Zinc in PDB 4c98: Thermus Thermophilus CAS6 (TTHB231)

The structure of Thermus Thermophilus CAS6 (TTHB231), PDB code: 4c98 was solved by M.Jinek, O.Niewoehner, J.A.Doudna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.465 / 2.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.540, 68.540, 133.740, 90.00, 90.00, 90.00
R / Rfree (%)	20.55 / 22.1

The binding sites of Zinc atom in the Thermus Thermophilus CAS6 (TTHB231) (pdb code 4c98). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Thermus Thermophilus CAS6 (TTHB231), PDB code: 4c98:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Thermus Thermophilus CAS6 (TTHB231)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermus Thermophilus CAS6 (TTHB231) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1265 b:0.3 occ:0.89 HE1 A:HIS23 1.4 0.0 1.0 HE1 A:HIS42 1.6 0.4 1.0 CE1 A:HIS42 2.0 0.3 1.0 NE2 A:HIS42 2.0 0.7 1.0 CE1 A:HIS23 2.1 0.2 1.0 NE2 A:HIS23 2.8 0.8 1.0 HE2 A:HIS23 2.8 0.4 1.0 ND1 A:HIS23 3.1 0.1 1.0 ND1 A:HIS42 3.3 0.2 1.0 CD2 A:HIS42 3.4 0.3 1.0 HD1 A:HIS23 3.4 1.0 1.0 HD1 A:HIS42 3.8 0.2 1.0 CG A:HIS42 3.9 0.3 1.0 CD2 A:HIS23 4.0 0.0 1.0 HD2 A:HIS42 4.0 0.2 1.0 CG A:HIS23 4.2 0.6 1.0 HA2 A:GLY24 4.7 0.2 1.0 HD2 A:HIS23 4.7 0.6 1.0

Zinc binding site 2 out of 5 in the Thermus Thermophilus CAS6 (TTHB231)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thermus Thermophilus CAS6 (TTHB231) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1266 b:23.6 occ:0.97 OE2 A:GLU127 2.0 81.0 1.0 CD A:GLU127 2.0 55.3 1.0 O A:HOH2048 2.1 20.6 1.0 OE1 A:GLU127 2.1 42.0 1.0 O A:HOH2045 2.2 4.8 1.0 CG A:GLU127 3.3 47.2 1.0 HG2 A:GLU127 3.4 56.6 1.0 HG3 A:GLU127 3.6 56.6 1.0 O A:HOH2015 4.0 40.2 1.0 HG2 A:GLU124 4.0 25.1 1.0 HA A:GLU124 4.2 26.7 1.0 O A:HOH2047 4.3 36.6 1.0 HB2 A:GLU127 4.4 43.8 1.0 CB A:GLU127 4.4 36.5 1.0 HG3 A:GLU124 4.5 25.1 1.0 HB3 A:GLU127 4.6 43.8 1.0 CG A:GLU124 4.7 21.0 1.0 HB3 A:GLU123 4.8 25.6 1.0

Zinc binding site 3 out of 5 in the Thermus Thermophilus CAS6 (TTHB231)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Thermus Thermophilus CAS6 (TTHB231) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1267 b:63.3 occ:0.60 NE2 A:HIS175 2.0 34.7 1.0 O A:HOH2088 2.7 56.5 1.0 CE1 A:HIS175 2.9 44.2 1.0 HE1 A:HIS175 3.0 53.0 1.0 CD2 A:HIS175 3.1 31.0 1.0 HD2 A:HIS175 3.4 37.2 1.0 HB2 A:ALA174 3.9 39.9 1.0 HB1 A:ALA174 4.0 39.9 1.0 ND1 A:HIS175 4.1 36.5 1.0 CG A:HIS175 4.2 30.3 1.0 CB A:ALA174 4.4 33.2 1.0 HG2 A:LYS171 4.6 30.9 1.0 HA A:LYS171 4.6 20.6 1.0 HB3 A:ALA174 4.7 39.9 1.0 HD13 A:LEU75 4.9 38.5 1.0

Zinc binding site 4 out of 5 in the Thermus Thermophilus CAS6 (TTHB231)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Thermus Thermophilus CAS6 (TTHB231) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1268 b:84.0 occ:0.59 ND1 A:HIS175 2.0 36.5 1.0 CE1 A:HIS175 2.7 44.2 1.0 HE1 A:HIS175 2.7 53.0 1.0 CG A:HIS175 3.2 30.3 1.0 HA A:HIS175 3.4 26.7 1.0 HB3 A:HIS175 3.6 27.3 1.0 OD2 A:ASP76 3.6 83.3 1.0 CB A:HIS175 3.8 22.7 1.0 NE2 A:HIS175 3.9 34.7 1.0 CA A:HIS175 4.1 22.2 1.0 CD2 A:HIS175 4.2 31.0 1.0 O A:ALA174 4.3 27.5 1.0 CG A:ASP76 4.3 74.5 1.0 OD1 A:ASP76 4.4 85.3 1.0 HB2 A:LEU75 4.7 28.3 1.0 HB2 A:HIS175 4.7 27.3 1.0 O A:HOH2087 4.9 55.0 1.0 C A:ALA174 4.9 31.5 1.0 N A:HIS175 4.9 22.8 1.0 O A:HIS175 5.0 27.6 1.0

Zinc binding site 5 out of 5 in the Thermus Thermophilus CAS6 (TTHB231)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Thermus Thermophilus CAS6 (TTHB231) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1269 b:0.7 occ:0.62 HZ3 A:TRP228 1.6 78.9 1.0 CZ3 A:TRP228 2.1 65.7 1.0 O A:HOH2105 2.4 44.4 1.0 HH2 A:TRP228 2.5 85.7 1.0 CH2 A:TRP228 2.6 71.4 1.0 CE3 A:TRP228 3.1 54.2 1.0 HE3 A:TRP228 3.4 65.1 1.0 OE2 A:GLU197 3.5 46.1 1.0 CZ2 A:TRP228 3.8 63.2 1.0 CD2 A:TRP228 4.2 54.3 1.0 CD A:GLU197 4.2 56.1 1.0 OE1 A:GLU197 4.3 49.2 1.0 HZ2 A:TRP228 4.4 75.8 1.0 CE2 A:TRP228 4.4 59.9 1.0

O.Niewoehner, M.Jinek, J.A.Doudna. Evolution of Crispr Rna Recognition and Processing By CAS6 Endonucleases. Nucleic Acids Res. V. 42 1341 2014.
ISSN: ISSN 0305-1048
PubMed: 24150936
DOI: 10.1093/NAR/GKT922