Nickel in PDB 5vvl: CAS1-CAS2 Bound to Full-Site Mimic with Ni

The structure of CAS1-CAS2 Bound to Full-Site Mimic with Ni, PDB code: 5vvl was solved by A.V.Wright, G.J.Knott, K.D.Doxzen, J.A.Doudna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.50 / 3.31
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.642, 197.728, 88.792, 90.00, 111.35, 90.00
R / Rfree (%)	22.4 / 26.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Nickel atom in the CAS1-CAS2 Bound to Full-Site Mimic with Ni (pdb code 5vvl). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 22 binding sites of Nickel where determined in the CAS1-CAS2 Bound to Full-Site Mimic with Ni, PDB code: 5vvl:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 22 in the CAS1-CAS2 Bound to Full-Site Mimic with Ni


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of CAS1-CAS2 Bound to Full-Site Mimic with Ni within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:0.2 occ:0.73 OD2 A:ASP221 2.0 0.7 1.0 OP2 J:DG17 2.0 0.7 1.0 NE2 A:HIS208 2.0 1.0 1.0 CE1 A:HIS208 2.5 0.5 1.0 CG A:ASP221 3.0 0.1 1.0 CD2 A:HIS208 3.2 0.2 1.0 OD1 A:ASP221 3.3 0.2 1.0 P J:DG17 3.4 0.5 1.0 O3' K:DC58 3.8 0.7 1.0 ND1 A:HIS208 3.8 0.8 1.0 C3' K:DC58 4.1 0.8 1.0 O5' J:DG17 4.1 0.4 1.0 CG A:HIS208 4.1 0.8 1.0 O3' J:DC16 4.2 0.1 1.0 O A:TYR217 4.2 0.5 1.0 CB A:ASP221 4.3 0.2 1.0 C3' J:DC16 4.4 0.1 1.0 OP1 J:DG17 4.4 0.7 1.0 CB A:TYR217 4.5 87.9 1.0 OE2 A:GLU141 4.7 0.2 1.0 NZ A:LYS224 4.8 0.7 1.0 C A:TYR217 4.9 0.1 1.0 C2' K:DC58 4.9 0.2 1.0

Nickel binding site 2 out of 22 in the CAS1-CAS2 Bound to Full-Site Mimic with Ni


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of CAS1-CAS2 Bound to Full-Site Mimic with Ni within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:0.8 occ:0.89 NZ A:LYS37 2.0 0.8 1.0 N7 H:DG1 2.0 90.1 1.0 CE A:LYS37 2.9 0.4 1.0 C8 H:DG1 2.9 85.8 1.0 C5 H:DG1 3.1 87.0 1.0 CD A:LYS37 3.2 0.9 1.0 O6 H:DG1 3.6 96.0 1.0 C6 H:DG1 3.7 86.4 1.0 N9 H:DG1 4.1 84.2 1.0 C4 H:DG1 4.2 85.9 1.0 CG A:LYS37 4.5 0.8 1.0

Nickel binding site 3 out of 22 in the CAS1-CAS2 Bound to Full-Site Mimic with Ni


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of CAS1-CAS2 Bound to Full-Site Mimic with Ni within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:0.5 occ:1.00 OD2 B:ASP221 2.0 0.1 1.0 NE2 B:HIS208 2.0 0.7 1.0 CE1 B:HIS208 2.6 0.3 1.0 CG B:ASP221 3.2 0.8 1.0 CD2 B:HIS208 3.2 0.6 1.0 ND1 B:HIS208 3.8 1.0 1.0 OE2 B:GLU141 3.8 1.0 1.0 OD1 B:ASP221 3.9 0.7 1.0 CG B:HIS208 4.2 0.7 1.0 CB B:ASP221 4.3 0.2 1.0 O B:TYR217 4.5 0.5 1.0 CB B:TYR217 4.7 0.5 1.0 CD B:GLU141 4.9 0.9 1.0 NH1 B:ARG123 5.0 0.4 1.0

Nickel binding site 4 out of 22 in the CAS1-CAS2 Bound to Full-Site Mimic with Ni


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of CAS1-CAS2 Bound to Full-Site Mimic with Ni within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni401 b:0.4 occ:0.99 OD2 C:ASP244 2.9 1.0 1.0 N6 K:DA14 3.6 0.4 1.0 CG C:ASP244 3.9 0.1 1.0 OD1 C:ASP244 4.4 0.5 1.0 N1 K:DA14 4.5 0.3 1.0 C6 K:DA14 4.5 0.0 1.0

Nickel binding site 5 out of 22 in the CAS1-CAS2 Bound to Full-Site Mimic with Ni


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of CAS1-CAS2 Bound to Full-Site Mimic with Ni within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni402 b:0.0 occ:0.28 OP2 K:DG17 2.0 0.4 1.0 O3' J:DA58 2.0 98.7 1.0 NE2 C:HIS208 2.0 0.0 1.0 OD2 C:ASP221 2.0 0.2 1.0 CE1 C:HIS208 2.5 0.1 1.0 CG C:ASP221 3.2 0.0 1.0 CD2 C:HIS208 3.3 97.8 1.0 C3' J:DA58 3.3 93.0 1.0 P K:DG17 3.4 0.4 1.0 OE2 C:GLU141 3.4 0.0 1.0 OD1 C:ASP221 3.7 0.8 1.0 ND1 C:HIS208 3.7 98.0 1.0 OP1 K:DG17 4.0 0.4 1.0 C2' J:DA58 4.1 88.2 1.0 CG C:HIS208 4.1 97.2 1.0 O5' K:DG17 4.2 0.4 1.0 CD C:GLU141 4.3 0.7 1.0 C4' J:DA58 4.4 91.9 1.0 CB C:ASP221 4.4 0.3 1.0 O3' K:DG16 4.4 0.7 1.0 OE1 C:GLU141 4.6 0.8 1.0 O C:TYR217 4.8 0.1 1.0 C3' K:DG16 4.8 0.7 1.0 C5' J:DA58 4.9 92.6 1.0 CB C:TYR217 5.0 71.4 1.0

Nickel binding site 6 out of 22 in the CAS1-CAS2 Bound to Full-Site Mimic with Ni


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of CAS1-CAS2 Bound to Full-Site Mimic with Ni within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni401 b:0.7 occ:1.00 NE2 D:HIS208 2.0 0.4 1.0 OD2 D:ASP221 2.0 99.4 1.0 CD2 D:HIS208 2.9 0.4 1.0 CE1 D:HIS208 3.0 0.4 1.0 CG D:ASP221 3.1 93.1 1.0 OD1 D:ASP221 3.7 87.5 1.0 CG D:HIS208 4.0 0.4 1.0 ND1 D:HIS208 4.1 0.4 1.0 CB D:ASP221 4.3 90.2 1.0 OE1 D:GLU141 4.5 0.9 1.0 O D:TYR217 4.9 82.8 1.0 NZ D:LYS224 4.9 0.1 1.0

Nickel binding site 7 out of 22 in the CAS1-CAS2 Bound to Full-Site Mimic with Ni


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of CAS1-CAS2 Bound to Full-Site Mimic with Ni within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni201 b:0.3 occ:1.00 O E:ALA28 4.7 85.4 1.0 O F:ALA28 4.9 85.6 1.0

Nickel binding site 8 out of 22 in the CAS1-CAS2 Bound to Full-Site Mimic with Ni


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of CAS1-CAS2 Bound to Full-Site Mimic with Ni within 5.0Å range: probe atom residue distance (Å) B Occ G:Ni101 b:0.0 occ:0.99 NZ C:LYS37 2.0 0.4 1.0 N7 G:DG1 2.0 79.9 1.0 CD C:LYS37 2.7 0.1 1.0 CE C:LYS37 2.7 0.1 1.0 C8 G:DG1 3.0 79.5 1.0 C5 G:DG1 3.0 77.9 1.0 O6 G:DG1 3.3 78.7 1.0 C6 G:DG1 3.5 77.4 1.0 CG C:LYS37 4.1 0.5 1.0 N9 G:DG1 4.2 77.3 1.0 C4 G:DG1 4.2 76.3 1.0 CB C:LYS37 4.7 0.8 1.0 N4 G:DC2 4.9 85.9 1.0 N1 G:DG1 4.9 75.3 1.0

Nickel binding site 9 out of 22 in the CAS1-CAS2 Bound to Full-Site Mimic with Ni


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of CAS1-CAS2 Bound to Full-Site Mimic with Ni within 5.0Å range: probe atom residue distance (Å) B Occ J:Ni101 b:0.7 occ:1.00 N7 J:DG17 2.0 0.5 1.0 C8 J:DG17 2.7 0.1 1.0 C5 J:DG17 3.2 0.8 1.0 O6 J:DG17 3.8 0.6 1.0 C6 J:DG17 3.8 0.4 1.0 N9 J:DG17 4.0 0.6 1.0 C4 J:DG17 4.2 0.1 1.0 N4 K:DC58 4.2 0.4 1.0 C5 K:DC58 4.4 0.4 1.0 C4 K:DC58 4.7 0.4 1.0

Nickel binding site 10 out of 22 in the CAS1-CAS2 Bound to Full-Site Mimic with Ni


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of CAS1-CAS2 Bound to Full-Site Mimic with Ni within 5.0Å range: probe atom residue distance (Å) B Occ J:Ni102 b:0.6 occ:1.00 N7 J:DG8 3.4 95.3 1.0 O6 J:DG9 3.6 92.6 1.0 NI J:NI104 3.9 0.0 1.0 NI J:NI103 4.0 0.3 1.0 O6 J:DG8 4.0 83.7 1.0 C5 J:DG8 4.2 93.8 1.0 C8 J:DG8 4.3 99.1 1.0 C6 J:DG8 4.5 87.0 1.0 N4 H:DC3 4.6 88.0 1.0 C6 J:DG9 4.7 90.7 1.0 C6 J:DT7 4.8 0.9 1.0 N7 J:DG9 4.9 90.1 1.0 C2' J:DT7 4.9 0.1 1.0 C5 J:DT7 5.0 98.4 1.0

A.V.Wright, J.J.Liu, G.J.Knott, K.W.Doxzen, E.Nogales, J.A.Doudna. Structures of the Crispr Genome Integration Complex. Science V. 357 1113 2017.
ISSN: ESSN 1095-9203
PubMed: 28729350
DOI: 10.1126/SCIENCE.AAO0679