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Iron in PDB 6dyd: Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3

Protein crystallography data

The structure of Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3, PDB code: 6dyd 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) 37.28 / 1.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 32.569, 87.770, 37.460, 90.00, 95.56, 90.00
R / Rfree (%) 19.6 / 24.7

Other elements in 6dyd:

The structure of Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3 also contains other interesting chemical elements:

Copper (Cu) 1 atom
Calcium (Ca) 5 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3 (pdb code 6dyd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3, PDB code: 6dyd:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6dyd

Go back to Iron Binding Sites List in 6dyd
Iron binding site 1 out of 2 in the Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:17.4
occ:1.00
FE A:HEC203 0.0 17.4 1.0
ND A:HEC203 2.0 13.5 1.0
NB A:HEC203 2.0 12.1 1.0
NA A:HEC203 2.0 16.1 1.0
NE2 A:HIS102 2.0 17.6 1.0
NC A:HEC203 2.1 18.4 1.0
SD A:MET7 2.3 16.9 1.0
CD2 A:HIS102 3.0 18.0 1.0
C4D A:HEC203 3.0 18.3 1.0
C1B A:HEC203 3.0 18.5 1.0
C4A A:HEC203 3.0 16.3 1.0
CE1 A:HIS102 3.0 16.7 1.0
C1A A:HEC203 3.1 19.5 1.0
C1D A:HEC203 3.1 15.3 1.0
C4B A:HEC203 3.1 17.0 1.0
C1C A:HEC203 3.1 15.3 1.0
C4C A:HEC203 3.1 15.9 1.0
CHA A:HEC203 3.4 20.3 1.0
CHB A:HEC203 3.4 19.4 1.0
CG A:MET7 3.4 14.2 1.0
CHC A:HEC203 3.5 14.3 1.0
CHD A:HEC203 3.5 17.3 1.0
CE A:MET7 3.5 17.0 1.0
ND1 A:HIS102 4.1 18.8 1.0
CG A:HIS102 4.2 20.3 1.0
CB A:MET7 4.2 19.7 1.0
C3A A:HEC203 4.2 21.1 1.0
C3D A:HEC203 4.3 21.2 1.0
C2A A:HEC203 4.3 24.2 1.0
C2B A:HEC203 4.3 16.2 1.0
C2D A:HEC203 4.3 17.2 1.0
C3B A:HEC203 4.3 15.8 1.0
C2C A:HEC203 4.3 16.3 1.0
C3C A:HEC203 4.3 14.6 1.0
CA A:MET7 5.0 18.7 1.0

Iron binding site 2 out of 2 in 6dyd

Go back to Iron Binding Sites List in 6dyd
Iron binding site 2 out of 2 in the Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe204

b:25.0
occ:1.00
FE C:HEC204 0.0 25.0 1.0
NB C:HEC204 2.0 26.6 1.0
NA C:HEC204 2.0 26.0 1.0
NC C:HEC204 2.1 22.0 1.0
ND C:HEC204 2.1 25.1 1.0
NE2 C:HIS102 2.1 25.3 1.0
SD C:MET7 2.4 24.2 1.0
C4B C:HEC204 3.0 22.3 1.0
C1B C:HEC204 3.0 25.1 1.0
C4A C:HEC204 3.0 24.7 1.0
C1C C:HEC204 3.1 25.7 1.0
C4D C:HEC204 3.1 25.4 1.0
C1A C:HEC204 3.1 31.9 1.0
C1D C:HEC204 3.1 21.6 1.0
CD2 C:HIS102 3.1 22.5 1.0
CE1 C:HIS102 3.1 25.4 1.0
C4C C:HEC204 3.1 20.4 1.0
CE C:MET7 3.3 27.7 1.0
CHC C:HEC204 3.4 20.2 1.0
CHB C:HEC204 3.4 24.1 1.0
CHA C:HEC204 3.4 30.0 1.0
CHD C:HEC204 3.5 21.0 1.0
CG C:MET7 3.5 26.1 1.0
ND1 C:HIS102 4.2 22.7 1.0
C3B C:HEC204 4.2 23.9 1.0
C2B C:HEC204 4.2 26.0 1.0
CG C:HIS102 4.2 25.6 1.0
CB C:MET7 4.3 26.5 1.0
C3A C:HEC204 4.3 27.8 1.0
C2A C:HEC204 4.3 26.4 1.0
C2C C:HEC204 4.3 18.1 1.0
C2D C:HEC204 4.3 25.3 1.0
C3D C:HEC204 4.3 27.5 1.0
C3C C:HEC204 4.3 17.1 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: Sun Dec 13 16:24:34 2020

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