Nickel in PDB 7qst: Crystal Structure of Homing Endonuclease-Associated Phovma Intein (C1A)

The structure of Crystal Structure of Homing Endonuclease-Associated Phovma Intein (C1A), PDB code: 7qst was solved by H.M.Beyer, H.Iwai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.51 / 2.49
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	91.08, 81.87, 67.69, 90, 112.85, 90
R / Rfree (%)	18.3 / 24.3

The structure of Crystal Structure of Homing Endonuclease-Associated Phovma Intein (C1A) also contains other interesting chemical elements:

Cadmium

(Cd)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of Homing Endonuclease-Associated Phovma Intein (C1A) (pdb code 7qst). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of Homing Endonuclease-Associated Phovma Intein (C1A), PDB code: 7qst:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure of Homing Endonuclease-Associated Phovma Intein (C1A)


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 Homing Endonuclease-Associated Phovma Intein (C1A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni403 b:116.1 occ:1.00 SG A:CYS171 2.0 134.6 1.0 CB A:CYS171 3.1 111.3 1.0 OD1 A:ASP172 3.6 178.1 1.0 CA A:CYS171 3.6 108.3 1.0 NZ A:LYS251 3.7 131.4 1.0 N A:ASP172 4.0 143.1 1.0 CG A:LYS251 4.2 124.9 1.0 C A:CYS171 4.4 122.9 1.0 O A:TYR170 4.5 100.1 1.0 OD1 A:ASN159 4.7 119.5 1.0 CG A:ASP172 4.7 177.8 1.0 N A:CYS171 4.8 104.9 1.0 CE A:LYS251 4.9 120.1 1.0 CD1 A:LEU176 5.0 86.5 1.0

Nickel binding site 2 out of 3 in the Crystal Structure of Homing Endonuclease-Associated Phovma Intein (C1A)


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 Homing Endonuclease-Associated Phovma Intein (C1A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni404 b:87.7 occ:1.00 NE2 A:HIS337 2.3 91.8 1.0 OD2 A:ASP124 2.3 97.9 1.0 OD1 A:ASP124 2.5 99.7 1.0 CG A:ASP124 2.7 90.6 1.0 CE1 A:HIS337 2.9 90.7 1.0 CD2 A:HIS337 3.4 76.4 1.0 ND1 A:HIS337 4.1 83.9 1.0 CB A:ASP124 4.2 71.5 1.0 CG A:LYS122 4.3 65.5 1.0 CG A:HIS337 4.3 78.8 1.0 CD A:LYS55 4.5 108.5 1.0 CE A:LYS122 4.8 75.6 1.0 NZ A:LYS122 4.8 75.8 1.0 CG A:LYS55 4.8 104.2 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of Homing Endonuclease-Associated Phovma Intein (C1A)


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 Homing Endonuclease-Associated Phovma Intein (C1A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni405 b:69.5 occ:1.00 OE2 A:GLU105 1.9 85.7 1.0 NE2 A:HIS375 2.3 75.3 1.0 CD A:GLU105 2.3 78.8 1.0 OE1 A:GLU105 2.4 64.4 1.0 O A:HOH508 2.8 63.0 1.0 CE1 A:HIS375 3.1 72.1 1.0 CD2 A:HIS375 3.3 69.1 1.0 CG A:GLU105 3.7 75.7 1.0 ND1 A:HIS375 4.3 81.0 1.0 CG A:HIS375 4.4 74.3 1.0 CB A:GLU105 4.8 66.7 1.0

H.M.Beyer, H.Iwai. Structural Basis For the Propagation of Homing Endonuclease-Associated Inteins. Front Mol Biosci V. 9 55511 2022.
ISSN: ESSN 2296-889X
PubMed: 35372505
DOI: 10.3389/FMOLB.2022.855511