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Iron in PDB 6vi7: Probing Extradiol Dioxygenase Mechanism in Nad(+) Biosynthesis By Viewing Reaction Cycle Intermediates - A Substrate Bidentately Bound Structure

Enzymatic activity of Probing Extradiol Dioxygenase Mechanism in Nad(+) Biosynthesis By Viewing Reaction Cycle Intermediates - A Substrate Bidentately Bound Structure

All present enzymatic activity of Probing Extradiol Dioxygenase Mechanism in Nad(+) Biosynthesis By Viewing Reaction Cycle Intermediates - A Substrate Bidentately Bound Structure:
1.13.11.6;

Protein crystallography data

The structure of Probing Extradiol Dioxygenase Mechanism in Nad(+) Biosynthesis By Viewing Reaction Cycle Intermediates - A Substrate Bidentately Bound Structure, PDB code: 6vi7 was solved by Y.Wang, F.Liu, Y.Yang, A.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.96 / 2.62
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.040, 58.040, 231.580, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 29

Iron Binding Sites:

The binding sites of Iron atom in the Probing Extradiol Dioxygenase Mechanism in Nad(+) Biosynthesis By Viewing Reaction Cycle Intermediates - A Substrate Bidentately Bound Structure (pdb code 6vi7). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Probing Extradiol Dioxygenase Mechanism in Nad(+) Biosynthesis By Viewing Reaction Cycle Intermediates - A Substrate Bidentately Bound Structure, PDB code: 6vi7:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6vi7

Go back to Iron Binding Sites List in 6vi7
Iron binding site 1 out of 2 in the Probing Extradiol Dioxygenase Mechanism in Nad(+) Biosynthesis By Viewing Reaction Cycle Intermediates - A Substrate Bidentately Bound Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Probing Extradiol Dioxygenase Mechanism in Nad(+) Biosynthesis By Viewing Reaction Cycle Intermediates - A Substrate Bidentately Bound Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:30.7
occ:1.00
 O11 A:3HA201 2.0 25.3 1.0
N10 A:3HA201 2.3 19.1 1.0
NE2 A:HIS95 2.4 10.4 1.0
ND1 A:HIS51 2.5 17.1 1.0
OE2 A:GLU57 2.5 18.6 1.0
OE1 A:GLU57 2.7 10.5 1.0
C4 A:3HA201 2.9 20.6 1.0
CD A:GLU57 2.9 13.6 1.0
C3 A:3HA201 3.0 16.8 1.0
CD2 A:HIS95 3.2 9.1 1.0
CE1 A:HIS51 3.4 14.0 1.0
CG A:HIS51 3.4 15.3 1.0
CE1 A:HIS95 3.5 11.7 1.0
CB A:HIS51 3.7 13.5 1.0
OE1 A:GLU110 4.0 19.6 1.0
C5 A:3HA201 4.1 22.1 1.0
C2 A:3HA201 4.3 17.2 1.0
CG A:GLU57 4.4 11.6 1.0
NE2 A:HIS51 4.4 18.5 1.0
CG A:HIS95 4.4 11.7 1.0
CD2 A:HIS51 4.4 17.4 1.0
ND1 A:HIS95 4.6 11.1 1.0
OD1 A:ASP53 4.8 13.2 1.0
CD A:GLU110 4.9 18.4 1.0
O8 A:3HA201 5.0 17.1 1.0

Iron binding site 2 out of 2 in 6vi7

Go back to Iron Binding Sites List in 6vi7
Iron binding site 2 out of 2 in the Probing Extradiol Dioxygenase Mechanism in Nad(+) Biosynthesis By Viewing Reaction Cycle Intermediates - A Substrate Bidentately Bound Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Probing Extradiol Dioxygenase Mechanism in Nad(+) Biosynthesis By Viewing Reaction Cycle Intermediates - A Substrate Bidentately Bound Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:30.0
occ:1.00
 SG A:CYS128 2.3 39.0 1.0
SG A:CYS165 2.3 41.0 1.0
SG A:CYS162 2.3 32.3 1.0
SG A:CYS125 2.3 31.6 1.0
CB A:CYS125 2.9 34.6 1.0
CB A:CYS128 3.3 37.5 1.0
CB A:CYS162 3.4 30.0 1.0
CB A:CYS165 3.5 33.2 1.0
N A:CYS128 3.6 32.1 1.0
N A:CYS165 3.7 39.9 1.0
CA A:CYS128 4.0 38.5 1.0
CA A:CYS165 4.1 40.7 1.0
CA A:CYS125 4.4 34.4 1.0
CB A:HIS164 4.4 42.1 1.0
N A:GLY129 4.5 50.6 1.0
C A:CYS128 4.5 41.2 1.0
C A:CYS165 4.6 40.5 1.0
O A:CYS165 4.6 37.7 1.0
N A:HIS130 4.7 38.0 1.0
C A:HIS164 4.8 39.8 1.0
N A:HIS164 4.8 41.8 1.0
C A:ALA127 4.8 34.8 1.0
CA A:CYS162 4.9 33.3 1.0
CB A:GLN167 4.9 30.9 1.0
CB A:ALA127 4.9 33.8 1.0
CA A:HIS164 4.9 40.0 1.0
C A:CYS125 5.0 36.9 1.0

Reference:

Y.Wang, F.Liu, Y.Yang, A.Liu. Probing Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Reaction Cycle Intermediates To Be Published.
Page generated: Wed Aug 6 15:02:14 2025

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