Iron in PDB 6vi5: Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State Structure

Enzymatic activity of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State Structure

All present enzymatic activity of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State Structure:
1.13.11.6;

Protein crystallography data

The structure of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State Structure, PDB code: 6vi5 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) 46.03 / 1.60
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 57.930, 57.930, 231.440, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 22.9

Other elements in 6vi5:

The structure of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State Structure also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State Structure (pdb code 6vi5). 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 - A Resting State Structure, PDB code: 6vi5:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6vi5

Go back to Iron Binding Sites List in 6vi5
Iron binding site 1 out of 2 in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State 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 - A Resting State Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:17.4
occ:1.00
NE2 A:HIS95 2.2 9.7 1.0
ND1 A:HIS51 2.2 14.5 1.0
O A:HOH314 2.3 14.7 1.0
OE2 A:GLU57 2.3 16.6 1.0
O A:HOH488 2.6 27.3 1.0
OE1 A:GLU57 2.6 15.9 1.0
CD A:GLU57 2.8 17.2 1.0
CE1 A:HIS95 3.1 8.5 1.0
CE1 A:HIS51 3.1 12.4 1.0
CD2 A:HIS95 3.2 10.6 1.0
CG A:HIS51 3.3 18.0 1.0
CB A:HIS51 3.6 11.2 1.0
O A:HOH482 4.0 58.9 1.0
OE1 A:GLU110 4.0 29.4 1.0
ND1 A:HIS95 4.3 9.4 1.0
O A:HOH460 4.3 55.7 1.0
NE2 A:HIS51 4.3 11.7 1.0
O A:HOH520 4.3 39.0 1.0
CG A:GLU57 4.3 12.4 1.0
CG A:HIS95 4.3 8.7 1.0
CD2 A:HIS51 4.4 14.1 1.0
OD2 A:ASP53 4.5 13.1 1.0
CB A:ASP53 4.8 8.6 1.0
CD A:GLU110 4.8 21.2 1.0

Iron binding site 2 out of 2 in 6vi5

Go back to Iron Binding Sites List in 6vi5
Iron binding site 2 out of 2 in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State 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 - A Resting State Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:26.2
occ:1.00
SG A:CYS165 2.3 34.2 1.0
SG A:CYS125 2.3 27.6 1.0
SG A:CYS128 2.3 37.4 1.0
SG A:CYS162 2.3 26.1 1.0
CB A:CYS125 3.1 22.6 1.0
CB A:CYS162 3.1 25.0 1.0
CB A:CYS128 3.4 39.3 1.0
CB A:CYS165 3.4 33.2 1.0
N A:CYS165 3.7 33.2 1.0
N A:CYS128 3.8 36.9 1.0
CA A:CYS165 4.1 34.0 1.0
CA A:CYS128 4.1 39.0 1.0
CB A:GLN167 4.5 34.9 0.6
CB A:HIS164 4.5 45.2 1.0
CA A:CYS125 4.6 20.3 1.0
CA A:CYS162 4.6 24.7 1.0
CB A:GLN167 4.6 35.4 0.4
CB A:ALA127 4.6 27.6 1.0
C A:CYS128 4.7 40.0 1.0
CB A:HIS130 4.7 33.4 1.0
C A:CYS165 4.7 34.7 1.0
O A:HOH419 4.7 26.9 1.0
N A:GLY166 4.8 29.9 1.0
C A:ALA127 4.8 42.7 1.0
C A:HIS164 4.8 38.0 1.0
N A:GLN167 4.8 29.6 1.0
N A:GLY129 4.8 30.9 1.0
N A:HIS130 4.9 26.7 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: Sun Dec 13 17:18:55 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy