Atomistry » Iron » PDB 6cxv-6dhz » 6dhy
Atomistry »
  Iron »
    PDB 6cxv-6dhz »
      6dhy »

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: Tue Aug 6 16:28:54 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy