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Iron in PDB 6x11: Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - An Enol Tautomer of Acms Monodentately Bound Structure

Enzymatic activity of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - An Enol Tautomer of Acms Monodentately Bound Structure

All present enzymatic activity of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - An Enol Tautomer of Acms Monodentately Bound Structure:
1.13.11.6;

Protein crystallography data

The structure of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - An Enol Tautomer of Acms Monodentately Bound Structure, PDB code: 6x11 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) 38.19 / 2.10
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.626, 58.626, 231.814, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / 27.9

Iron Binding Sites:

The binding sites of Iron atom in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - An Enol Tautomer of Acms Monodentately Bound Structure (pdb code 6x11). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - An Enol Tautomer of Acms Monodentately Bound Structure, PDB code: 6x11:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6x11

Go back to Iron Binding Sites List in 6x11
Iron binding site 1 out of 2 in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - An Enol Tautomer of Acms Monodentately Bound Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - An Enol Tautomer of Acms Monodentately Bound Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:37.7
occ:1.00
 NE2 A:HIS95 2.3 19.6 1.0
ND1 A:HIS51 2.3 27.8 1.0
OE2 A:GLU57 2.4 29.1 1.0
O A:2FO204 2.4 32.1 1.0
OE1 A:GLU57 2.5 22.2 1.0
CD A:GLU57 2.8 27.3 1.0
C1 A:2FO204 3.1 43.9 1.0
CD2 A:HIS95 3.2 21.9 1.0
CE1 A:HIS51 3.3 26.7 1.0
CE1 A:HIS95 3.3 24.2 1.0
CG A:HIS51 3.3 26.2 1.0
N A:2FO204 3.4 38.7 1.0
CB A:HIS51 3.6 20.5 1.0
C A:2FO204 3.7 43.6 1.0
OE1 A:GLU110 3.7 38.8 1.0
O1 A:2FO204 4.0 45.8 1.0
CG A:GLU57 4.3 19.6 1.0
NE2 A:HIS51 4.4 28.7 1.0
CG A:HIS95 4.4 21.0 1.0
ND1 A:HIS95 4.4 23.0 1.0
CD2 A:HIS51 4.4 26.6 1.0
OD2 A:ASP53 4.6 27.1 1.0
CD A:GLU110 4.6 35.3 1.0
CB A:ASP53 4.7 25.9 1.0
OE2 A:GLU110 5.0 30.8 1.0

Iron binding site 2 out of 2 in 6x11

Go back to Iron Binding Sites List in 6x11
Iron binding site 2 out of 2 in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - An Enol Tautomer of Acms Monodentately Bound Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - An Enol Tautomer of Acms Monodentately Bound Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:35.4
occ:1.00
 SG A:CYS162 2.3 31.2 1.0
SG A:CYS128 2.3 48.9 1.0
SG A:CYS125 2.3 39.1 1.0
SG A:CYS165 2.3 39.2 1.0
CB A:CYS125 3.1 35.0 1.0
CB A:CYS165 3.2 39.2 1.0
CB A:CYS162 3.2 33.8 1.0
CB A:CYS128 3.3 42.3 1.0
N A:CYS128 3.7 40.6 1.0
N A:CYS165 3.8 40.4 1.0
CA A:CYS128 4.0 43.5 1.0
CA A:CYS165 4.1 41.4 1.0
CB A:GLN167 4.6 38.4 1.0
CA A:CYS125 4.6 35.3 1.0
CB A:ALA127 4.6 43.6 1.0
C A:CYS128 4.7 44.1 1.0
C A:ALA127 4.7 42.6 1.0
O A:HOH377 4.7 36.0 1.0
CA A:CYS162 4.7 32.2 1.0
C A:CYS165 4.7 41.1 1.0
CB A:HIS130 4.8 45.0 1.0
CB A:HIS164 4.8 46.9 1.0
C A:HIS164 4.8 42.1 1.0
N A:GLY129 4.8 39.4 1.0
N A:GLN167 4.8 41.2 1.0
N A:HIS130 4.9 38.4 1.0

Reference:

Y.Wang, F.Liu, Y.Yang, A.Liu. Probing Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Reaction Cycle Intermediates Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.2005327117
Page generated: Wed Aug 7 14:37:26 2024

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