Iron in PDB 6dhy: Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines

Protein crystallography data

The structure of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines, PDB code: 6dhy was solved by F.A.Tezcan, L.A.Churchfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.84 / 2.22
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 52.510, 52.510, 255.670, 90.00, 90.00, 120.00
R / Rfree (%) 22.9 / 25.8

Other elements in 6dhy:

The structure of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines also contains other interesting chemical elements:

Calcium (Ca) 3 atoms
Zinc (Zn) 10 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines (pdb code 6dhy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines, PDB code: 6dhy:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6dhy

Go back to Iron Binding Sites List in 6dhy
Iron binding site 1 out of 4 in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:29.5
occ:1.00
FE A:HEM201 0.0 29.5 1.0
ND A:HEM201 1.9 29.6 1.0
NA A:HEM201 2.0 31.1 1.0
NB A:HEM201 2.1 30.0 1.0
NC A:HEM201 2.1 30.0 1.0
NE2 A:HIS102 2.2 28.2 1.0
SD A:MET7 2.2 25.4 1.0
C4D A:HEM201 2.9 30.4 1.0
C1D A:HEM201 2.9 30.1 1.0
C1A A:HEM201 3.0 30.9 1.0
C4B A:HEM201 3.1 29.2 1.0
C1B A:HEM201 3.1 30.2 1.0
C4A A:HEM201 3.1 31.5 1.0
C4C A:HEM201 3.1 30.3 1.0
C1C A:HEM201 3.1 29.4 1.0
CD2 A:HIS102 3.1 29.2 1.0
CE1 A:HIS102 3.2 28.4 1.0
CG A:MET7 3.4 25.4 1.0
CHA A:HEM201 3.4 30.7 1.0
CHD A:HEM201 3.4 29.6 1.0
CHB A:HEM201 3.4 30.9 1.0
CHC A:HEM201 3.5 29.3 1.0
CE A:MET7 3.6 25.3 1.0
C3D A:HEM201 4.2 29.9 1.0
C2D A:HEM201 4.2 29.9 1.0
CB A:MET7 4.2 25.7 1.0
C3A A:HEM201 4.3 32.0 1.0
C2A A:HEM201 4.3 32.6 1.0
C2B A:HEM201 4.3 29.6 1.0
CG A:HIS102 4.3 30.1 1.0
ND1 A:HIS102 4.3 29.3 1.0
C2C A:HEM201 4.3 30.0 1.0
C3B A:HEM201 4.3 30.0 1.0
C3C A:HEM201 4.3 30.4 1.0
CA A:MET7 5.0 25.9 1.0
NE A:ARG106 5.0 48.1 1.0

Iron binding site 2 out of 4 in 6dhy

Go back to Iron Binding Sites List in 6dhy
Iron binding site 2 out of 4 in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:39.0
occ:1.00
FE B:HEM201 0.0 39.0 1.0
ND B:HEM201 1.9 37.6 1.0
NA B:HEM201 2.0 39.4 1.0
NB B:HEM201 2.1 37.2 1.0
NC B:HEM201 2.1 35.9 1.0
NE2 B:HIS102 2.4 33.5 1.0
SD B:MET7 2.4 41.8 1.0
C4D B:HEM201 2.9 37.8 1.0
C1D B:HEM201 2.9 36.6 1.0
C1A B:HEM201 3.0 39.7 1.0
C4A B:HEM201 3.0 40.1 1.0
C4B B:HEM201 3.0 36.5 1.0
C1B B:HEM201 3.0 38.1 1.0
C4C B:HEM201 3.1 35.6 1.0
C1C B:HEM201 3.1 34.7 1.0
CE1 B:HIS102 3.3 33.5 1.0
CG B:MET7 3.3 41.5 1.0
CD2 B:HIS102 3.4 34.1 1.0
CHA B:HEM201 3.4 38.9 1.0
CHB B:HEM201 3.4 39.1 1.0
CHD B:HEM201 3.4 36.0 1.0
CHC B:HEM201 3.5 34.8 1.0
CE B:MET7 3.6 39.9 1.0
CB B:MET7 4.0 42.4 1.0
C3D B:HEM201 4.2 38.0 1.0
C2D B:HEM201 4.2 36.9 1.0
C2A B:HEM201 4.2 41.5 1.0
C3A B:HEM201 4.2 40.9 1.0
C2B B:HEM201 4.3 37.5 1.0
C3B B:HEM201 4.3 36.3 1.0
C2C B:HEM201 4.3 33.7 1.0
C3C B:HEM201 4.3 33.1 1.0
ND1 B:HIS102 4.4 33.7 1.0
CG B:HIS102 4.5 34.2 1.0
CA B:MET7 4.7 43.1 1.0

Iron binding site 3 out of 4 in 6dhy

Go back to Iron Binding Sites List in 6dhy
Iron binding site 3 out of 4 in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:25.3
occ:1.00
FE C:HEM201 0.0 25.3 1.0
ND C:HEM201 1.9 26.1 1.0
NA C:HEM201 2.0 26.1 1.0
NE2 C:HIS102 2.1 23.3 1.0
NC C:HEM201 2.1 25.3 1.0
NB C:HEM201 2.1 24.0 1.0
SD C:MET7 2.5 30.5 1.0
C4D C:HEM201 2.9 26.7 1.0
C1D C:HEM201 2.9 26.2 1.0
CE1 C:HIS102 3.0 23.7 1.0
C1A C:HEM201 3.0 26.6 1.0
C4B C:HEM201 3.0 24.2 1.0
C4A C:HEM201 3.1 26.3 1.0
C1C C:HEM201 3.1 25.0 1.0
C1B C:HEM201 3.1 24.1 1.0
C4C C:HEM201 3.1 25.8 1.0
CD2 C:HIS102 3.1 24.0 1.0
CHA C:HEM201 3.3 26.8 1.0
CHC C:HEM201 3.4 24.4 1.0
CHD C:HEM201 3.5 25.7 1.0
CHB C:HEM201 3.5 25.1 1.0
CE C:MET7 3.5 29.7 1.0
CG C:MET7 3.6 30.7 1.0
ND1 C:HIS102 4.1 23.7 1.0
C3D C:HEM201 4.2 27.1 1.0
C2D C:HEM201 4.2 26.2 1.0
C2A C:HEM201 4.2 28.0 1.0
CG C:HIS102 4.2 24.6 1.0
C3A C:HEM201 4.2 27.4 1.0
CB C:MET7 4.3 31.1 1.0
C2C C:HEM201 4.3 25.6 1.0
C2B C:HEM201 4.3 23.0 1.0
C3C C:HEM201 4.3 25.9 1.0
C3B C:HEM201 4.3 23.5 1.0
NH1 C:ARG106 4.4 26.5 1.0

Iron binding site 4 out of 4 in 6dhy

Go back to Iron Binding Sites List in 6dhy
Iron binding site 4 out of 4 in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:36.9
occ:1.00
FE D:HEM201 0.0 36.9 1.0
ND D:HEM201 1.9 35.6 1.0
NA D:HEM201 2.0 36.0 1.0
NC D:HEM201 2.1 34.9 1.0
NB D:HEM201 2.1 34.2 1.0
NE2 D:HIS102 2.4 37.4 1.0
SD D:MET7 2.6 41.0 1.0
C4D D:HEM201 2.9 34.8 1.0
C1D D:HEM201 2.9 35.5 1.0
C4A D:HEM201 3.0 36.3 1.0
C1A D:HEM201 3.0 35.8 1.0
C1B D:HEM201 3.0 35.1 1.0
C4B D:HEM201 3.1 33.8 1.0
C1C D:HEM201 3.1 34.4 1.0
C4C D:HEM201 3.1 35.2 1.0
CD2 D:HIS102 3.3 38.6 1.0
CE D:MET7 3.4 39.1 1.0
CHA D:HEM201 3.4 35.1 1.0
CHB D:HEM201 3.4 35.6 1.0
CHD D:HEM201 3.4 35.5 1.0
CHC D:HEM201 3.5 33.7 1.0
CE1 D:HIS102 3.5 36.7 1.0
CG D:MET7 3.6 43.3 1.0
C3D D:HEM201 4.2 35.9 1.0
C2D D:HEM201 4.2 35.5 1.0
C3A D:HEM201 4.2 36.5 1.0
C2A D:HEM201 4.2 36.3 1.0
C2C D:HEM201 4.3 34.5 1.0
C3C D:HEM201 4.3 34.6 1.0
C2B D:HEM201 4.3 34.2 1.0
C3B D:HEM201 4.3 33.9 1.0
CB D:MET7 4.4 45.3 1.0
CG D:HIS102 4.5 38.9 1.0
ND1 D:HIS102 4.5 38.1 1.0

Reference:

L.A.Churchfield, R.G.Alberstein, L.M.Williamson, F.A.Tezcan. Determining the Structural and Energetic Basis of Allostery in A De Novo Designed Metalloprotein Assembly. J. Am. Chem. Soc. V. 140 10043 2018.
ISSN: ESSN 1520-5126
PubMed: 29996654
DOI: 10.1021/JACS.8B05812
Page generated: Sun Dec 13 16:24:18 2020

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