Nickel in PDB 4q2d: Crystal Structure of Crispr-Associated Protein in Complex with 2'- Deoxyadenosine 5'-Triphosphate

The structure of Crystal Structure of Crispr-Associated Protein in Complex with 2'- Deoxyadenosine 5'-Triphosphate, PDB code: 4q2d 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)	45.66 / 2.77
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	105.684, 211.630, 104.272, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 24.7

The structure of Crystal Structure of Crispr-Associated Protein in Complex with 2'- Deoxyadenosine 5'-Triphosphate also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Nickel atom in the Crystal Structure of Crispr-Associated Protein in Complex with 2'- Deoxyadenosine 5'-Triphosphate (pdb code 4q2d). 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 in Complex with 2'- Deoxyadenosine 5'-Triphosphate, PDB code: 4q2d:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure of Crispr-Associated Protein in Complex with 2'- Deoxyadenosine 5'-Triphosphate


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 in Complex with 2'- Deoxyadenosine 5'-Triphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1001 b:25.7 occ:1.00 OD1 A:ASP237 1.9 33.3 1.0 OD2 A:ASP99 1.9 24.6 1.0 NE2 A:HIS52 2.1 26.4 1.0 NE2 A:HIS98 2.4 23.9 1.0 NI A:NI1003 2.8 40.0 1.0 CG A:ASP237 2.9 30.6 1.0 CG A:ASP99 3.0 24.6 1.0 CD2 A:HIS52 3.0 29.5 1.0 CE1 A:HIS52 3.1 29.1 1.0 CE1 A:HIS98 3.3 24.4 1.0 OD2 A:ASP237 3.4 32.0 1.0 CD2 A:HIS98 3.4 23.7 1.0 NI A:NI1002 3.5 23.7 1.0 OD1 A:ASP99 3.6 24.4 1.0 NZ A:LYS102 3.6 25.0 1.0 CB A:ASP99 4.1 25.1 1.0 CG A:HIS52 4.2 27.6 1.0 NZ A:LYS37 4.2 43.5 1.0 ND1 A:HIS52 4.2 27.1 1.0 CB A:ASP237 4.2 27.4 1.0 ND1 A:HIS98 4.4 24.4 1.0 CE A:LYS102 4.5 26.7 1.0 CG A:HIS98 4.5 24.0 1.0 CE A:LYS37 4.5 39.1 1.0 NE2 A:HIS171 4.5 27.3 1.0

Nickel binding site 2 out of 3 in the Crystal Structure of Crispr-Associated Protein in Complex with 2'- Deoxyadenosine 5'-Triphosphate


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 in Complex with 2'- Deoxyadenosine 5'-Triphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1002 b:23.7 occ:1.00 NE2 A:HIS138 2.1 28.0 1.0 NE2 A:HIS171 2.3 27.3 1.0 NE2 A:HIS172 2.3 30.4 1.0 OD1 A:ASP99 2.4 24.4 1.0 NI A:NI1003 2.9 40.0 1.0 CE1 A:HIS138 3.0 30.1 1.0 CD2 A:HIS172 3.0 26.3 1.0 CE1 A:HIS171 3.1 28.6 1.0 CD2 A:HIS138 3.2 29.4 1.0 CG A:ASP99 3.2 24.6 1.0 OD2 A:ASP99 3.3 24.6 1.0 CE1 A:HIS172 3.3 31.8 1.0 CD2 A:HIS171 3.4 28.2 1.0 NI A:NI1001 3.5 25.7 1.0 CE A:LYS102 3.8 26.7 1.0 NZ A:LYS102 3.9 25.0 1.0 ND1 A:HIS138 4.1 33.8 1.0 CD2 A:HIS98 4.1 23.7 1.0 CG A:HIS172 4.2 25.5 1.0 CG A:HIS138 4.3 25.4 1.0 ND1 A:HIS172 4.3 26.8 1.0 NE2 A:HIS98 4.3 23.9 1.0 ND1 A:HIS171 4.3 28.8 1.0 CG A:HIS171 4.5 29.0 1.0 OD1 A:ASP237 4.6 33.3 1.0 CB A:ASP99 4.6 25.1 1.0 OD2 A:ASP237 4.7 32.0 1.0 CG A:ASP237 4.9 30.6 1.0 CD A:LYS102 4.9 25.7 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of Crispr-Associated Protein in Complex with 2'- Deoxyadenosine 5'-Triphosphate


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 in Complex with 2'- Deoxyadenosine 5'-Triphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1003 b:40.0 occ:1.00 NI A:NI1001 2.8 25.7 1.0 NI A:NI1002 2.9 23.7 1.0 NZ A:LYS102 3.1 25.0 1.0 OD2 A:ASP237 3.3 32.0 1.0 NE2 A:HIS172 3.3 30.4 1.0 CE1 A:HIS172 3.3 31.8 1.0 NZ A:LYS37 3.4 43.5 1.0 OD2 A:ASP99 3.7 24.6 1.0 OD1 A:ASP237 3.7 33.3 1.0 N A:TYR415 3.8 23.9 1.0 CG A:ASP237 3.9 30.6 1.0 CE A:LYS102 4.0 26.7 1.0 O A:GLY413 4.0 26.8 1.0 CA A:VAL414 4.2 23.5 1.0 CE A:LYS37 4.4 39.1 1.0 NE2 A:HIS52 4.4 26.4 1.0 NE2 A:HIS138 4.4 28.0 1.0 OD1 A:ASP99 4.5 24.4 1.0 CG A:ASP99 4.5 24.6 1.0 C A:VAL414 4.5 23.6 1.0 CE1 A:HIS138 4.6 30.1 1.0 NE2 A:HIS171 4.6 27.3 1.0 ND1 A:HIS172 4.6 26.8 1.0 CD2 A:HIS172 4.7 26.3 1.0 CB A:TYR415 4.7 24.7 1.0 CD1 A:TYR415 4.8 25.2 1.0 CA A:TYR415 4.8 24.2 1.0 CG1 A:VAL414 4.8 22.5 1.0 NE2 A:HIS98 4.9 23.9 1.0 OG A:SER241 5.0 33.8 1.0 C A:GLY413 5.0 24.5 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