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Iron in PDB 6dyh: Vanadyl-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y

Protein crystallography data

The structure of Vanadyl-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y, PDB code: 6dyh was solved by F.A.Tezcan, J.Rittle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.37 / 1.83
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 31.973, 83.482, 39.033, 90.00, 100.57, 90.00
R / Rfree (%) 18.3 / 23.4

Other elements in 6dyh:

The structure of Vanadyl-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y also contains other interesting chemical elements:

Vanadium (V) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Vanadyl-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y (pdb code 6dyh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Vanadyl-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y, PDB code: 6dyh:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6dyh

Go back to Iron Binding Sites List in 6dyh
Iron binding site 1 out of 2 in the Vanadyl-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Vanadyl-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:23.1
occ:1.00
FE A:HEC202 0.0 23.1 1.0
NA A:HEC202 2.0 27.1 1.0
NC A:HEC202 2.0 20.6 1.0
NE2 A:HIS102 2.0 25.7 1.0
NB A:HEC202 2.0 25.9 1.0
ND A:HEC202 2.1 25.9 1.0
SD A:MET7 2.4 20.8 1.0
CD2 A:HIS102 3.0 24.5 1.0
C4A A:HEC202 3.0 27.0 1.0
C1C A:HEC202 3.0 22.7 1.0
C1B A:HEC202 3.1 21.1 1.0
C1A A:HEC202 3.1 25.9 1.0
C4C A:HEC202 3.1 20.2 1.0
CE1 A:HIS102 3.1 27.5 1.0
C4B A:HEC202 3.1 21.2 1.0
C1D A:HEC202 3.1 21.9 1.0
C4D A:HEC202 3.1 25.1 1.0
CE A:MET7 3.3 23.5 1.0
CHB A:HEC202 3.4 25.8 1.0
CG A:MET7 3.4 22.5 1.0
CHC A:HEC202 3.4 22.6 1.0
CHD A:HEC202 3.4 21.2 1.0
CHA A:HEC202 3.5 26.1 1.0
CG A:HIS102 4.1 22.3 1.0
ND1 A:HIS102 4.1 22.0 1.0
CB A:MET7 4.3 23.3 1.0
C3A A:HEC202 4.3 27.5 1.0
C2A A:HEC202 4.3 27.5 1.0
C2C A:HEC202 4.3 21.0 1.0
C2B A:HEC202 4.3 26.0 1.0
C3C A:HEC202 4.3 17.8 1.0
C3B A:HEC202 4.3 21.1 1.0
C2D A:HEC202 4.3 23.2 1.0
C3D A:HEC202 4.3 24.8 1.0
NH1 A:ARG106 4.9 35.2 1.0

Iron binding site 2 out of 2 in 6dyh

Go back to Iron Binding Sites List in 6dyh
Iron binding site 2 out of 2 in the Vanadyl-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Vanadyl-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:22.6
occ:1.00
FE D:HEC201 0.0 22.6 1.0
NE2 D:HIS102 1.9 22.0 1.0
NB D:HEC201 2.0 24.2 1.0
NC D:HEC201 2.0 21.9 1.0
ND D:HEC201 2.1 21.9 1.0
NA D:HEC201 2.1 19.1 1.0
SD D:MET7 2.3 23.6 1.0
CE1 D:HIS102 2.9 20.2 1.0
CD2 D:HIS102 3.0 20.8 1.0
C4B D:HEC201 3.0 24.6 1.0
C1B D:HEC201 3.1 22.2 1.0
C1C D:HEC201 3.1 21.7 1.0
C4C D:HEC201 3.1 21.6 1.0
C1D D:HEC201 3.1 19.8 1.0
C1A D:HEC201 3.1 23.2 1.0
C4D D:HEC201 3.1 21.9 1.0
C4A D:HEC201 3.1 23.4 1.0
CE D:MET7 3.4 26.8 1.0
CHC D:HEC201 3.4 20.3 1.0
CHD D:HEC201 3.4 21.7 1.0
CHB D:HEC201 3.5 25.0 1.0
CG D:MET7 3.5 21.5 1.0
CHA D:HEC201 3.5 24.6 1.0
ND1 D:HIS102 4.0 25.1 1.0
CG D:HIS102 4.1 23.0 1.0
CB D:MET7 4.2 23.0 1.0
C3B D:HEC201 4.2 22.4 1.0
C2B D:HEC201 4.2 24.1 1.0
C3C D:HEC201 4.3 17.4 1.0
C2C D:HEC201 4.3 20.1 1.0
C2D D:HEC201 4.3 20.8 1.0
C2A D:HEC201 4.3 22.2 1.0
C3D D:HEC201 4.3 20.9 1.0
C3A D:HEC201 4.3 23.0 1.0
CA D:MET7 5.0 22.5 1.0

Reference:

J.Rittle, M.J.Field, M.T.Green, F.A.Tezcan. An Efficient, Step-Economical Strategy For the Design of Functional Metalloproteins. Nat.Chem. V. 11 434 2019.
ISSN: ESSN 1755-4349
PubMed: 30778140
DOI: 10.1038/S41557-019-0218-9
Page generated: Wed Oct 28 18:19:01 2020

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