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Iron in PDB 6dhz: Crystallographic Octamer of A Metal-Free RIDC1 Variant Bearing Two Disulfide Bonded Cysteines

Protein crystallography data

The structure of Crystallographic Octamer of A Metal-Free RIDC1 Variant Bearing Two Disulfide Bonded Cysteines, PDB code: 6dhz 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) 78.55 / 2.80
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 78.550, 78.550, 168.330, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 27.7

Other elements in 6dhz:

The structure of Crystallographic Octamer of A Metal-Free RIDC1 Variant Bearing Two Disulfide Bonded Cysteines also contains other interesting chemical elements:

Calcium (Ca) 7 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 4 in 6dhz

Go back to Iron Binding Sites List in 6dhz
Iron binding site 1 out of 4 in the Crystallographic Octamer of A Metal-Free 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 Crystallographic Octamer of A Metal-Free RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:42.7
occ:1.00
FE A:HEM201 0.0 42.7 1.0
ND A:HEM201 1.9 43.6 1.0
NA A:HEM201 2.0 45.1 1.0
NE2 A:HIS102 2.0 38.7 1.0
NC A:HEM201 2.1 45.4 1.0
NB A:HEM201 2.1 44.3 1.0
SD A:MET7 2.1 40.7 1.0
C4D A:HEM201 2.9 45.6 1.0
C1D A:HEM201 2.9 43.5 1.0
CD2 A:HIS102 3.0 37.0 1.0
C4A A:HEM201 3.0 47.0 1.0
CE1 A:HIS102 3.0 38.3 1.0
C1A A:HEM201 3.0 46.0 1.0
C4B A:HEM201 3.0 46.0 1.0
C1C A:HEM201 3.0 45.0 1.0
C1B A:HEM201 3.0 45.8 1.0
C4C A:HEM201 3.1 46.9 1.0
CE A:MET7 3.1 45.3 1.0
CHA A:HEM201 3.4 45.6 1.0
CHD A:HEM201 3.4 46.8 1.0
CHB A:HEM201 3.4 45.7 1.0
CHC A:HEM201 3.4 47.5 1.0
CG A:MET7 3.5 42.9 1.0
ND1 A:HIS102 4.1 38.4 1.0
CG A:HIS102 4.1 38.2 1.0
C2D A:HEM201 4.2 44.0 1.0
C3D A:HEM201 4.2 43.6 1.0
C2A A:HEM201 4.2 48.5 1.0
C3A A:HEM201 4.2 50.9 1.0
C2C A:HEM201 4.2 46.5 1.0
CB A:MET7 4.3 45.7 1.0
C3C A:HEM201 4.3 46.5 1.0
C2B A:HEM201 4.3 47.0 1.0
C3B A:HEM201 4.3 46.9 1.0

Iron binding site 2 out of 4 in 6dhz

Go back to Iron Binding Sites List in 6dhz
Iron binding site 2 out of 4 in the Crystallographic Octamer of A Metal-Free 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 Crystallographic Octamer of A Metal-Free RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:43.8
occ:1.00
FE B:HEM201 0.0 43.8 1.0
ND B:HEM201 1.9 41.7 1.0
NA B:HEM201 2.0 43.9 1.0
NC B:HEM201 2.0 39.3 1.0
NE2 B:HIS102 2.1 49.9 1.0
NB B:HEM201 2.1 48.0 1.0
SD B:MET7 2.2 43.5 1.0
C1D B:HEM201 2.9 42.5 1.0
C4D B:HEM201 2.9 44.5 1.0
C1A B:HEM201 3.0 46.6 1.0
C4A B:HEM201 3.0 43.3 1.0
C4C B:HEM201 3.0 42.0 1.0
C1C B:HEM201 3.0 39.6 1.0
CD2 B:HIS102 3.0 50.1 1.0
CE1 B:HIS102 3.0 46.1 1.0
C4B B:HEM201 3.1 45.5 1.0
C1B B:HEM201 3.1 46.8 1.0
CE B:MET7 3.1 45.9 1.0
CHD B:HEM201 3.4 43.1 1.0
CHA B:HEM201 3.4 46.9 1.0
CHB B:HEM201 3.4 44.6 1.0
CHC B:HEM201 3.4 40.0 1.0
CG B:MET7 3.5 45.6 1.0
ND1 B:HIS102 4.1 47.1 1.0
CG B:HIS102 4.2 45.7 1.0
C2A B:HEM201 4.2 48.4 1.0
C3A B:HEM201 4.2 44.2 1.0
C2D B:HEM201 4.2 43.2 1.0
C2C B:HEM201 4.2 42.8 1.0
C3D B:HEM201 4.2 46.1 1.0
C3C B:HEM201 4.2 42.0 1.0
C2B B:HEM201 4.3 46.5 1.0
CB B:MET7 4.3 48.4 1.0
C3B B:HEM201 4.3 47.0 1.0

Iron binding site 3 out of 4 in 6dhz

Go back to Iron Binding Sites List in 6dhz
Iron binding site 3 out of 4 in the Crystallographic Octamer of A Metal-Free 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 Crystallographic Octamer of A Metal-Free RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:45.6
occ:1.00
FE C:HEM201 0.0 45.6 1.0
ND C:HEM201 1.9 43.9 1.0
NA C:HEM201 2.0 47.9 1.0
NE2 C:HIS102 2.0 49.2 1.0
NB C:HEM201 2.1 42.3 1.0
NC C:HEM201 2.1 44.7 1.0
SD C:MET7 2.3 46.2 1.0
C4D C:HEM201 2.9 49.2 1.0
CE1 C:HIS102 2.9 44.8 1.0
C1D C:HEM201 2.9 43.8 1.0
C1A C:HEM201 3.0 49.7 1.0
C4A C:HEM201 3.0 49.8 1.0
C4B C:HEM201 3.0 42.5 1.0
C1B C:HEM201 3.1 44.7 1.0
C4C C:HEM201 3.1 43.6 1.0
CD2 C:HIS102 3.1 48.9 1.0
C1C C:HEM201 3.1 43.9 1.0
CE C:MET7 3.3 41.1 1.0
CHA C:HEM201 3.4 48.8 1.0
CHD C:HEM201 3.4 44.2 1.0
CHB C:HEM201 3.4 46.5 1.0
CHC C:HEM201 3.4 42.3 1.0
CG C:MET7 3.6 47.0 1.0
ND1 C:HIS102 4.1 47.7 1.0
CG C:HIS102 4.2 49.7 1.0
C3A C:HEM201 4.2 52.8 1.0
C3D C:HEM201 4.2 54.4 1.0
C2D C:HEM201 4.2 48.3 1.0
C2A C:HEM201 4.2 57.0 1.0
C2B C:HEM201 4.3 42.2 1.0
C2C C:HEM201 4.3 44.8 1.0
C3C C:HEM201 4.3 45.2 1.0
C3B C:HEM201 4.3 45.5 1.0
CB C:MET7 4.4 43.8 1.0

Iron binding site 4 out of 4 in 6dhz

Go back to Iron Binding Sites List in 6dhz
Iron binding site 4 out of 4 in the Crystallographic Octamer of A Metal-Free 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 Crystallographic Octamer of A Metal-Free RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:70.7
occ:1.00
FE D:HEM201 0.0 70.7 1.0
ND D:HEM201 1.9 70.0 1.0
NA D:HEM201 2.0 67.0 1.0
NB D:HEM201 2.1 58.4 1.0
SD D:MET7 2.1 81.3 1.0
NC D:HEM201 2.1 59.0 1.0
NE2 D:HIS102 2.2 66.4 1.0
C4D D:HEM201 2.9 70.8 1.0
C1D D:HEM201 2.9 66.7 1.0
C1A D:HEM201 3.0 68.3 1.0
C4B D:HEM201 3.0 56.3 1.0
C4A D:HEM201 3.0 70.3 1.0
C1B D:HEM201 3.0 64.7 1.0
C4C D:HEM201 3.1 60.0 1.0
CE D:MET7 3.1 80.6 1.0
C1C D:HEM201 3.1 55.6 1.0
CE1 D:HIS102 3.2 67.2 1.0
CD2 D:HIS102 3.2 65.6 1.0
CHA D:HEM201 3.4 64.8 1.0
CHD D:HEM201 3.4 66.9 1.0
CHB D:HEM201 3.4 70.1 1.0
CHC D:HEM201 3.4 54.5 1.0
CG D:MET7 3.5 81.8 1.0
C3D D:HEM201 4.1 75.1 1.0
C2D D:HEM201 4.2 69.9 1.0
C2A D:HEM201 4.2 75.9 1.0
C3A D:HEM201 4.2 73.5 1.0
C2B D:HEM201 4.3 62.7 1.0
C2C D:HEM201 4.3 56.3 1.0
C3C D:HEM201 4.3 57.5 1.0
ND1 D:HIS102 4.3 67.8 1.0
CB D:MET7 4.3 78.6 1.0
C3B D:HEM201 4.3 61.2 1.0
CG D:HIS102 4.3 69.1 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: Wed Aug 6 05:23:49 2025

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