058 2.7 36.7 1.0
CD A:GLU63 3.0 36.0 1.0
OE2 A:GLU63 3.2 30.6 1.0
O A:GLY62 3.9 31.6 1.0
CB A:ASP40 4.2 28.5 1.0
O A:ASP40 4.3 28.3 1.0
CG A:GLU63 4.3 32.4 1.0
CA A:ASP40 4.8 28.3 1.0
C A:ASP40 4.9 28.5 1.0
C A:GLY62 5.0 33.9 1.0

Zinc binding site 4 out of 6 in 3pn2

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Zinc binding site 4 out of 6 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) (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) (Crystallized in Peg-550-Mme) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1004

b:33.8
occ:1.00
 OE2 A:GLU160 1.7 24.1 1.0
OE1 A:GLU179 2.0 40.8 1.0
O A:HOH1150 2.2 46.0 1.0
CD A:GLU160 2.7 30.1 1.0
CD A:GLU179 2.9 44.4 1.0
OE1 A:GLU160 3.0 25.2 1.0
CG A:GLU179 3.1 45.9 1.0
O A:HOH1201 3.8 49.7 1.0
OE2 A:GLU179 4.0 47.5 1.0
CG A:GLU160 4.1 26.8 1.0
O A:HOH1132 4.5 31.0 1.0
CB A:GLU179 4.6 48.0 1.0
OE1 A:GLU157 4.7 28.0 1.0

Zinc binding site 5 out of 6 in 3pn2

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Zinc binding site 5 out of 6 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) (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) (Crystallized in Peg-550-Mme) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1005

b:40.0
occ:1.00
 OD2 A:ASP34 2.0 36.5 1.0
OD1 A:ASP30 2.1 44.2 1.0
CG A:ASP30 2.8 40.1 1.0
OD2 A:ASP30 2.8 38.8 1.0
CG A:ASP34 3.0 35.5 1.0
OD1 A:ASP34 3.3 34.0 1.0
O A:HOH1046 4.0 34.8 1.0
O A:ASP30 4.1 36.6 1.0
CB A:ASP30 4.2 41.6 1.0
O A:HOH1045 4.3 53.0 1.0
CB A:ASP34 4.4 30.1 1.0
C A:ASP30 4.5 37.6 1.0
CA A:ASP30 4.8 39.9 1.0

Zinc binding site 6 out of 6 in 3pn2

Go back to Zinc Binding Sites List in 3pn2
Zinc binding site 6 out of 6 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) (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 6 of Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) (Crystallized in Peg-550-Mme) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1006

b:36.1
occ:1.00
 N A:MET1 1.9 25.4 1.0
O A:MET1 2.1 27.6 1.0
C A:MET1 2.8 27.8 1.0
CA A:MET1 2.9 28.8 1.0
N A:GLU2 4.0 26.8 1.0
CB A:MET1 4.2 26.6 1.0
O A:HOH1008 4.6 55.7 1.0
CB A:GLU2 4.6 31.5 1.0
CA A:GLU2 4.7 29.9 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: Sat Oct 26 11:31:37 2024

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