Nickel in PDB 4q2c: Crystal Structure of Crispr-Associated Protein

The structure of Crystal Structure of Crispr-Associated Protein, PDB code: 4q2c was solved by B.Gong, M.Shin, J.Sun, J.Van Der Oost, J.-S.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	93.78 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	104.268, 214.558, 102.196, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 22.9

The binding sites of Nickel atom in the Crystal Structure of Crispr-Associated Protein (pdb code 4q2c). 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 Crispr-Associated Protein, PDB code: 4q2c:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure of Crispr-Associated Protein


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 Crispr-Associated Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1001 b:34.1 occ:1.00 NE2 A:HIS52 2.0 40.6 1.0 OD2 A:ASP237 2.1 34.0 1.0 OD1 A:ASP99 2.1 40.7 1.0 NE2 A:HIS98 2.2 28.4 1.0 NI A:NI1003 2.8 57.6 1.0 CD2 A:HIS52 3.0 37.5 1.0 CE1 A:HIS52 3.0 40.5 1.0 CG A:ASP99 3.1 38.6 1.0 CG A:ASP237 3.1 31.9 1.0 CE1 A:HIS98 3.1 34.6 1.0 CD2 A:HIS98 3.2 30.3 1.0 OD1 A:ASP237 3.6 34.4 1.0 OD2 A:ASP99 3.6 39.6 1.0 NI A:NI1002 3.9 30.0 1.0 CB A:ASP99 4.1 36.8 1.0 CG A:HIS52 4.1 36.0 1.0 ND1 A:HIS52 4.1 37.8 1.0 NZ A:LYS102 4.1 27.8 1.0 CB A:ASP237 4.2 29.0 1.0 ND1 A:HIS98 4.3 28.4 1.0 CG A:HIS98 4.4 30.0 1.0 NZ A:LYS37 4.7 36.7 1.0 CE A:LYS102 4.8 27.8 1.0 CG2 A:VAL56 4.9 29.9 1.0 CE A:LYS37 4.9 34.6 1.0 NE2 A:HIS171 4.9 32.4 1.0

Nickel binding site 2 out of 3 in the Crystal Structure of Crispr-Associated Protein


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 Crispr-Associated Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1002 b:30.0 occ:1.00 NE2 A:HIS138 2.1 34.6 1.0 NE2 A:HIS171 2.1 32.4 1.0 NE2 A:HIS172 2.3 38.9 1.0 OD2 A:ASP99 2.4 39.6 1.0 CD2 A:HIS172 3.0 31.5 1.0 CD2 A:HIS138 3.0 39.1 1.0 CD2 A:HIS171 3.0 27.0 1.0 NI A:NI1003 3.1 57.6 1.0 CE1 A:HIS138 3.1 34.6 1.0 CE1 A:HIS171 3.2 28.1 1.0 CE1 A:HIS172 3.2 38.5 1.0 CG A:ASP99 3.3 38.6 1.0 OD1 A:ASP99 3.5 40.7 1.0 NI A:NI1001 3.9 34.1 1.0 CE A:LYS102 4.0 27.8 1.0 CG A:HIS172 4.1 32.0 1.0 CD2 A:HIS98 4.1 30.3 1.0 ND1 A:HIS172 4.2 35.7 1.0 ND1 A:HIS138 4.2 39.3 1.0 CG A:HIS138 4.2 41.0 1.0 CG A:HIS171 4.2 31.9 1.0 ND1 A:HIS171 4.2 29.3 1.0 NZ A:LYS102 4.4 27.8 1.0 NE2 A:HIS98 4.4 28.4 1.0 CB A:ASP99 4.7 36.8 1.0 OD1 A:ASP237 4.9 34.4 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of Crispr-Associated Protein


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 Crispr-Associated Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1003 b:57.6 occ:1.00 NI A:NI1001 2.8 34.1 1.0 NI A:NI1002 3.1 30.0 1.0 NZ A:LYS102 3.4 27.8 1.0 OD1 A:ASP237 3.4 34.4 1.0 CE1 A:HIS172 3.5 38.5 1.0 OD1 A:ASP99 3.5 40.7 1.0 NE2 A:HIS172 3.6 38.9 1.0 OD2 A:ASP237 3.6 34.0 1.0 NZ A:LYS37 3.9 36.7 1.0 CG A:ASP237 3.9 31.9 1.0 N A:TYR415 4.0 35.4 1.0 O A:GLY413 4.1 39.4 1.0 CE A:LYS102 4.1 27.8 1.0 OD2 A:ASP99 4.3 39.6 1.0 CG A:ASP99 4.3 38.6 1.0 NE2 A:HIS52 4.3 40.6 1.0 CA A:VAL414 4.4 26.2 1.0 NE2 A:HIS138 4.5 34.6 1.0 CE A:LYS37 4.6 34.6 1.0 NE2 A:HIS98 4.7 28.4 1.0 ND1 A:HIS172 4.7 35.7 1.0 C A:VAL414 4.8 31.2 1.0 NE2 A:HIS171 4.8 32.4 1.0 CB A:TYR415 4.9 34.3 1.0 CD2 A:HIS172 4.9 31.5 1.0 CE1 A:HIS138 4.9 34.6 1.0 OG A:SER241 4.9 30.9 1.0 CD1 A:TYR415 4.9 34.2 1.0 CE1 A:HIS52 4.9 40.5 1.0 CA A:TYR415 5.0 36.5 1.0 CD2 A:HIS171 5.0 27.0 1.0

B.Gong, M.Shin, J.Sun, C.H.Jung, E.L.Bolt, J.Van Der Oost, J.-S.Kim. Molecular Insights Into Dna Interference By Crispr-Associated Nuclease-Helicase CAS3 Proc.Natl.Acad.Sci.Usa 2014.
ISSN: ESSN 1091-6490
PubMed: 25368186
DOI: 10.1073/PNAS.1410806111