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Iron in PDB 4l2n: Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - Ligand-Free Structure

Enzymatic activity of Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - Ligand-Free Structure

All present enzymatic activity of Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - Ligand-Free Structure:
1.13.11.6;

Protein crystallography data

The structure of Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - Ligand-Free Structure, PDB code: 4l2n was solved by F.Liu, A.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.13 / 1.74
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.340, 58.340, 231.426, 90.00, 90.00, 120.00
R / Rfree (%) 21.1 / 25.4

Other elements in 4l2n:

The structure of Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - Ligand-Free Structure also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - Ligand-Free Structure (pdb code 4l2n). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - Ligand-Free Structure, PDB code: 4l2n:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 4l2n

Go back to Iron Binding Sites List in 4l2n
Iron binding site 1 out of 2 in the Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - Ligand-Free Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - Ligand-Free Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:21.2
occ:1.00
 NE2 A:HIS95 2.2 20.2 1.0
OE2 A:GLU57 2.2 23.3 1.0
ND1 A:HIS51 2.2 23.6 1.0
O A:HOH305 2.3 31.2 1.0
O A:HOH308 2.7 34.9 1.0
OE1 A:GLU57 2.7 22.6 1.0
CD A:GLU57 2.8 24.8 1.0
CE1 A:HIS95 3.0 19.9 1.0
CE1 A:HIS51 3.2 22.4 1.0
CG A:HIS51 3.2 24.7 1.0
CD2 A:HIS95 3.2 21.9 1.0
O A:HOH417 3.4 40.4 1.0
CB A:HIS51 3.5 21.6 1.0
ND1 A:HIS95 4.2 20.6 1.0
OE1 A:GLU110 4.2 41.1 1.0
CG A:GLU57 4.3 21.7 1.0
NE2 A:HIS51 4.3 23.6 1.0
CG A:HIS95 4.3 20.3 1.0
CD2 A:HIS51 4.3 24.6 1.0
OD2 A:ASP53 4.4 22.6 1.0
CB A:ASP53 4.6 23.0 1.0
O A:HOH416 4.6 41.5 1.0
CA A:HIS51 4.9 22.4 1.0
CG A:ASP53 5.0 23.8 1.0

Iron binding site 2 out of 2 in 4l2n

Go back to Iron Binding Sites List in 4l2n
Iron binding site 2 out of 2 in the Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - Ligand-Free Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - Ligand-Free Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:34.5
occ:1.00
 SG A:CYS162 2.5 37.4 1.0
SG A:CYS165 2.5 40.8 1.0
SG A:CYS125 2.6 37.4 1.0
SG A:CYS128 2.7 47.9 1.0
CB A:CYS125 3.1 38.0 1.0
CB A:CYS162 3.2 31.8 1.0
CB A:CYS165 3.3 46.5 1.0
CB A:CYS128 3.5 44.9 1.0
N A:CYS165 3.8 44.5 1.0
N A:CYS128 3.8 40.8 1.0
CA A:CYS165 4.0 43.5 1.0
CA A:CYS128 4.2 41.5 1.0
CB A:HIS164 4.5 47.8 1.0
CA A:CYS125 4.6 32.8 1.0
C A:CYS165 4.7 42.2 1.0
CA A:CYS162 4.7 33.0 1.0
CB A:ALA127 4.7 42.9 1.0
CB A:HIS130 4.7 40.1 1.0
N A:GLY166 4.7 39.2 1.0
C A:CYS128 4.8 42.3 1.0
CB A:GLN167 4.8 40.6 1.0
C A:HIS164 4.8 46.5 1.0
N A:GLY129 4.8 41.6 1.0
C A:ALA127 4.9 45.2 1.0
N A:GLN167 4.9 36.6 1.0
N A:HIS130 4.9 36.5 1.0

Reference:

F.Liu, J.Geng, R.H.Gumpper, A.Barman, I.Davis, A.Ozarowski, D.Hamelberg, A.Liu. An Iron Reservoir to the Catalytic Metal: the Rubredoxin Iron in An Extradiol Dioxygenase J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
Page generated: Mon Aug 5 06:02:55 2024

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