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

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

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

Iron

(Fe)

4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystallographic Octamer of A Metal-Free RIDC1 Variant Bearing Two Disulfide Bonded Cysteines, PDB code: 6dhz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 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 Calcium with other atoms in the Ca 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:Ca202 b:82.5 occ:1.00 O A:LYS19 3.1 76.0 1.0 O A:HOH301 3.1 44.4 1.0 OD2 A:ASP21 3.8 81.4 1.0 OD1 A:ASP21 3.9 84.0 1.0 C A:LYS19 4.2 65.9 1.0 CG A:ASP21 4.2 83.0 1.0 CB A:LYS19 4.3 71.5 1.0 CD A:LYS19 4.4 86.9 1.0 CG A:LYS19 4.5 79.8 1.0 CE A:LYS19 4.8 86.9 1.0 CA A:LYS19 4.8 69.1 1.0

Calcium binding site 2 out of 7 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 Calcium with other atoms in the Ca 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 A:Ca203 b:72.6 occ:1.00 OD2 A:ASP2 2.8 57.6 1.0 OD2 A:ASP5 2.8 62.9 1.0 OD1 A:ASP5 3.2 65.5 1.0 CG A:ASP5 3.3 59.4 1.0 CG A:ASP2 4.0 58.5 1.0 CB A:ASP2 4.5 59.0 1.0 CB A:ASP5 4.8 57.0 1.0 OD1 A:ASP2 4.9 59.6 1.0

Calcium binding site 3 out of 7 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 Calcium with other atoms in the Ca 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 B:Ca202 b:0.5 occ:1.00 O1A B:HEM201 2.6 66.7 1.0 OE1 B:GLU4 3.0 57.8 1.0 CGA B:HEM201 3.6 62.7 1.0 CD B:GLU4 3.7 62.5 1.0 O2A B:HEM201 3.9 63.8 1.0 O2D B:HEM201 4.3 70.1 1.0 CG B:GLU4 4.3 61.8 1.0 OE2 B:GLU4 4.4 70.3 1.0 O B:HOH301 4.5 41.7 1.0 CBA B:HEM201 4.9 58.7 1.0

Calcium binding site 4 out of 7 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 Calcium with other atoms in the Ca 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 B:Ca203 b:77.6 occ:1.00 O B:ALA1 2.5 61.3 1.0 OD2 B:ASP39 2.5 57.0 1.0 OD1 B:ASP39 2.7 57.0 1.0 CG B:ASP39 3.0 55.6 1.0 N B:ALA1 3.2 74.5 1.0 C B:ALA1 3.4 59.5 1.0 CA B:ALA1 3.9 67.3 1.0 CB B:ASP39 4.5 48.6 1.0 N B:ASP2 4.6 52.5 1.0 O B:ASP39 4.8 53.8 1.0

Calcium binding site 5 out of 7 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 Calcium with other atoms in the Ca binding site number 5 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:Ca202 b:91.5 occ:1.00 OD1 C:ASP21 3.0 94.4 1.0 OD2 C:ASP21 3.3 86.0 1.0 CG C:ASP21 3.6 90.4 1.0 O C:LYS19 4.3 63.4 1.0

Calcium binding site 6 out of 7 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 Calcium with other atoms in the Ca binding site number 6 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:Ca203 b:80.1 occ:1.00 OD1 C:ASP5 2.1 80.7 1.0 OE2 C:GLU8 2.5 1.0 1.0 CG C:ASP5 3.1 77.0 1.0 OD2 C:ASP5 3.5 0.5 1.0 CD C:GLU8 3.6 87.5 1.0 OE1 C:GLU8 4.0 99.2 1.0 CB C:ASP5 4.5 61.9 1.0 CA C:ASP5 4.8 54.8 1.0 CG C:GLU8 5.0 70.5 1.0

Calcium binding site 7 out of 7 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 Calcium with other atoms in the Ca binding site number 7 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:Ca202 b:64.2 occ:1.00 OD1 D:ASP39 2.3 94.3 1.0 CG D:ASP39 3.1 79.8 1.0 O D:ALA1 3.1 64.5 1.0 N D:ALA1 3.3 83.5 1.0 OD2 D:ASP39 3.3 82.9 1.0 C D:ALA1 4.1 77.2 1.0 CA D:ALA1 4.3 79.9 1.0 O D:ASP39 4.5 92.5 1.0 CB D:ASP39 4.5 76.7 1.0 C D:ASP39 4.8 85.3 1.0 CA D:ASP39 4.8 76.8 1.0

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