Calcium in PDB 6jk4: CA2+-Dependent Type II Antifreeze Protein

The structure of CA2+-Dependent Type II Antifreeze Protein, PDB code: 6jk4 was solved by T.Arai, S.Tsuda, H.Kondo, Y.Nishimiya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.04 / 1.06
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	65.952, 65.952, 49.794, 90.00, 90.00, 120.00
R / Rfree (%)	15.4 / 17.4

The binding sites of Calcium atom in the CA2+-Dependent Type II Antifreeze Protein (pdb code 6jk4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the CA2+-Dependent Type II Antifreeze Protein, PDB code: 6jk4:

Calcium binding site 1 out of 1 in the CA2+-Dependent Type II Antifreeze Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of CA2+-Dependent Type II Antifreeze Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:7.3 occ:1.00 O A:ASP114 2.3 8.1 1.0 OD2 A:ASP94 2.3 8.8 1.0 OE1 A:GLU99 2.4 10.1 1.0 OE1 A:GLN92 2.4 7.8 1.0 O A:HOH422 2.4 10.9 1.0 OD1 A:ASP114 2.4 7.1 1.0 OD1 A:ASP113 2.5 9.3 1.0 CD A:GLN92 3.3 7.6 1.0 C A:ASP114 3.4 6.7 1.0 CG A:ASP94 3.4 8.3 1.0 CG A:ASP113 3.4 8.3 1.0 CD A:GLU99 3.5 9.9 1.0 CG A:ASP114 3.5 6.5 1.0 NE2 A:GLN92 3.5 9.3 1.0 N A:ASP114 3.5 6.2 1.0 CA A:ASP114 3.9 6.1 1.0 OD2 A:ASP113 3.9 9.6 1.0 CB A:ASP94 4.0 8.9 1.0 CG A:GLU99 4.1 9.6 1.0 O A:HOH443 4.1 15.1 1.0 O A:HOH456 4.2 23.1 1.0 CB A:ASP114 4.2 6.3 1.0 N A:ASP94 4.2 7.1 1.0 C A:ASP113 4.2 6.5 1.0 O A:HOH460 4.3 20.1 1.0 OD2 A:ASP114 4.5 7.0 1.0 OD1 A:ASP94 4.5 10.4 1.0 N A:THR115 4.5 6.6 1.0 OE2 A:GLU99 4.5 15.8 1.0 CB A:ASP113 4.6 8.0 1.0 CA A:ASP113 4.6 6.5 1.0 CB A:GLU99 4.6 7.9 1.0 CG A:GLN92 4.7 7.0 1.0 CA A:ASP94 4.8 8.5 1.0 O A:GLU99 4.9 7.7 1.0 CA A:THR115 5.0 6.6 1.0

T.Arai, Y.Nishimiya, Y.Ohyama, H.Kondo, S.Tsuda. Calcium-Binding Generates the Semi-Clathrate Waters on A Type II Antifreeze Protein to Adsorb Onto An Ice Crystal Surface. Biomolecules V. 9 2019.
ISSN: ESSN 2218-273X
PubMed: 31035615
DOI: 10.3390/BIOM9050162