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Zinc in PDB 3pn3: Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 21

Enzymatic activity of Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 21

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 21:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 21, PDB code: 3pn3 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) 44.62 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.600, 55.610, 149.530, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 16.9

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 21 (pdb code 3pn3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 15 binding sites of Zinc where determined in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 21, PDB code: 3pn3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 15 in 3pn3

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Zinc binding site 1 out of 15 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 21


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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 Inhibitor 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:6.5
occ:1.00
 O A:HOH1312 2.0 7.0 1.0
NE2 A:HIS133 2.0 7.1 1.0
NE2 A:HIS137 2.1 6.8 1.0
SG A:CYS91 2.3 6.6 1.0
CD2 A:HIS133 3.0 6.4 1.0
CE1 A:HIS133 3.0 7.5 1.0
CD2 A:HIS137 3.1 5.5 1.0
CE1 A:HIS137 3.1 6.5 1.0
CB A:CYS91 3.3 7.4 1.0
NE2 A:GLN48 3.3 7.4 1.0
ZN A:ZN1002 3.5 8.1 1.0
O A:HOH1061 3.6 7.4 1.0
CA A:CYS91 3.7 7.5 1.0
CD A:GLN48 3.8 7.3 1.0
OE1 A:GLN48 3.9 8.1 1.0
OE2 A:GLU134 4.1 8.3 1.0
O A:HOH1221 4.1 10.7 1.0
ND1 A:HIS133 4.1 7.2 1.0
CG A:HIS133 4.1 6.5 1.0
ND1 A:HIS137 4.2 5.7 1.0
CG A:HIS137 4.2 5.8 1.0
N A:LEU92 4.2 7.6 1.0
C A:CYS91 4.3 7.6 1.0
O A:HOH1359 4.5 7.2 1.0
O A:GLY90 4.7 9.2 1.0
N A:SER93 4.8 7.1 1.0
CD A:GLU134 4.9 7.4 1.0
N A:CYS91 4.9 8.2 1.0
OG A:SER93 5.0 7.7 1.0
CG A:GLN48 5.0 7.4 1.0

Zinc binding site 2 out of 15 in 3pn3

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Zinc binding site 2 out of 15 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 21


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 Inhibitor 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:8.1
occ:1.00
 O A:HOH1312 1.9 7.0 1.0
OE2 A:GLU134 1.9 8.3 1.0
O A:HOH1043 1.9 10.6 1.0
OE1 A:GLN48 2.0 8.1 1.0
CD A:GLU134 2.7 7.4 1.0
OE1 A:GLU134 2.9 8.6 1.0
CD A:GLN48 2.9 7.3 1.0
O A:HOH1362 3.2 14.5 1.0
NE2 A:GLN48 3.2 7.4 1.0
ZN A:ZN1001 3.5 6.5 1.0
O A:HOH1221 3.7 10.7 1.0
O A:HOH1238 3.9 11.3 1.0
CD2 A:HIS137 4.0 5.5 1.0
NE2 A:HIS137 4.0 6.8 1.0
O A:GLY43 4.1 7.4 1.0
CG A:GLU134 4.2 7.6 1.0
CG A:GLN48 4.3 7.4 1.0
CD2 A:HIS133 4.3 6.4 1.0
CD1 A:LEU44 4.4 9.0 1.0
O A:HOH1363 4.4 20.6 1.0
NE2 A:HIS133 4.5 7.1 1.0
CA A:LEU44 4.6 6.7 1.0
OG A:SER45 4.7 9.2 1.0
N A:SER45 4.8 6.4 1.0
CB A:GLN48 4.9 7.4 1.0
C A:GLY43 5.0 6.9 1.0

Zinc binding site 3 out of 15 in 3pn3

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Zinc binding site 3 out of 15 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 21


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 Inhibitor 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1005

b:12.0
occ:1.00
 OE1 A:GLU63 1.9 9.9 1.0
OD1 A:ASP40 1.9 9.6 1.0
O A:HOH1316 1.9 14.8 1.0
O A:HOH1315 2.1 17.3 1.0
O A:HOH1040 2.6 12.9 1.0
CG A:ASP40 2.7 10.0 1.0
OD2 A:ASP40 2.7 12.8 1.0
CD A:GLU63 2.9 9.3 1.0
OE2 A:GLU63 3.1 9.9 1.0
NZ B:LYS38 3.7 10.8 1.0
O A:GLY62 3.9 7.9 1.0
O A:HOH1317 4.0 26.6 1.0
CB A:ASP40 4.1 9.0 1.0
CG A:GLU63 4.3 9.0 1.0
O A:ASP40 4.3 8.4 1.0
CA A:ASP40 4.7 8.4 1.0
C A:ASP40 4.9 8.4 1.0
CE B:LYS38 4.9 10.9 1.0
O B:HOH1287 5.0 16.3 1.0
C A:GLY62 5.0 7.8 1.0

Zinc binding site 4 out of 15 in 3pn3

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Zinc binding site 4 out of 15 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 21


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 Inhibitor 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1007

b:9.0
occ:1.00
 OE1 A:GLU179 1.9 17.4 1.0
O A:HOH1319 1.9 10.1 1.0
OE1 A:GLU160 1.9 8.0 1.0
CD A:GLU160 2.8 8.1 1.0
CD A:GLU179 2.9 17.8 1.0
OE2 A:GLU160 3.0 8.4 1.0
CG A:GLU179 3.2 17.7 1.0
O A:HOH1323 3.7 23.3 1.0
O A:HOH1322 3.7 19.1 1.0
OE2 A:GLU179 4.0 19.3 1.0
CG A:GLU160 4.1 8.6 1.0
O A:HOH1321 4.3 41.0 1.0
O A:HOH1320 4.4 29.7 1.0
O A:HOH1604 4.5 0.8 1.0
O A:HOH1118 4.5 11.8 1.0
CB A:GLU179 4.7 17.2 1.0
OE1 A:GLU157 4.7 10.3 1.0
O A:HOH1453 5.0 25.7 1.0

Zinc binding site 5 out of 15 in 3pn3

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Zinc binding site 5 out of 15 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 21


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 Inhibitor 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1009

b:7.3
occ:1.00
 O A:HOH1328 1.9 6.9 1.0
OE1 B:GLU69 1.9 7.5 1.0
OD1 A:ASP30 2.0 9.8 1.0
OD2 A:ASP34 2.0 6.7 1.0
CD B:GLU69 2.7 8.1 1.0
OE2 B:GLU69 2.8 9.1 1.0
CG A:ASP30 2.8 9.7 1.0
OD2 A:ASP30 2.9 11.2 1.0
CG A:ASP34 3.0 6.5 1.0
ZN A:ZN1010 3.2 6.8 1.0
OD1 A:ASP34 3.2 6.4 1.0
CE1 B:TYR37 3.8 7.0 1.0
O A:HOH1075 3.8 10.7 1.0
O A:HOH1331 4.0 15.0 1.0
O B:HOH1329 4.1 14.6 1.0
O A:ASP30 4.1 7.6 1.0
CG B:GLU69 4.1 8.0 1.0
CB A:ASP30 4.2 8.8 1.0
OH B:TYR37 4.2 7.7 1.0
CB A:ASP34 4.4 6.2 1.0
CZ B:TYR37 4.4 6.8 1.0
O B:HOH1271 4.4 33.8 1.0
O A:HOH1150 4.5 39.6 1.0
O B:HOH1330 4.5 7.0 1.0
C A:ASP30 4.5 7.8 1.0
CD1 B:TYR37 4.6 6.6 1.0
CA A:ASP30 4.7 8.2 1.0
CB B:PHE33 4.9 6.5 1.0
OD1 B:ASP34 4.9 6.4 1.0

Zinc binding site 6 out of 15 in 3pn3

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Zinc binding site 6 out of 15 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 21


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) in Complex with Inhibitor 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1010

b:6.8
occ:1.00
 O B:HOH1330 1.9 7.0 1.0
O A:HOH1328 2.0 6.9 1.0
OD1 B:ASP34 2.0 6.4 1.0
OD1 A:ASP34 2.0 6.4 1.0
CG A:ASP34 3.0 6.5 1.0
CG B:ASP34 3.0 5.9 1.0
ZN A:ZN1009 3.2 7.3 1.0
ZN B:ZN1011 3.2 7.2 1.0
OD2 B:ASP34 3.4 6.6 1.0
OD2 A:ASP34 3.4 6.7 1.0
O B:HOH1329 3.7 14.6 1.0
O A:HOH1331 3.7 15.0 1.0
OD1 B:ASP30 3.9 9.7 1.0
OD1 A:ASP30 3.9 9.8 1.0
CB A:ASP34 4.3 6.2 1.0
CB B:ASP34 4.4 6.1 1.0
CD1 B:TYR37 4.4 6.6 1.0
CD1 A:TYR37 4.5 6.5 1.0
CE1 B:TYR37 4.5 7.0 1.0
CE1 A:TYR37 4.5 6.9 1.0
CA A:ASP34 4.6 6.2 1.0
CA B:ASP34 4.6 6.0 1.0
O B:ASP30 4.6 7.5 1.0
CB B:PHE33 4.6 6.5 1.0
O A:ASP30 4.6 7.6 1.0
N B:ASP34 4.6 5.9 1.0
N A:ASP34 4.6 6.1 1.0
CB A:PHE33 4.6 6.6 1.0
OE1 B:GLU69 4.8 7.5 1.0
OE1 A:GLU69 4.8 7.5 1.0
C B:PHE33 4.9 5.9 1.0
C A:PHE33 4.9 6.1 1.0

Zinc binding site 7 out of 15 in 3pn3

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Zinc binding site 7 out of 15 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 21


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) in Complex with Inhibitor 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1012

b:8.4
occ:1.00
 N A:MET1 2.1 8.5 1.0
O A:MET1 2.2 8.9 1.0
C A:MET1 2.9 9.2 1.0
CA A:MET1 3.0 8.9 1.0
OE1 B:GLU66 3.7 9.4 1.0
O B:HOH1016 4.0 10.6 1.0
N A:GLU2 4.1 10.0 1.0
O A:HOH1375 4.2 16.9 1.0
O A:HOH1568 4.2 25.0 1.0
CB A:MET1 4.3 8.8 1.0
CD B:GLU66 4.6 9.6 1.0
CA A:GLU2 4.8 11.9 1.0
CB A:GLU2 4.9 12.2 1.0

Zinc binding site 8 out of 15 in 3pn3

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Zinc binding site 8 out of 15 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 21


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 Petide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1014

b:13.2
occ:1.00
 O A:HOH1556 2.0 13.0 1.0
O A:HOH1555 2.0 20.7 1.0
O4 A:PN3194 2.0 11.5 1.0
O2 A:PN3194 2.1 13.4 1.0
O A:HOH1553 2.1 18.2 1.0
O A:HOH1554 2.2 14.9 1.0
N3 A:PN3194 2.8 11.9 1.0
C1 A:PN3194 2.8 13.3 1.0
O A:HOH1435 4.1 12.8 1.0
O16 A:PN3194 4.1 10.9 1.0
O A:HOH1059 4.1 35.1 1.0
NH1 A:ARG146 4.2 10.1 1.0
OE2 A:GLU139 4.2 14.1 1.0
C5 A:PN3194 4.2 10.9 1.0
O A:HOH1360 4.3 15.0 1.0
O A:HOH1387 4.3 30.5 1.0
C6 A:PN3194 4.9 10.0 1.0
C15 A:PN3194 4.9 10.8 1.0
NH2 A:ARG146 4.9 11.0 1.0
CZ A:ARG146 5.0 10.4 1.0

Zinc binding site 9 out of 15 in 3pn3

Go back to Zinc Binding Sites List in 3pn3
Zinc binding site 9 out of 15 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 21


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 Petide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1003

b:6.6
occ:1.00
 O B:HOH1313 2.0 6.7 1.0
NE2 B:HIS133 2.0 6.9 1.0
NE2 B:HIS137 2.1 6.3 1.0
SG B:CYS91 2.3 6.7 1.0
CD2 B:HIS133 3.0 6.3 1.0
CE1 B:HIS133 3.0 7.7 1.0
CD2 B:HIS137 3.1 5.6 1.0
CE1 B:HIS137 3.1 6.5 1.0
CB B:CYS91 3.3 7.5 1.0
NE2 B:GLN48 3.3 7.4 1.0
ZN B:ZN1004 3.5 8.1 1.0
O B:HOH1078 3.6 7.5 1.0
CA B:CYS91 3.7 7.5 1.0
CD B:GLN48 3.8 7.4 1.0
OE1 B:GLN48 3.9 8.2 1.0
OE1 B:GLU134 4.1 8.4 1.0
ND1 B:HIS133 4.1 7.4 1.0
O B:HOH1365 4.1 10.7 1.0
CG B:HIS133 4.1 6.7 1.0
ND1 B:HIS137 4.2 5.9 1.0
CG B:HIS137 4.2 5.7 1.0
N B:LEU92 4.2 7.5 1.0
C B:CYS91 4.3 7.5 1.0
O B:HOH1364 4.5 7.0 1.0
O B:GLY90 4.7 9.3 1.0
N B:SER93 4.9 7.1 1.0
N B:CYS91 4.9 8.1 1.0
CD B:GLU134 5.0 7.6 1.0
CG B:GLN48 5.0 7.6 1.0
OG B:SER93 5.0 7.5 1.0

Zinc binding site 10 out of 15 in 3pn3

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Zinc binding site 10 out of 15 in the Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Arabidopsis Thaliana Petide Deformylase 1B (ATPDF1B) in Complex with Inhibitor 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1004

b:8.1
occ:1.00
 O B:HOH1313 1.9 6.7 1.0
OE1 B:GLU134 1.9 8.4 1.0
O B:HOH1079 1.9 10.7 1.0
OE1 B:GLN48 2.0 8.2 1.0
CD B:GLU134 2.7 7.6 1.0
OE2 B:GLU134 2.9 8.4 1.0
CD B:GLN48 2.9 7.4 1.0
O B:HOH1366 3.2 15.1 1.0
NE2 B:GLN48 3.2 7.4 1.0
ZN B:ZN1003 3.5 6.6 1.0
O B:HOH1365 3.7 10.7 1.0
O B:HOH1314 4.0 11.6 1.0
CD2 B:HIS137 4.0 5.6 1.0
NE2 B:HIS137 4.0 6.3 1.0
O B:GLY43 4.1 7.1 1.0
CG B:GLU134 4.2 7.4 1.0
CG B:GLN48 4.3 7.6 1.0
CD2 B:HIS133 4.3 6.3 1.0
CD1 B:LEU44 4.4 8.7 1.0
O B:HOH1367 4.4 20.8 1.0
NE2 B:HIS133 4.4 6.9 1.0
CA B:LEU44 4.6 6.8 1.0
OG B:SER45 4.7 9.4 1.0
N B:SER45 4.8 6.8 1.0
CB B:GLN48 4.9 7.3 1.0
C B:GLY43 5.0 6.8 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 11:31:37 2024

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