Atomistry » Iron » PDB 5utd-5ve3 » 5vcp
Atomistry »
  Iron »
    PDB 5utd-5ve3 »
      5vcp »

Iron in PDB 5vcp: Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin

Enzymatic activity of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin

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

Protein crystallography data

The structure of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin, PDB code: 5vcp was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.54 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.110, 90.330, 140.210, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.2

Other elements in 5vcp:

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

Magnesium (Mg) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin (pdb code 5vcp). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin, PDB code: 5vcp:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5vcp

Go back to Iron Binding Sites List in 5vcp
Iron binding site 1 out of 4 in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:41.5
occ:0.92
 NE2 A:HIS145 2.3 34.4 1.0
NE2 A:HIS141 2.4 32.3 1.0
SG A:CYS99 2.4 34.3 1.0
O2 A:BB2202 2.5 51.0 0.9
O4 A:BB2202 2.6 55.2 0.9
C3 A:BB2202 3.1 65.3 0.9
N1 A:BB2202 3.1 54.8 0.9
CD2 A:HIS141 3.1 37.5 1.0
CE1 A:HIS145 3.2 33.2 1.0
CB A:CYS99 3.3 34.0 1.0
CD2 A:HIS145 3.3 30.8 1.0
O A:HOH369 3.4 32.4 1.0
CE1 A:HIS141 3.5 30.8 1.0
NE2 A:GLN51 3.6 31.2 1.0
CA A:CYS99 3.9 32.5 1.0
CD A:GLN51 4.1 34.7 1.0
OE1 A:GLN51 4.3 29.8 1.0
CG A:HIS141 4.3 31.0 1.0
ND1 A:HIS145 4.4 28.2 1.0
C5 A:BB2202 4.4 72.9 0.9
O A:HOH364 4.4 27.6 1.0
CG A:HIS145 4.5 33.8 1.0
N A:LEU100 4.5 35.7 1.0
ND1 A:HIS141 4.5 33.9 1.0
C A:CYS99 4.6 37.8 1.0
C6 A:BB2202 4.7 66.7 0.9
OE1 A:GLU142 4.8 44.5 1.0
OE2 A:GLU142 4.8 42.2 1.0
O A:GLY98 4.9 37.1 1.0

Iron binding site 2 out of 4 in 5vcp

Go back to Iron Binding Sites List in 5vcp
Iron binding site 2 out of 4 in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:43.0
occ:0.93
 NE2 B:HIS141 2.4 33.1 1.0
NE2 B:HIS145 2.4 31.6 1.0
SG B:CYS99 2.4 37.4 1.0
O2 B:BB2202 2.5 38.6 0.9
O4 B:BB2202 2.6 61.6 0.9
N1 B:BB2202 2.8 45.9 0.9
C3 B:BB2202 3.0 60.7 0.9
CD2 B:HIS141 3.1 34.6 1.0
CB B:CYS99 3.3 32.5 1.0
CE1 B:HIS145 3.4 29.4 1.0
NE2 B:GLN51 3.4 28.7 1.0
CD2 B:HIS145 3.4 26.9 1.0
O B:HOH370 3.5 27.5 1.0
CE1 B:HIS141 3.5 36.1 1.0
CA B:CYS99 3.8 39.0 1.0
CD B:GLN51 4.0 34.6 1.0
OE1 B:GLN51 4.2 32.5 1.0
C5 B:BB2202 4.3 62.1 0.9
CG B:HIS141 4.4 34.3 1.0
N B:LEU100 4.4 36.0 1.0
ND1 B:HIS145 4.5 28.3 1.0
ND1 B:HIS141 4.5 38.5 1.0
CG B:HIS145 4.5 31.4 1.0
C B:CYS99 4.6 39.5 1.0
OE2 B:GLU142 4.6 43.5 1.0
O B:HOH350 4.7 28.9 1.0
C6 B:BB2202 4.7 57.9 0.9
OE1 B:GLU142 4.8 41.8 1.0
O B:GLY98 4.9 39.1 1.0

Iron binding site 3 out of 4 in 5vcp

Go back to Iron Binding Sites List in 5vcp
Iron binding site 3 out of 4 in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:39.6
occ:0.85
 NE2 C:HIS141 2.4 35.6 1.0
NE2 C:HIS145 2.4 33.9 1.0
SG C:CYS99 2.4 37.8 1.0
O2 C:BB2202 2.5 35.3 0.8
O4 C:BB2202 2.7 52.5 0.8
N1 C:BB2202 2.7 46.9 0.8
C3 C:BB2202 2.9 56.6 0.8
CD2 C:HIS141 3.1 35.2 1.0
CB C:CYS99 3.2 29.3 1.0
CD2 C:HIS145 3.3 32.3 1.0
CE1 C:HIS145 3.4 38.8 1.0
CE1 C:HIS141 3.5 41.5 1.0
O C:HOH343 3.5 28.7 1.0
NE2 C:GLN51 3.5 31.9 1.0
CA C:CYS99 3.8 33.8 1.0
CD C:GLN51 4.1 34.5 1.0
OE1 C:GLN51 4.3 36.1 1.0
C5 C:BB2202 4.3 56.9 0.8
CG C:HIS141 4.3 36.4 1.0
N C:LEU100 4.4 38.4 1.0
ND1 C:HIS141 4.5 34.6 1.0
CG C:HIS145 4.5 32.3 1.0
C C:CYS99 4.5 38.9 1.0
ND1 C:HIS145 4.5 30.1 1.0
C6 C:BB2202 4.6 62.6 0.8
O C:HOH337 4.6 33.2 1.0
OE2 C:GLU142 4.7 50.7 1.0
O C:GLY98 4.8 44.3 1.0
OE1 C:GLU142 4.8 44.2 1.0

Iron binding site 4 out of 4 in 5vcp

Go back to Iron Binding Sites List in 5vcp
Iron binding site 4 out of 4 in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:45.0
occ:0.85
 NE2 D:HIS141 2.4 39.0 1.0
O2 D:BB2202 2.5 42.5 0.8
NE2 D:HIS145 2.5 32.6 1.0
SG D:CYS99 2.5 40.5 1.0
O4 D:BB2202 2.6 49.5 0.8
C3 D:BB2202 3.1 57.0 0.8
CD2 D:HIS141 3.2 40.1 1.0
N1 D:BB2202 3.2 53.7 0.8
CD2 D:HIS145 3.3 34.0 1.0
CB D:CYS99 3.3 32.0 1.0
O D:HOH353 3.4 30.1 1.0
NE2 D:GLN51 3.4 34.3 1.0
CE1 D:HIS141 3.5 46.7 1.0
CE1 D:HIS145 3.5 38.2 1.0
CA D:CYS99 3.9 34.0 1.0
CD D:GLN51 4.0 40.4 1.0
OE1 D:GLN51 4.2 41.4 1.0
C5 D:BB2202 4.4 62.0 0.8
CG D:HIS141 4.4 34.9 1.0
N D:LEU100 4.5 37.7 1.0
CG D:HIS145 4.5 30.2 1.0
ND1 D:HIS141 4.6 37.0 1.0
O D:HOH319 4.6 29.7 1.0
ND1 D:HIS145 4.6 31.6 1.0
C6 D:BB2202 4.6 64.1 0.8
C D:CYS99 4.7 37.0 1.0
O D:GLY98 4.8 41.1 1.0
OE2 D:GLU142 4.9 53.5 1.0
OE1 D:GLU142 4.9 50.4 1.0

Reference:

D.G.Conrady, J.Abendroth, D.D.Lorimer, T.E.Edwards. Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin To Be Published.
Page generated: Tue Aug 6 10:17:59 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy