Atomistry » Iron » PDB 6dhz-6e42 » 6dy8
Atomistry »
  Iron »
    PDB 6dhz-6e42 »
      6dy8 »

Iron in PDB 6dy8: Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY

Protein crystallography data

The structure of Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY, PDB code: 6dy8 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) 37.59 / 1.90
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 75.661, 37.591, 77.323, 90.00, 104.39, 90.00
R / Rfree (%) 22.6 / 27.8

Other elements in 6dy8:

The structure of Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY (pdb code 6dy8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY, PDB code: 6dy8:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6dy8

Go back to Iron Binding Sites List in 6dy8
Iron binding site 1 out of 4 in the Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:23.7
occ:1.00
FE A:HEC201 0.0 23.7 1.0
NE2 A:HIS102 1.9 18.8 1.0
NC A:HEC201 2.1 27.1 1.0
NA A:HEC201 2.1 24.5 1.0
NB A:HEC201 2.1 19.6 1.0
ND A:HEC201 2.1 21.6 1.0
SD A:MET7 2.4 23.1 1.0
CD2 A:HIS102 2.9 20.8 1.0
CE1 A:HIS102 2.9 19.4 1.0
C4C A:HEC201 3.1 24.8 1.0
C1A A:HEC201 3.1 21.8 1.0
C1C A:HEC201 3.1 24.8 1.0
C4A A:HEC201 3.1 26.1 1.0
C4B A:HEC201 3.1 23.8 1.0
C1B A:HEC201 3.1 26.8 1.0
C1D A:HEC201 3.1 25.1 1.0
C4D A:HEC201 3.1 25.7 1.0
CE A:MET7 3.4 16.1 1.0
CG A:MET7 3.4 28.3 1.0
CHD A:HEC201 3.4 21.2 1.0
CHA A:HEC201 3.4 27.3 1.0
CHC A:HEC201 3.4 28.2 1.0
CHB A:HEC201 3.5 22.4 1.0
ND1 A:HIS102 4.0 13.6 1.0
CG A:HIS102 4.0 23.5 1.0
CB A:MET7 4.1 24.0 1.0
C3C A:HEC201 4.3 21.1 1.0
C2A A:HEC201 4.3 21.8 1.0
C2C A:HEC201 4.3 25.5 1.0
C3A A:HEC201 4.3 21.0 1.0
C3B A:HEC201 4.3 21.9 1.0
C2B A:HEC201 4.3 28.9 1.0
C2D A:HEC201 4.3 23.5 1.0
C3D A:HEC201 4.3 26.9 1.0

Iron binding site 2 out of 4 in 6dy8

Go back to Iron Binding Sites List in 6dy8
Iron binding site 2 out of 4 in the Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:48.1
occ:1.00
FE B:HEC202 0.0 48.1 1.0
NA B:HEC202 2.1 62.1 1.0
NC B:HEC202 2.1 56.9 1.0
NB B:HEC202 2.1 52.5 1.0
NE2 B:HIS102 2.1 52.2 1.0
ND B:HEC202 2.1 53.4 1.0
SD B:MET7 2.2 63.5 1.0
CE B:MET7 2.6 51.5 1.0
CD2 B:HIS102 3.0 52.8 1.0
C1C B:HEC202 3.1 57.2 1.0
C1A B:HEC202 3.1 57.4 1.0
C4B B:HEC202 3.1 62.6 1.0
C4A B:HEC202 3.1 60.3 1.0
C1B B:HEC202 3.1 58.3 1.0
C4D B:HEC202 3.1 59.6 1.0
C4C B:HEC202 3.1 56.0 1.0
CE1 B:HIS102 3.1 53.0 1.0
C1D B:HEC202 3.1 54.6 1.0
CHC B:HEC202 3.4 60.3 1.0
CHA B:HEC202 3.4 60.2 1.0
CHB B:HEC202 3.5 62.5 1.0
CHD B:HEC202 3.5 50.4 1.0
CG B:MET7 3.6 55.1 1.0
CB B:MET7 4.1 56.6 1.0
CG B:HIS102 4.2 54.9 1.0
ND1 B:HIS102 4.2 59.9 1.0
C2A B:HEC202 4.3 61.7 1.0
C3B B:HEC202 4.3 58.9 1.0
C2C B:HEC202 4.3 51.9 1.0
C3A B:HEC202 4.3 64.1 1.0
C2B B:HEC202 4.3 59.5 1.0
C3C B:HEC202 4.3 45.5 1.0
C3D B:HEC202 4.3 57.4 1.0
C2D B:HEC202 4.3 50.7 1.0

Iron binding site 3 out of 4 in 6dy8

Go back to Iron Binding Sites List in 6dy8
Iron binding site 3 out of 4 in the Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:29.1
occ:1.00
FE C:HEC202 0.0 29.1 1.0
NE2 C:HIS102 1.9 25.4 1.0
NA C:HEC202 2.1 26.4 1.0
NC C:HEC202 2.1 20.7 1.0
NB C:HEC202 2.1 27.3 1.0
ND C:HEC202 2.1 29.6 1.0
SD C:MET7 2.3 27.5 1.0
CE1 C:HIS102 2.8 28.3 1.0
CD2 C:HIS102 3.0 28.3 1.0
C1A C:HEC202 3.1 29.1 1.0
C1C C:HEC202 3.1 23.9 1.0
C4D C:HEC202 3.1 27.0 1.0
C4B C:HEC202 3.1 31.0 1.0
C1D C:HEC202 3.1 27.3 1.0
C4C C:HEC202 3.1 26.6 1.0
C4A C:HEC202 3.1 31.9 1.0
C1B C:HEC202 3.1 30.7 1.0
CE C:MET7 3.3 26.7 1.0
CHA C:HEC202 3.4 31.8 1.0
CHC C:HEC202 3.4 26.8 1.0
CG C:MET7 3.4 28.4 1.0
CHD C:HEC202 3.4 31.1 1.0
CHB C:HEC202 3.5 34.8 1.0
ND1 C:HIS102 4.0 32.1 1.0
CG C:HIS102 4.1 29.9 1.0
CB C:MET7 4.2 35.8 1.0
C2A C:HEC202 4.3 34.9 1.0
C2C C:HEC202 4.3 21.7 1.0
C3A C:HEC202 4.3 37.1 1.0
C3C C:HEC202 4.3 23.4 1.0
C3B C:HEC202 4.3 28.2 1.0
C3D C:HEC202 4.3 26.6 1.0
C2D C:HEC202 4.3 27.6 1.0
C2B C:HEC202 4.3 25.0 1.0
CA C:MET7 5.0 36.0 1.0

Iron binding site 4 out of 4 in 6dy8

Go back to Iron Binding Sites List in 6dy8
Iron binding site 4 out of 4 in the Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:37.2
occ:1.00
FE D:HEC201 0.0 37.2 1.0
NE2 D:HIS102 1.9 33.3 1.0
NC D:HEC201 2.1 34.4 1.0
NA D:HEC201 2.1 42.6 1.0
ND D:HEC201 2.1 37.8 1.0
NB D:HEC201 2.1 41.0 1.0
SD D:MET7 2.4 33.0 1.0
CD2 D:HIS102 2.9 32.2 1.0
CE1 D:HIS102 2.9 40.4 1.0
C1A D:HEC201 3.1 42.6 1.0
C4D D:HEC201 3.1 36.4 1.0
C1C D:HEC201 3.1 35.5 1.0
C4B D:HEC201 3.1 38.5 1.0
C1D D:HEC201 3.1 36.5 1.0
C4C D:HEC201 3.1 33.0 1.0
C4A D:HEC201 3.1 40.5 1.0
C1B D:HEC201 3.1 41.3 1.0
CE D:MET7 3.2 41.6 1.0
CHA D:HEC201 3.4 37.8 1.0
CHC D:HEC201 3.4 34.6 1.0
CHD D:HEC201 3.4 36.0 1.0
CG D:MET7 3.5 39.1 1.0
CHB D:HEC201 3.5 36.7 1.0
ND1 D:HIS102 4.0 34.6 1.0
CG D:HIS102 4.0 39.8 1.0
C2A D:HEC201 4.3 45.9 1.0
C2C D:HEC201 4.3 33.5 1.0
C3D D:HEC201 4.3 41.7 1.0
C3B D:HEC201 4.3 39.5 1.0
C3A D:HEC201 4.3 44.8 1.0
C2D D:HEC201 4.3 37.3 1.0
C3C D:HEC201 4.3 31.5 1.0
C2B D:HEC201 4.3 41.8 1.0
CB D:MET7 4.3 32.2 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 16:24:32 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