Atomistry » Iron » PDB 3m38-3mma » 3mi1
Atomistry »
  Iron »
    PDB 3m38-3mma »
      3mi1 »

Iron in PDB 3mi1: Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase

Enzymatic activity of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase

All present enzymatic activity of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase:
1.13.11.3;

Protein crystallography data

The structure of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase, PDB code: 3mi1 was solved by V.M.Purpero, J.D.Lipscomb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.52 / 1.74
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 128.046, 140.876, 168.048, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 17.4

Other elements in 3mi1:

The structure of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase (pdb code 3mi1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase, PDB code: 3mi1:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 3mi1

Go back to Iron Binding Sites List in 3mi1
Iron binding site 1 out of 3 in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe600

b:24.8
occ:0.45
O A:HOH1055 2.6 27.3 1.0
O M:HOH1067 2.6 23.6 1.0
OH M:TYR462 2.7 17.7 1.0
NH1 M:ARG457 3.4 15.3 1.0
NE2 M:GLN477 3.4 13.1 1.0
CA A:GLY14 3.6 13.9 1.0
CG2 A:THR12 3.7 14.0 1.0
CZ M:TYR462 3.7 14.7 1.0
CD1 M:ILE491 3.8 16.3 1.0
CE1 M:TYR462 3.8 14.7 1.0
O A:HOH1084 4.1 23.6 0.5
CD M:GLN477 4.2 16.3 1.0
CD A:PRO15 4.2 16.0 1.0
O M:HOH1093 4.2 27.4 1.0
OE1 M:GLN477 4.2 15.1 1.0
N A:GLY14 4.3 13.9 1.0
O1 A:SO4203 4.4 30.4 0.7
O A:THR12 4.5 13.2 1.0
CZ M:ARG457 4.5 15.1 1.0
NE2 M:HIS460 4.8 16.1 1.0
C A:GLY14 4.9 14.3 1.0
OH M:TYR324 4.9 15.2 1.0
OH M:TYR447 4.9 16.5 1.0
CG2 M:ILE491 5.0 15.7 1.0
CB A:THR12 5.0 13.2 1.0

Iron binding site 2 out of 3 in 3mi1

Go back to Iron Binding Sites List in 3mi1
Iron binding site 2 out of 3 in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe600

b:24.2
occ:0.45
O N:HOH1077 2.7 27.4 1.0
OH N:TYR462 2.7 18.3 1.0
O B:HOH1060 3.0 33.2 1.0
NH2 N:ARG457 3.3 16.7 1.0
NE2 N:GLN477 3.4 14.3 1.0
CZ N:TYR462 3.7 14.1 1.0
CA B:GLY14 3.7 15.8 1.0
CG2 B:THR12 3.7 14.5 1.0
CE1 N:TYR462 3.8 13.1 1.0
CD1 N:ILE491 3.8 16.4 1.0
CD N:GLN477 4.1 17.4 1.0
OE1 N:GLN477 4.1 16.2 1.0
CD B:PRO15 4.2 18.4 1.0
O N:HOH1198 4.2 23.7 0.5
N B:GLY14 4.3 15.2 1.0
CZ N:ARG457 4.4 17.1 1.0
O B:THR12 4.6 13.0 1.0
O4 B:SO4202 4.6 32.0 0.7
NE2 N:HIS460 4.7 16.2 1.0
OH N:TYR447 4.9 17.9 1.0
C B:GLY14 4.9 16.5 1.0
OH N:TYR324 4.9 14.8 1.0
CE2 N:TYR462 5.0 13.9 1.0
CG2 N:ILE491 5.0 17.0 1.0
O N:HOH1236 5.0 33.8 1.0
CB B:THR12 5.0 12.9 1.0

Iron binding site 3 out of 3 in 3mi1

Go back to Iron Binding Sites List in 3mi1
Iron binding site 3 out of 3 in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe600

b:24.0
occ:0.45
OH O:TYR462 2.6 20.6 1.0
O O:HOH1078 2.7 26.1 1.0
O C:HOH1058 2.7 30.2 1.0
NH1 O:ARG457 3.4 15.3 1.0
NE2 O:GLN477 3.4 14.9 1.0
CA C:GLY14 3.6 14.6 1.0
CZ O:TYR462 3.7 16.0 1.0
CG2 C:THR12 3.7 14.7 1.0
CD1 O:ILE491 3.8 17.3 1.0
CE1 O:TYR462 3.8 14.8 1.0
O C:HOH665 4.0 35.3 1.0
CD O:GLN477 4.1 15.4 1.0
OE1 O:GLN477 4.1 17.5 1.0
O O:HOH11 4.2 28.5 1.0
CD C:PRO15 4.2 16.8 1.0
N C:GLY14 4.2 13.8 1.0
O4 C:SO4202 4.4 32.8 0.8
CZ O:ARG457 4.5 15.4 1.0
O C:THR12 4.5 13.5 1.0
NE2 O:HIS460 4.7 15.7 1.0
OH O:TYR447 4.9 17.1 1.0
C C:GLY14 4.9 15.6 1.0
CE2 O:TYR462 4.9 15.1 1.0
OH O:TYR324 4.9 14.3 1.0
O O:HOH835 5.0 31.0 1.0
CG2 O:ILE491 5.0 15.2 1.0
CB C:THR12 5.0 14.0 1.0
C C:ALA13 5.0 13.3 1.0

Reference:

V.M.Purpero, J.D.Lipscomb. Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase To Be Published.
Page generated: Sun Aug 4 14:48:17 2024

Last articles

F in 5JI6
F in 5JCZ
F in 5JHB
F in 5JHA
F in 5JFO
F in 5JFS
F in 5JCP
F in 5JFR
F in 5JEI
F in 5JAJ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy