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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

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