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Iron in PDB 6dyj: Iron-Bound Structure of the Engineered Cyt B562 Variant, CH3Y*

Protein crystallography data

The structure of Iron-Bound Structure of the Engineered Cyt B562 Variant, CH3Y*, PDB code: 6dyj 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) 49.24 / 1.96
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 48.719, 98.490, 179.249, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 25.2

Other elements in 6dyj:

The structure of Iron-Bound Structure of the Engineered Cyt B562 Variant, CH3Y* also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Iron-Bound Structure of the Engineered Cyt B562 Variant, CH3Y* (pdb code 6dyj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Iron-Bound Structure of the Engineered Cyt B562 Variant, CH3Y*, PDB code: 6dyj:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6dyj

Go back to Iron Binding Sites List in 6dyj
Iron binding site 1 out of 2 in the Iron-Bound Structure of the Engineered Cyt B562 Variant, CH3Y*


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Iron-Bound Structure of the Engineered Cyt B562 Variant, CH3Y* within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:23.3
occ:1.00
NE2 E:HIS71 2.2 15.1 1.0
NE2 A:HIS67 2.2 12.5 1.0
NE2 E:HIS67 2.2 16.8 1.0
NE2 A:HIS71 2.2 14.6 1.0
NE2 E:HIS97 2.3 14.5 1.0
O E:HOH344 2.4 15.8 1.0
CD2 A:HIS67 3.0 12.9 1.0
CE1 A:HIS71 3.1 17.4 1.0
CE1 E:HIS71 3.1 15.4 1.0
CE1 E:HIS67 3.2 18.0 1.0
CD2 E:HIS71 3.2 14.2 1.0
CD2 E:HIS67 3.2 13.8 1.0
CD2 E:HIS97 3.2 14.1 1.0
CE1 E:HIS97 3.2 19.8 1.0
CE1 A:HIS67 3.3 14.9 1.0
CD2 A:HIS71 3.3 11.8 1.0
CG A:HIS67 4.2 16.5 1.0
ND1 E:HIS71 4.2 16.0 1.0
ND1 A:HIS71 4.3 16.1 1.0
ND1 E:HIS67 4.3 16.8 1.0
ND1 A:HIS67 4.3 12.4 1.0
CG E:HIS71 4.3 17.2 1.0
ND1 E:HIS97 4.3 15.4 1.0
CG E:HIS67 4.3 20.5 1.0
CG E:HIS97 4.3 17.5 1.0
O E:HOH354 4.3 24.5 1.0
CG A:HIS71 4.4 15.2 1.0
CD1 A:TYR70 4.7 18.2 1.0
CE1 A:HIS97 4.8 17.7 1.0
CE1 A:TYR70 4.8 18.4 1.0

Iron binding site 2 out of 2 in 6dyj

Go back to Iron Binding Sites List in 6dyj
Iron binding site 2 out of 2 in the Iron-Bound Structure of the Engineered Cyt B562 Variant, CH3Y*


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Iron-Bound Structure of the Engineered Cyt B562 Variant, CH3Y* within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe201

b:22.6
occ:1.00
NE2 G:HIS97 2.1 13.5 1.0
NE2 G:HIS71 2.2 15.1 1.0
O C:HOH255 2.2 13.5 1.0
NE2 G:HIS67 2.2 11.9 1.0
NE2 C:HIS71 2.2 16.3 1.0
NE2 C:HIS67 2.3 14.1 1.0
CE1 G:HIS97 3.0 19.1 1.0
CD2 C:HIS67 3.1 12.0 1.0
CE1 G:HIS67 3.1 15.6 1.0
CD2 G:HIS71 3.1 17.1 1.0
CD2 G:HIS97 3.2 12.2 1.0
CE1 G:HIS71 3.2 18.6 1.0
CD2 C:HIS71 3.2 13.2 1.0
CE1 C:HIS71 3.2 19.1 1.0
CD2 G:HIS67 3.3 13.5 1.0
CE1 C:HIS67 3.3 16.8 1.0
ND1 G:HIS97 4.1 16.1 1.0
ND1 G:HIS67 4.3 15.5 1.0
CG G:HIS97 4.3 13.6 1.0
CG C:HIS67 4.3 14.5 1.0
ND1 G:HIS71 4.3 16.9 1.0
CG G:HIS71 4.3 18.6 1.0
ND1 C:HIS71 4.3 15.8 1.0
CG G:HIS67 4.4 15.6 1.0
ND1 C:HIS67 4.4 14.3 1.0
CG C:HIS71 4.4 18.3 1.0
O G:HOH366 4.4 21.6 1.0
CE1 C:HIS97 4.7 20.7 1.0
CD1 C:TYR70 4.7 22.4 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 16:24:38 2020

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