Nickel in PDB 5fsh: Crystal Structure of Thermus Thermophilus CSM6

The structure of Crystal Structure of Thermus Thermophilus CSM6, PDB code: 5fsh was solved by O.Niewoehner, M.Jinek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.701 / 2.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.309, 207.070, 58.903, 90.00, 90.00, 90.00
R / Rfree (%)	21.89 / 24.38

The binding sites of Nickel atom in the Crystal Structure of Thermus Thermophilus CSM6 (pdb code 5fsh). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Crystal Structure of Thermus Thermophilus CSM6, PDB code: 5fsh:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the Crystal Structure of Thermus Thermophilus CSM6


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Thermus Thermophilus CSM6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1465 b:68.7 occ:1.00 ND2 A:ASN-1 2.0 0.0 1.0 OD2 A:ASP3 2.0 0.3 1.0 OD1 A:ASN-1 2.1 0.5 1.0 CG A:ASN-1 2.3 1.0 1.0 O A:HOH2001 2.6 56.0 1.0 CG A:ASP3 3.2 0.6 1.0 OD1 A:ASP3 3.6 0.3 1.0 CB A:ASN-1 3.8 94.7 1.0 CB A:ASP3 4.6 89.8 1.0 CA A:ASN-1 4.8 79.2 1.0

Nickel binding site 2 out of 6 in the Crystal Structure of Thermus Thermophilus CSM6


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Thermus Thermophilus CSM6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1466 b:72.6 occ:0.16 NE2 A:HIS422 2.0 93.9 1.0 NE2 B:HIS422 2.0 70.1 1.0 OD1 A:ASN416 2.1 88.2 1.0 OD1 B:ASN416 2.1 99.6 1.0 CD2 A:HIS422 2.7 85.0 1.0 CD2 B:HIS422 2.7 65.1 1.0 CE1 A:HIS422 3.0 92.3 1.0 CE1 B:HIS422 3.1 68.5 1.0 CG A:ASN416 3.3 88.7 1.0 CG B:ASN416 3.3 91.7 1.0 CG A:HIS422 3.8 83.2 1.0 CG B:HIS422 3.9 70.1 1.0 ND1 A:HIS422 3.9 88.5 1.0 CG2 A:VAL421 3.9 66.5 1.0 ND2 A:ASN416 4.0 91.9 1.0 ND1 B:HIS422 4.0 70.0 1.0 CG2 B:VAL421 4.0 65.3 1.0 ND2 B:ASN416 4.1 83.3 1.0 CB B:ASN416 4.5 84.5 1.0 CB A:ASN416 4.5 89.7 1.0

Nickel binding site 3 out of 6 in the Crystal Structure of Thermus Thermophilus CSM6


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Thermus Thermophilus CSM6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1467 b:92.1 occ:0.28 OD1 A:ASP195 2.0 0.0 1.0 NE2 A:HIS188 2.0 0.6 1.0 CE1 A:HIS188 2.1 0.1 1.0 CG A:ASP195 2.8 0.8 1.0 OD2 A:ASP195 3.0 0.4 1.0 CD2 A:HIS188 3.2 1.0 1.0 ND1 A:HIS188 3.3 0.8 1.0 CG A:HIS188 3.9 0.5 1.0 CE1 A:TYR214 4.1 72.1 1.0 CB A:ASP195 4.2 81.0 1.0 NH2 A:ARG221 4.3 0.5 1.0 CD1 A:TYR214 4.5 70.7 1.0 CA A:ASP195 4.8 62.8 1.0 O A:HIS188 5.0 68.2 1.0

Nickel binding site 4 out of 6 in the Crystal Structure of Thermus Thermophilus CSM6


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Thermus Thermophilus CSM6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1468 b:91.7 occ:0.62 O A:HOH2035 2.0 76.4 1.0 NE2 A:HIS310 2.0 0.5 1.0 OE2 A:GLU314 2.0 0.7 1.0 CE1 A:HIS310 2.9 95.2 1.0 CD2 A:HIS310 3.1 90.2 1.0 CD A:GLU314 3.2 0.7 1.0 NH1 A:ARG241 3.5 78.8 1.0 NH2 A:ARG241 3.6 75.1 1.0 OE1 A:GLU314 3.9 0.5 1.0 CZ A:ARG241 4.0 80.2 1.0 ND1 A:HIS310 4.0 87.1 1.0 OE2 A:GLU458 4.0 99.7 1.0 CG A:HIS310 4.2 77.1 1.0 CG A:GLU314 4.3 86.8 1.0

Nickel binding site 5 out of 6 in the Crystal Structure of Thermus Thermophilus CSM6


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Thermus Thermophilus CSM6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1469 b:0.7 occ:1.00 OE2 A:GLU207 2.0 0.1 1.0 OE2 B:GLU207 2.0 0.8 1.0 CD B:GLU207 3.1 0.7 1.0 CD A:GLU207 3.2 0.2 1.0 OE1 B:GLU207 3.7 0.6 1.0 OE1 A:GLU207 3.8 0.8 1.0 CG A:GLU207 4.3 90.5 1.0 CG B:GLU207 4.4 92.2 1.0

Nickel binding site 6 out of 6 in the Crystal Structure of Thermus Thermophilus CSM6


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of Thermus Thermophilus CSM6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1465 b:0.7 occ:1.00 NE2 B:HIS310 2.0 89.3 1.0 OE2 B:GLU314 2.0 90.6 1.0 OE2 B:GLU458 2.0 0.8 1.0 CE1 B:HIS310 2.2 93.6 1.0 CD B:GLU314 3.2 82.6 1.0 CD B:GLU458 3.3 0.7 1.0 CD2 B:HIS310 3.3 82.5 1.0 ND1 B:HIS310 3.5 87.7 1.0 CG B:GLU314 3.9 74.1 1.0 NH2 B:ARG241 4.0 74.7 1.0 CG B:HIS310 4.0 77.9 1.0 OE1 B:GLU458 4.1 0.7 1.0 OE1 B:GLU314 4.2 81.5 1.0 CG B:GLU458 4.3 97.9 1.0

O.Niewoehner, M.Jinek. Structural Basis For the Endoribonuclease Activity of the Type III-A Crispr-Associated Protein CSM6. Rna V. 22 318 2016.
ISSN: ISSN 1355-8382
PubMed: 26763118
DOI: 10.1261/RNA.054098.115