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Iron in PDB 5hgw: Crystal Structure of A Peptide Deformylase From Burkholderia Ambifaria

Enzymatic activity of Crystal Structure of A Peptide Deformylase From Burkholderia Ambifaria

All present enzymatic activity of Crystal Structure of A Peptide Deformylase From Burkholderia Ambifaria:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of A Peptide Deformylase From Burkholderia Ambifaria, PDB code: 5hgw 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) 50.00 / 1.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 116.690, 121.350, 71.290, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 17.8

Iron Binding Sites:

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

Iron binding site 1 out of 2 in 5hgw

Go back to Iron Binding Sites List in 5hgw
Iron binding site 1 out of 2 in the Crystal Structure of A Peptide Deformylase From Burkholderia Ambifaria


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 Ambifaria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:12.0
occ:0.68
NE2 A:HIS145 2.1 13.0 1.0
O A:HOH311 2.2 18.8 1.0
SG A:CYS99 2.2 13.0 1.0
NE2 A:HIS141 2.2 16.0 1.0
CD2 A:HIS141 3.0 16.2 1.0
CE1 A:HIS145 3.1 12.9 1.0
CD2 A:HIS145 3.2 11.1 1.0
CB A:CYS99 3.2 8.9 1.0
CE1 A:HIS141 3.2 15.8 1.0
O A:HOH393 3.5 14.7 1.0
O1 A:SO4201 3.7 16.9 0.9
NE2 A:GLN51 3.8 13.3 1.0
CA A:CYS99 3.8 9.8 1.0
ND1 A:HIS145 4.2 11.6 1.0
CG A:HIS141 4.2 13.0 1.0
CD A:GLN51 4.2 12.1 1.0
O A:HOH441 4.3 10.7 1.0
ND1 A:HIS141 4.3 14.5 1.0
CG A:HIS145 4.3 10.7 1.0
OE1 A:GLN51 4.3 12.1 1.0
N A:LEU100 4.4 10.0 1.0
C A:CYS99 4.5 9.2 1.0
OE2 A:GLU142 4.5 18.2 1.0
O A:GLY98 4.6 12.9 1.0
O2 A:SO4201 4.7 22.0 0.9
OE1 A:GLU142 4.7 20.5 1.0
S A:SO4201 4.7 17.1 0.9
CD A:GLU142 4.9 14.9 1.0
N A:SER101 5.0 11.9 1.0

Iron binding site 2 out of 2 in 5hgw

Go back to Iron Binding Sites List in 5hgw
Iron binding site 2 out of 2 in the Crystal Structure of A Peptide Deformylase From Burkholderia Ambifaria


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 Ambifaria within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe200

b:11.4
occ:0.70
NE2 B:HIS145 2.1 10.8 1.0
SG B:CYS99 2.2 14.6 1.0
NE2 B:HIS141 2.2 11.2 1.0
O B:HOH311 2.2 20.2 1.0
CD2 B:HIS141 3.0 13.7 1.0
CE1 B:HIS145 3.1 12.9 1.0
CD2 B:HIS145 3.1 9.5 1.0
CB B:CYS99 3.2 12.9 1.0
CE1 B:HIS141 3.3 13.1 1.0
O B:HOH388 3.5 11.9 1.0
O4 B:SO4201 3.6 38.0 0.8
NE2 B:GLN51 3.7 11.4 1.0
CA B:CYS99 3.8 13.4 1.0
CD B:GLN51 4.1 11.0 1.0
OE1 B:GLN51 4.1 12.2 1.0
CG B:HIS141 4.2 11.0 1.0
ND1 B:HIS145 4.2 10.2 1.0
CG B:HIS145 4.3 9.8 1.0
ND1 B:HIS141 4.3 12.1 1.0
O B:HOH410 4.3 9.5 1.0
OE2 B:GLU142 4.4 14.7 1.0
N B:LEU100 4.5 13.0 1.0
C B:CYS99 4.6 14.4 1.0
O B:GLY98 4.6 16.6 1.0
OE1 B:GLU142 4.7 14.8 1.0
S B:SO4201 4.8 29.8 0.8
O2 B:SO4201 4.8 30.4 0.8
CD B:GLU142 4.8 11.9 1.0

Reference:

Seattle Structural Genomics Center For Infectious Disease(Ssgcid), J.Abendroth, S.J.Mayclin, D.D.Lorimer, T.E.Edwards. Crystal Structure of A Peptide Deformylase From Burkholderia Ambifaria To Be Published.
Page generated: Tue Aug 6 01:52:32 2024

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