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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: Wed Aug 6 02:08:30 2025

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