Atomistry » Zinc » PDB 4dr3-4dz7 » 4dr9
Atomistry »
  Zinc »
    PDB 4dr3-4dz7 »
      4dr9 »

Zinc in PDB 4dr9: Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin

Enzymatic activity of Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin

All present enzymatic activity of Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin, PDB code: 4dr9 was solved by D.Lorimer, J.Abendroth, T.Craig, A.Burgin, A.Segall, F.Rohwler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 43.250, 65.780, 68.290, 80.87, 76.82, 82.75
R / Rfree (%) 18.2 / 23.5

Other elements in 4dr9:

The structure of Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin also contains other interesting chemical elements:

Bromine (Br) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin (pdb code 4dr9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin, PDB code: 4dr9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4dr9

Go back to Zinc Binding Sites List in 4dr9
Zinc binding site 1 out of 4 in the Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin


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 A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:10.3
occ:1.00
 O4 A:BB2203 2.1 13.7 1.0
NE2 A:HIS155 2.1 6.4 1.0
NE2 A:HIS151 2.1 6.6 1.0
O2 A:BB2203 2.2 14.6 1.0
SG A:CYS109 2.3 7.9 1.0
C3 A:BB2203 2.8 14.1 1.0
N1 A:BB2203 2.9 14.2 1.0
CE1 A:HIS155 3.0 6.7 1.0
CD2 A:HIS151 3.0 6.3 1.0
CD2 A:HIS155 3.1 6.4 1.0
CE1 A:HIS151 3.2 6.8 1.0
CB A:CYS109 3.3 8.4 1.0
NE2 A:GLN66 3.4 8.8 1.0
O A:HOH304 3.5 7.7 1.0
CA A:CYS109 3.8 8.8 1.0
CD A:GLN66 3.8 9.0 1.0
OE1 A:GLN66 3.9 9.3 1.0
ND1 A:HIS155 4.1 6.7 1.0
C5 A:BB2203 4.2 15.0 1.0
CG A:HIS151 4.2 6.3 1.0
CG A:HIS155 4.2 6.5 1.0
ND1 A:HIS151 4.3 6.8 1.0
N A:LEU110 4.3 9.2 1.0
C A:CYS109 4.5 9.3 1.0
C6 A:BB2203 4.5 14.8 1.0
O A:HOH302 4.5 7.7 1.0
OE1 A:GLU152 4.7 9.0 1.0
O A:GLY108 4.8 9.7 1.0
OE2 A:GLU152 4.9 10.3 1.0
N A:SER111 4.9 9.6 1.0
CG A:GLN66 4.9 9.2 1.0
C7 A:BB2203 5.0 15.1 1.0

Zinc binding site 2 out of 4 in 4dr9

Go back to Zinc Binding Sites List in 4dr9
Zinc binding site 2 out of 4 in the Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin


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 A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:11.9
occ:1.00
 NE2 B:HIS155 2.1 7.9 1.0
NE2 B:HIS151 2.1 8.5 1.0
O4 B:BB2203 2.1 14.7 1.0
SG B:CYS109 2.3 8.5 1.0
O2 B:BB2203 2.3 14.0 1.0
C3 B:BB2203 2.8 14.9 1.0
N1 B:BB2203 2.9 13.9 1.0
CD2 B:HIS151 3.0 8.2 1.0
CD2 B:HIS155 3.1 7.6 1.0
CE1 B:HIS155 3.1 8.2 1.0
CE1 B:HIS151 3.2 8.9 1.0
CB B:CYS109 3.3 9.3 1.0
NE2 B:GLN66 3.4 9.8 1.0
O B:HOH306 3.6 6.5 1.0
CA B:CYS109 3.8 9.8 1.0
CD B:GLN66 3.9 9.5 1.0
OE1 B:GLN66 4.0 10.3 1.0
N B:LEU110 4.2 10.1 1.0
C5 B:BB2203 4.2 15.0 1.0
CG B:HIS151 4.2 8.2 1.0
ND1 B:HIS155 4.2 8.1 1.0
CG B:HIS155 4.3 7.7 1.0
ND1 B:HIS151 4.3 8.9 1.0
C B:CYS109 4.4 10.2 1.0
O B:HOH314 4.5 8.2 1.0
C6 B:BB2203 4.6 15.6 1.0
OE1 B:GLU152 4.7 12.2 1.0
O B:GLY108 4.8 10.7 1.0
CG B:GLN66 5.0 9.1 1.0
OE2 B:GLU152 5.0 12.5 1.0
N B:SER111 5.0 10.4 1.0

Zinc binding site 3 out of 4 in 4dr9

Go back to Zinc Binding Sites List in 4dr9
Zinc binding site 3 out of 4 in the Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin


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 A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:14.9
occ:1.00
 NE2 C:HIS155 2.1 11.0 1.0
NE2 C:HIS151 2.1 11.1 1.0
O4 C:BB2204 2.2 15.1 1.0
SG C:CYS109 2.4 11.8 1.0
O2 C:BB2204 2.4 15.5 1.0
C3 C:BB2204 2.9 16.0 1.0
CD2 C:HIS151 2.9 11.0 1.0
N1 C:BB2204 3.0 15.6 1.0
CD2 C:HIS155 3.1 10.9 1.0
CE1 C:HIS155 3.2 11.4 1.0
CE1 C:HIS151 3.3 11.2 1.0
NE2 C:GLN66 3.3 10.8 1.0
CB C:CYS109 3.3 11.9 1.0
O C:HOH304 3.5 7.3 1.0
CA C:CYS109 3.8 12.1 1.0
CD C:GLN66 3.9 11.2 1.0
OE1 C:GLN66 4.1 10.9 1.0
CG C:HIS151 4.2 11.0 1.0
N C:LEU110 4.2 12.3 1.0
C5 C:BB2204 4.3 16.8 1.0
CG C:HIS155 4.3 11.2 1.0
ND1 C:HIS151 4.3 11.3 1.0
ND1 C:HIS155 4.3 11.6 1.0
O C:HOH301 4.4 7.6 1.0
C C:CYS109 4.5 12.4 1.0
OE1 C:GLU152 4.5 12.3 1.0
C6 C:BB2204 4.6 17.1 1.0
O C:GLY108 4.9 12.6 1.0
OE2 C:GLU152 5.0 12.6 1.0
CG C:GLN66 5.0 11.7 1.0

Zinc binding site 4 out of 4 in 4dr9

Go back to Zinc Binding Sites List in 4dr9
Zinc binding site 4 out of 4 in the Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin


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 A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:12.6
occ:1.00
 NE2 D:HIS155 2.1 7.8 1.0
NE2 D:HIS151 2.1 7.5 1.0
O4 D:BB2203 2.2 13.1 1.0
SG D:CYS109 2.3 8.2 1.0
O2 D:BB2203 2.3 13.9 1.0
C3 D:BB2203 2.9 13.7 1.0
CD2 D:HIS151 2.9 7.5 1.0
CD2 D:HIS155 3.1 7.9 1.0
N1 D:BB2203 3.1 13.7 1.0
CE1 D:HIS155 3.1 8.1 1.0
CE1 D:HIS151 3.2 7.7 1.0
CB D:CYS109 3.2 8.6 1.0
NE2 D:GLN66 3.3 9.2 1.0
O D:HOH302 3.5 8.1 1.0
CA D:CYS109 3.8 9.1 1.0
CD D:GLN66 3.9 9.3 1.0
OE1 D:GLN66 4.0 9.6 1.0
CG D:HIS151 4.2 7.2 1.0
N D:LEU110 4.2 9.8 1.0
CG D:HIS155 4.3 8.0 1.0
ND1 D:HIS155 4.3 8.1 1.0
C5 D:BB2203 4.3 13.9 1.0
ND1 D:HIS151 4.3 7.4 1.0
C D:CYS109 4.4 9.5 1.0
O D:HOH312 4.6 6.0 1.0
C6 D:BB2203 4.6 14.0 1.0
OE1 D:GLU152 4.7 9.8 1.0
O D:GLY108 4.9 10.1 1.0
N D:SER111 4.9 9.8 1.0
CG D:GLN66 4.9 9.5 1.0
N D:CYS109 5.0 9.5 1.0

Reference:

J.A.Frank, D.Lorimer, M.Youle, P.Witte, T.Craig, J.Abendroth, F.Rohwer, R.A.Edwards, A.M.Segall, A.B.Burgin. Structure and Function of A Cyanophage-Encoded Peptide Deformylase. Isme J V. 7 1150 2013.
ISSN: ISSN 1751-7362
PubMed: 23407310
DOI: 10.1038/ISMEJ.2013.4
Page generated: Sat Oct 26 21:35:17 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy