Zinc in PDB 6tly: Crystal Structure of the Unconventional Kinetochore Protein Bodo Saltans KKT2 Central Domain

The structure of Crystal Structure of the Unconventional Kinetochore Protein Bodo Saltans KKT2 Central Domain, PDB code: 6tly was solved by G.Marciano, O.Nerusheva, M.Ishii, B.Akiyoshi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.00 / 1.80
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	38.961, 53.512, 83.294, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.5

The structure of Crystal Structure of the Unconventional Kinetochore Protein Bodo Saltans KKT2 Central Domain also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Unconventional Kinetochore Protein Bodo Saltans KKT2 Central Domain (pdb code 6tly). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Unconventional Kinetochore Protein Bodo Saltans KKT2 Central Domain, PDB code: 6tly:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Unconventional Kinetochore Protein Bodo Saltans KKT2 Central Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Unconventional Kinetochore Protein Bodo Saltans KKT2 Central Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:24.5 occ:0.66 ND1 A:HIS584 2.1 26.3 1.0 SG A:CYS623 2.4 23.8 1.0 SG A:CYS620 2.4 23.7 1.0 SG A:CYS580 2.5 23.2 1.0 CE1 A:HIS584 3.0 28.1 1.0 CG A:HIS584 3.1 26.3 1.0 CB A:CYS623 3.2 23.5 1.0 CB A:CYS620 3.3 21.4 1.0 CB A:HIS584 3.4 24.1 1.0 CB A:CYS580 3.4 22.8 1.0 CG A:LYS622 4.0 37.0 1.0 O A:HOH864 4.1 24.5 1.0 NE2 A:HIS584 4.1 28.7 1.0 N A:CYS623 4.1 24.1 1.0 CD2 A:HIS584 4.2 28.1 1.0 CA A:CYS623 4.3 23.6 1.0 CB A:ASN582 4.4 23.1 1.0 N A:HIS584 4.5 24.9 1.0 CD A:LYS622 4.5 44.1 1.0 CA A:HIS584 4.5 24.2 1.0 O A:HOH858 4.7 31.5 1.0 CA A:CYS620 4.7 20.9 1.0 N A:ASN582 4.8 22.0 1.0 CA A:CYS580 4.8 22.7 1.0 ND2 A:ASN582 4.9 22.9 1.0 C A:LYS622 4.9 26.0 1.0 CA A:ASN582 5.0 23.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Unconventional Kinetochore Protein Bodo Saltans KKT2 Central Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Unconventional Kinetochore Protein Bodo Saltans KKT2 Central Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:24.2 occ:0.69 SG A:CYS631 2.3 25.0 1.0 SG A:CYS628 2.3 23.6 1.0 SG A:CYS604 2.3 24.7 1.0 SG A:CYS601 2.4 22.9 1.0 CB A:CYS601 3.2 22.7 1.0 CB A:CYS631 3.2 25.0 1.0 CB A:CYS604 3.3 23.6 1.0 CB A:CYS628 3.5 21.2 1.0 N A:CYS604 3.7 23.8 1.0 N A:CYS628 4.0 20.0 1.0 CA A:CYS604 4.1 24.2 1.0 N A:CYS631 4.1 25.3 1.0 CA A:CYS631 4.3 25.3 1.0 CA A:CYS628 4.3 20.5 1.0 O A:HOH883 4.5 39.6 1.0 CG2 A:VAL627 4.6 21.9 0.5 CA A:CYS601 4.7 21.7 1.0 OE1 A:GLN606 4.7 45.4 1.0 CB A:VAL603 4.7 22.9 1.0 O A:CYS628 4.8 20.5 1.0 C A:VAL603 4.8 24.0 1.0 C A:CYS628 4.8 21.0 1.0 C A:CYS604 4.9 24.2 1.0 CG1 A:VAL627 4.9 20.5 0.5

Zinc binding site 3 out of 3 in the Crystal Structure of the Unconventional Kinetochore Protein Bodo Saltans KKT2 Central Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Unconventional Kinetochore Protein Bodo Saltans KKT2 Central Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:27.3 occ:0.56 NE2 A:HIS660 1.9 27.3 1.0 SG A:CYS647 2.3 28.2 1.0 SG A:CYS664 2.3 27.8 1.0 SG A:CYS644 2.4 25.9 1.0 CD2 A:HIS660 2.9 26.4 1.0 CE1 A:HIS660 3.0 27.8 1.0 CB A:CYS664 3.2 27.5 1.0 CB A:CYS644 3.3 23.6 1.0 CB A:CYS647 3.3 29.3 1.0 N A:CYS647 3.7 29.1 1.0 CG A:HIS660 4.0 26.1 1.0 ND1 A:HIS660 4.1 27.6 1.0 CA A:CYS647 4.1 29.4 1.0 CB A:LYS646 4.5 30.1 1.0 C A:LYS646 4.5 28.9 1.0 CA A:CYS664 4.7 27.6 1.0 CA A:CYS644 4.7 22.5 1.0 CA A:LYS646 4.9 28.3 1.0 N A:LYS646 4.9 27.0 1.0 CB A:LYS649 4.9 28.2 1.0 C A:CYS647 4.9 29.9 1.0

G.Marciano, O.Nerusheva, M.Ishii, B.Akiyoshi. Unconventional Kinetochore Kinases KKT2 and KKT3 Have A Unique Zinc Finger That Promotes Their Kinetochore Localization Biorxiv 2019.
DOI: 10.1101/2019.12.13.875419V1