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Zinc in PDB 3pn6: Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) G41M Mutant

Enzymatic activity of Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) G41M Mutant

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) G41M Mutant:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) G41M Mutant, PDB code: 3pn6 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) 48.56 / 2.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 66.280, 66.280, 194.290, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) G41M Mutant (pdb code 3pn6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) G41M Mutant, PDB code: 3pn6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 3pn6

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Zinc binding site 1 out of 7 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) G41M Mutant


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) G41M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:19.4
occ:1.00
 O A:HOH472 1.9 20.3 1.0
NE2 A:HIS133 2.1 19.1 1.0
NE2 A:HIS137 2.1 18.4 1.0
SG A:CYS91 2.2 17.0 1.0
CD2 A:HIS133 3.0 17.0 1.0
CE1 A:HIS133 3.0 17.7 1.0
CD2 A:HIS137 3.0 15.1 1.0
CE1 A:HIS137 3.1 17.7 1.0
CB A:CYS91 3.2 17.8 1.0
NE2 A:GLN48 3.5 29.6 1.0
O A:HOH329 3.6 18.4 1.0
CA A:CYS91 3.7 18.9 1.0
OE1 A:GLU134 3.8 21.4 1.0
CD A:GLN48 3.9 32.2 1.0
OE1 A:GLN48 4.1 38.4 1.0
ND1 A:HIS133 4.1 18.3 1.0
CG A:HIS133 4.2 17.0 1.0
N A:LEU92 4.2 18.8 1.0
ND1 A:HIS137 4.2 16.5 1.0
CG A:HIS137 4.2 16.6 1.0
C A:CYS91 4.3 18.8 1.0
O A:HOH403 4.5 14.6 1.0
CD A:GLU134 4.6 20.6 1.0
O A:HOH374 4.7 32.5 1.0
CG A:GLN48 4.7 26.1 1.0
N A:SER93 4.8 21.0 1.0
OG A:SER93 4.8 23.4 1.0
O A:GLY90 4.8 18.9 1.0
OE2 A:GLU134 4.9 22.3 1.0
O A:HOH390 5.0 33.7 1.0
N A:CYS91 5.0 19.4 1.0

Zinc binding site 2 out of 7 in 3pn6

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Zinc binding site 2 out of 7 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) G41M Mutant


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) G41M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:0.6
occ:1.00
 OD1 A:ASP40 2.2 33.8 1.0
OE1 A:GLU63 2.7 45.4 1.0
CG A:ASP40 3.0 30.0 1.0
OD2 A:ASP40 3.2 36.5 1.0
NZ B:LYS38 3.3 24.3 1.0
CD A:GLU63 3.9 40.9 1.0
O A:HOH316 4.3 52.2 1.0
OE2 A:GLU63 4.4 44.4 1.0
CE B:LYS38 4.4 26.3 1.0
CB A:ASP40 4.5 23.5 1.0
O A:GLY62 4.6 27.5 1.0
O A:ASP40 4.9 21.7 1.0
O B:HOH305 4.9 30.9 1.0
CA A:ASP40 5.0 22.7 1.0

Zinc binding site 3 out of 7 in 3pn6

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Zinc binding site 3 out of 7 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) G41M Mutant


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) G41M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:50.4
occ:1.00
 O A:HOH479 1.9 29.7 1.0
OE1 A:GLU160 2.3 40.5 1.0
OE2 A:GLU160 2.6 42.5 1.0
CD A:GLU160 2.8 39.1 1.0
OE1 A:GLU179 3.0 44.8 1.0
CD A:GLU179 3.7 46.1 1.0
CG A:GLU179 4.3 44.1 1.0
OE2 A:GLU157 4.3 57.0 1.0
CG A:GLU160 4.3 34.5 1.0
OE2 A:GLU179 4.4 47.1 1.0
OE1 A:GLU157 4.6 54.8 1.0
CD A:GLU157 4.9 53.2 1.0

Zinc binding site 4 out of 7 in 3pn6

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Zinc binding site 4 out of 7 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) G41M Mutant


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) G41M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:20.7
occ:1.00
 O A:HOH484 1.9 19.9 1.0
OE2 B:GLU69 2.0 16.4 1.0
OD1 A:ASP34 2.0 18.1 1.0
OD2 A:ASP30 2.1 23.1 1.0
CD B:GLU69 2.7 21.0 1.0
OE1 B:GLU69 2.8 18.1 1.0
CG A:ASP30 2.8 18.1 1.0
OD1 A:ASP30 2.9 22.3 1.0
CG A:ASP34 3.0 16.3 1.0
OD2 A:ASP34 3.3 15.8 1.0
ZN A:ZN205 3.4 24.7 1.0
O A:HOH332 3.8 23.5 1.0
CE2 B:TYR37 3.9 14.0 1.0
O B:HOH410 4.0 32.8 1.0
O A:HOH418 4.0 36.4 1.0
O A:ASP30 4.0 17.5 1.0
CG B:GLU69 4.2 19.4 1.0
CB A:ASP30 4.2 17.7 1.0
OH B:TYR37 4.4 15.9 1.0
CB A:ASP34 4.4 13.6 1.0
CZ B:TYR37 4.5 15.1 1.0
C A:ASP30 4.5 16.4 1.0
CD2 B:TYR37 4.7 14.7 1.0
CA A:ASP30 4.8 16.1 1.0
CB B:PHE33 4.8 12.3 1.0
O B:HOH381 4.9 30.7 1.0
O B:HOH487 5.0 16.5 1.0

Zinc binding site 5 out of 7 in 3pn6

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Zinc binding site 5 out of 7 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) G41M Mutant


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) G41M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:24.7
occ:1.00
 OD2 A:ASP34 2.0 15.8 1.0
OD2 B:ASP34 2.1 12.6 1.0
O B:HOH487 2.1 16.5 1.0
O A:HOH484 2.2 19.9 1.0
CG A:ASP34 3.1 16.3 1.0
CG B:ASP34 3.2 15.7 1.0
ZN B:ZN202 3.3 16.1 1.0
ZN A:ZN204 3.4 20.7 1.0
O B:HOH410 3.4 32.8 1.0
O A:HOH418 3.5 36.4 1.0
OD1 A:ASP34 3.5 18.1 1.0
OD1 B:ASP34 3.6 15.6 1.0
OD2 B:ASP30 3.8 16.8 1.0
OD2 A:ASP30 3.9 23.1 1.0
CB A:PHE33 4.4 11.9 1.0
CB A:ASP34 4.4 13.6 1.0
CB B:ASP34 4.4 13.8 1.0
O A:ASP30 4.5 17.5 1.0
N A:ASP34 4.5 13.1 1.0
O B:ASP30 4.6 17.2 1.0
CA A:ASP34 4.6 14.0 1.0
CD2 A:TYR37 4.6 14.8 1.0
N B:ASP34 4.6 13.1 1.0
CA B:ASP34 4.6 13.8 1.0
CB B:PHE33 4.7 12.3 1.0
CE2 A:TYR37 4.7 15.2 1.0
CD2 B:TYR37 4.7 14.7 1.0
CG B:ASP30 4.7 18.6 1.0
CE2 B:TYR37 4.8 14.0 1.0
C A:PHE33 4.8 13.2 1.0
CG A:ASP30 4.9 18.1 1.0

Zinc binding site 6 out of 7 in 3pn6

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Zinc binding site 6 out of 7 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) G41M Mutant


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) G41M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:15.3
occ:1.00
 NE2 B:HIS137 2.1 10.9 1.0
O B:HOH482 2.2 17.4 1.0
NE2 B:HIS133 2.2 12.8 1.0
SG B:CYS91 2.2 13.7 1.0
CD2 B:HIS133 3.0 13.8 1.0
CD2 B:HIS137 3.1 9.3 1.0
CE1 B:HIS137 3.1 11.3 1.0
CB B:CYS91 3.2 14.3 1.0
CE1 B:HIS133 3.3 14.5 1.0
NE2 B:GLN48 3.6 10.7 1.0
O B:HOH302 3.6 11.3 1.0
CA B:CYS91 3.9 14.9 1.0
OE1 B:GLN48 3.9 12.9 1.0
CD B:GLN48 4.0 13.4 1.0
O B:HOH411 4.1 19.1 1.0
OE2 B:GLU134 4.1 15.4 1.0
ND1 B:HIS137 4.2 10.8 1.0
CG B:HIS137 4.2 11.5 1.0
CG B:HIS133 4.2 14.5 1.0
ND1 B:HIS133 4.3 13.4 1.0
OE1 B:GLU134 4.4 12.7 1.0
O B:HOH395 4.5 12.4 1.0
CD B:GLU134 4.6 13.8 1.0
N B:LEU92 4.6 13.8 1.0
C B:CYS91 4.6 14.7 1.0
O B:GLY90 4.7 17.0 1.0

Zinc binding site 7 out of 7 in 3pn6

Go back to Zinc Binding Sites List in 3pn6
Zinc binding site 7 out of 7 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) G41M Mutant


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 Petide Deformylase 1B (ATPDF1B) G41M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:16.1
occ:1.00
 O B:HOH487 1.8 16.5 1.0
OD1 B:ASP34 2.0 15.6 1.0
OE2 A:GLU69 2.0 16.9 1.0
OD2 B:ASP30 2.1 16.8 1.0
OD1 B:ASP30 2.5 25.6 1.0
CG B:ASP30 2.6 18.6 1.0
CD A:GLU69 2.7 17.2 1.0
OE1 A:GLU69 2.7 14.7 1.0
CG B:ASP34 2.9 15.7 1.0
OD2 B:ASP34 3.2 12.6 1.0
ZN A:ZN205 3.3 24.7 1.0
O A:HOH402 3.8 26.3 1.0
CE2 A:TYR37 3.8 15.2 1.0
O B:HOH410 4.1 32.8 1.0
CB B:ASP30 4.1 16.7 1.0
CG A:GLU69 4.2 14.6 1.0
O B:ASP30 4.2 17.2 1.0
O A:HOH418 4.2 36.4 1.0
CB B:ASP34 4.3 13.8 1.0
OH A:TYR37 4.3 15.0 1.0
C B:ASP30 4.5 16.4 1.0
CZ A:TYR37 4.5 15.7 1.0
O B:HOH499 4.5 39.1 1.0
CD2 A:TYR37 4.7 14.8 1.0
CA B:ASP30 4.7 16.5 1.0
CB A:PHE33 4.8 11.9 1.0
O A:HOH484 4.9 19.9 1.0
O A:HOH420 5.0 34.0 1.0
CG A:PHE33 5.0 11.0 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 11:34:07 2024

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