Calcium in PDB 7df2: Crystal Structure of A C2 Domain Protein From Ramazzottius Varieornatus

The structure of Crystal Structure of A C2 Domain Protein From Ramazzottius Varieornatus, PDB code: 7df2 was solved by Y.Fukuda, T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.68 / 1.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.916, 62.916, 100.499, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 21.2

The binding sites of Calcium atom in the Crystal Structure of A C2 Domain Protein From Ramazzottius Varieornatus (pdb code 7df2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of A C2 Domain Protein From Ramazzottius Varieornatus, PDB code: 7df2:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of A C2 Domain Protein From Ramazzottius Varieornatus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A C2 Domain Protein From Ramazzottius Varieornatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:19.5 occ:1.00 O A:CYS63 2.3 21.4 1.0 OD2 A:ASP135 2.3 18.7 1.0 O A:HOH546 2.4 22.9 1.0 OD1 A:ASP64 2.4 20.0 1.0 OD2 A:ASP142 2.5 21.6 1.0 OD2 A:ASP137 2.5 21.8 1.0 OD1 A:ASP137 2.5 22.1 1.0 CG A:ASP137 2.9 21.2 1.0 C A:CYS63 3.3 19.2 1.0 CG A:ASP142 3.5 23.6 1.0 CG A:ASP135 3.6 19.5 1.0 CG A:ASP64 3.6 20.6 1.0 CA A:CA302 3.7 19.1 1.0 CB A:ASP142 3.8 23.6 1.0 N A:ASP64 4.1 18.7 1.0 CA A:ASP64 4.2 18.6 1.0 CA A:CYS63 4.3 20.6 1.0 OD1 A:ASP135 4.4 18.8 1.0 CB A:ASP137 4.4 22.2 1.0 O A:HOH556 4.4 44.5 1.0 OD2 A:ASP64 4.4 19.9 1.0 CB A:ASP64 4.5 18.2 1.0 CB A:ASP135 4.5 19.4 1.0 O A:HOH565 4.6 34.9 1.0 OD1 A:ASP142 4.6 24.2 1.0 CB A:CYS63 4.7 20.7 1.0 O A:HOH415 4.7 30.8 1.0 O A:HOH548 5.0 21.9 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of A C2 Domain Protein From Ramazzottius Varieornatus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A C2 Domain Protein From Ramazzottius Varieornatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:19.1 occ:1.00 OD2 A:ASP70 2.3 19.2 1.0 O A:LYS136 2.4 19.9 0.5 O A:LYS136 2.4 19.9 0.5 O A:HOH548 2.4 21.9 1.0 OD1 A:ASP135 2.5 18.8 1.0 OD1 A:ASP137 2.5 22.1 1.0 OD2 A:ASP64 2.5 19.9 1.0 OD1 A:ASP64 2.7 20.0 1.0 OD2 A:ASP135 2.7 18.7 1.0 CG A:ASP135 2.9 19.5 1.0 CG A:ASP64 2.9 20.6 1.0 C A:LYS136 3.4 21.0 0.5 C A:LYS136 3.4 21.0 0.5 CG A:ASP70 3.5 21.2 1.0 CA A:CA301 3.7 19.5 1.0 CG A:ASP137 3.7 21.2 1.0 CA A:CA303 4.0 21.2 1.0 CB A:ASP70 4.1 20.6 1.0 CA A:ASP137 4.1 21.1 1.0 N A:ASP137 4.1 20.4 1.0 N A:LYS136 4.3 18.5 0.5 N A:LYS136 4.3 18.5 0.5 CB A:ASP135 4.4 19.4 1.0 CB A:ASP64 4.5 18.2 1.0 C A:ASP135 4.5 18.6 1.0 OD1 A:ASP70 4.5 21.7 1.0 CA A:LYS136 4.5 19.5 0.5 CA A:LYS136 4.5 19.5 0.5 O A:HOH512 4.5 32.8 1.0 N A:ASP70 4.5 17.6 1.0 CB A:ASP137 4.5 22.2 1.0 OD2 A:ASP137 4.5 21.8 1.0 O A:HOH552 4.7 28.6 1.0 O A:ASP135 4.8 19.6 1.0 O A:HOH556 4.8 44.5 1.0 O A:LYS68 4.9 21.5 1.0 CA A:ASP70 4.9 18.0 1.0 CA A:ASP135 4.9 17.6 1.0 O A:HOH550 4.9 47.5 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of A C2 Domain Protein From Ramazzottius Varieornatus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A C2 Domain Protein From Ramazzottius Varieornatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:21.2 occ:1.00 OD1 A:ASP67 2.3 22.4 1.0 O A:LYS68 2.3 21.5 1.0 OD1 A:ASN104 2.4 24.4 1.0 OD2 A:ASP64 2.4 19.9 1.0 O A:HOH552 2.5 28.6 1.0 OD1 A:ASP70 2.5 21.7 1.0 OD2 A:ASP70 2.6 19.2 1.0 CG A:ASP70 2.9 21.2 1.0 CG A:ASP67 3.3 31.1 1.0 CG A:ASN104 3.4 26.4 1.0 C A:LYS68 3.5 19.1 1.0 CG A:ASP64 3.5 20.6 1.0 O A:HOH512 3.9 32.8 1.0 N A:LYS68 3.9 23.2 1.0 CA A:CA302 4.0 19.1 1.0 CB A:ASP67 4.0 23.9 1.0 ND2 A:ASN104 4.1 28.3 1.0 CB A:ASP64 4.1 18.2 1.0 C A:ASP67 4.1 23.5 1.0 O A:HOH548 4.1 21.9 1.0 OD2 A:ASP67 4.3 41.2 1.0 CB A:ASP70 4.3 20.6 1.0 CA A:LYS68 4.3 24.1 1.0 C A:CYS69 4.4 21.9 0.7 C A:CYS69 4.4 21.8 0.3 N A:ASP70 4.4 17.6 1.0 O A:ASP67 4.5 22.2 1.0 N A:CYS69 4.5 19.2 0.7 N A:CYS69 4.5 19.3 0.3 CA A:ASN104 4.5 20.4 1.0 N A:ASN104 4.5 19.0 1.0 CB A:ASN104 4.6 22.5 1.0 OD1 A:ASP64 4.6 20.0 1.0 O A:CYS69 4.6 21.3 0.3 O A:HOH543 4.6 46.1 1.0 O A:CYS69 4.6 21.2 0.7 CA A:CYS69 4.6 19.9 0.7 CA A:ASP67 4.7 23.5 1.0 CA A:CYS69 4.7 20.2 0.3 OD1 A:ASP135 4.8 18.8 1.0 CA A:ASP70 4.9 18.0 1.0

Y.Fukuda, T.Inoue. Structural Insights Into A C2 Domain Protein Specifically Found in Tardigrades. Protein Sci. 2020.
ISSN: ESSN 1469-896X
PubMed: 33226149
DOI: 10.1002/PRO.4002