Iodine in PDB 5w1h: Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer)

The structure of Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer), PDB code: 5w1h was solved by G.J.Knott, J.A.Doudna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.12 / 1.99
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	150.842, 92.213, 115.858, 90.00, 92.42, 90.00
R / Rfree (%)	18.5 / 21.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer) (pdb code 5w1h). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 23 binding sites of Iodine where determined in the Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer), PDB code: 5w1h:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 23 in the Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1501 b:48.6 occ:0.67 O A:HOH1821 3.3 35.5 1.0 O A:HOH2041 3.3 54.3 1.0 CA A:PHE854 4.0 32.6 1.0 CG A:GLU857 4.2 50.6 1.0 N A:PHE854 4.3 32.3 1.0 CG2 A:VAL735 4.3 36.5 1.0 CB A:GLU857 4.4 39.3 1.0 CD1 A:PHE854 4.4 34.3 1.0 O A:GLU853 4.4 32.9 1.0 CB A:ASN734 4.4 46.5 1.0 CB A:PHE854 4.4 32.2 1.0 ND2 A:ASN858 4.5 35.8 1.0 C A:GLU853 4.5 37.2 1.0 N A:VAL735 4.6 38.0 1.0 CD A:ARG738 4.6 57.1 1.0 C A:ASN734 4.6 43.8 1.0 O A:ASN734 4.7 41.1 1.0 CA A:VAL735 4.7 38.8 1.0 OD2 A:ASP732 4.9 39.9 1.0 CG A:PHE854 5.0 30.6 1.0

Iodine binding site 2 out of 23 in the Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1502 b:42.2 occ:0.68 O A:HOH2236 3.3 49.2 1.0 NH1 A:ARG1126 3.5 25.3 1.0 NH1 A:ARG1243 4.0 32.2 1.0 CA A:GLU1127 4.0 21.8 1.0 CD A:ARG1126 4.0 22.7 1.0 CG A:ARG1126 4.1 23.7 1.0 N A:GLU1127 4.1 20.2 1.0 CB A:GLU1127 4.1 25.5 1.0 O A:HOH2086 4.3 45.5 1.0 CB A:ARG1126 4.4 21.2 1.0 C A:ARG1126 4.4 19.8 1.0 O A:ILE1123 4.5 19.7 1.0 CZ A:ARG1126 4.6 28.0 1.0 CD2 A:LEU1130 4.6 22.8 1.0 CG A:ARG1243 4.7 29.9 1.0 CG A:GLU1127 4.7 24.2 1.0 O A:ARG1126 4.8 20.9 1.0 NE A:ARG1126 4.8 23.6 1.0 OE2 A:GLU1127 4.8 30.6 1.0 CZ A:PHE1270 4.9 24.3 1.0

Iodine binding site 3 out of 23 in the Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1503 b:47.6 occ:0.57 O A:HOH1703 3.5 38.6 1.0 O A:HOH2160 3.6 39.9 1.0 CD A:PRO886 3.7 35.0 1.0 N A:TYR887 3.7 33.9 1.0 CA A:LYS885 3.8 40.5 1.0 N A:PRO886 3.9 34.5 1.0 C A:LYS885 3.9 37.4 1.0 CB A:TYR887 4.1 32.2 1.0 CD2 A:TYR887 4.2 32.6 1.0 CG A:LYS885 4.3 49.2 1.0 CG A:PRO886 4.4 32.6 1.0 CA A:TYR887 4.4 32.8 1.0 CB A:LYS885 4.4 42.4 1.0 O A:THR629 4.5 31.6 1.0 O A:LYS885 4.6 34.9 1.0 CG A:TYR887 4.6 33.2 1.0 O A:VAL884 4.7 45.0 1.0 C A:PRO886 4.7 33.5 1.0 C A:TYR887 4.7 35.5 1.0 N A:ALA888 4.8 35.4 1.0 CA A:PRO886 4.8 32.6 1.0 N A:LYS885 4.9 42.6 1.0

Iodine binding site 4 out of 23 in the Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1504 b:37.5 occ:0.73 N A:ASP210 3.5 31.1 1.0 NZ A:LYS198 3.7 32.4 1.0 CA A:PRO211 3.7 33.8 1.0 N A:PRO211 3.8 31.7 1.0 C A:ASP210 3.9 32.5 1.0 CA A:SER209 3.9 30.4 1.0 CE A:LYS198 4.1 31.1 1.0 CB A:PRO211 4.2 33.7 1.0 O A:ASP210 4.2 30.4 1.0 CB A:SER209 4.2 32.3 1.0 C A:SER209 4.2 31.9 1.0 OG A:SER209 4.2 30.2 1.0 CD A:PRO211 4.3 33.4 1.0 CA A:ASP210 4.4 31.6 1.0 O A:HOH1990 4.5 33.1 1.0 O A:TYR208 4.8 31.8 1.0 CG A:PRO211 4.8 35.2 1.0

Iodine binding site 5 out of 23 in the Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1505 b:56.7 occ:0.52 O A:HOH1822 3.4 34.8 1.0 NE A:ARG848 3.6 45.5 1.0 N A:VAL680 3.7 31.2 1.0 O A:VAL678 3.7 34.7 1.0 CZ A:ARG848 3.9 45.9 1.0 ND2 A:ASN683 4.0 40.4 1.0 CG2 A:VAL680 4.0 33.9 1.0 NH2 A:ARG848 4.0 44.7 1.0 CB A:VAL680 4.1 36.2 1.0 CD1 A:LEU687 4.1 49.6 1.0 CB A:ASN683 4.2 38.3 1.0 CD A:ARG848 4.3 41.5 1.0 CA A:PHE679 4.4 31.3 1.0 CA A:VAL680 4.5 29.7 1.0 C A:PHE679 4.6 31.2 1.0 CG A:ASN683 4.7 40.7 1.0 C A:VAL678 4.7 33.9 1.0 O A:VAL680 4.7 33.0 1.0 NH1 A:ARG848 4.8 46.5 1.0

Iodine binding site 6 out of 23 in the Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1506 b:45.7 occ:0.50 N A:SER1201 3.4 29.1 1.0 NZ A:LYS528 3.5 47.5 1.0 CB A:SER1201 3.7 29.8 1.0 OG A:SER1201 3.7 32.9 1.0 CA A:GLU1200 4.1 28.6 1.0 CA A:SER1201 4.2 30.4 1.0 CE A:LYS528 4.2 44.0 1.0 CB A:GLU1200 4.3 28.2 1.0 C A:GLU1200 4.3 31.2 1.0 O A:HOH1685 4.3 48.2 1.0 CB A:ALA1204 4.4 28.7 1.0 CD2 A:LEU526 4.7 33.3 1.0

Iodine binding site 7 out of 23 in the Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1507 b:71.0 occ:0.61 O A:HOH1627 3.2 54.1 1.0 OG A:SER39 4.0 41.6 1.0 N A:ARG40 4.0 36.7 1.0 CG2 A:VAL796 4.3 47.0 1.0 CB A:LYS43 4.3 32.4 1.0 CB A:ARG40 4.3 41.0 1.0 NE A:ARG40 4.5 56.6 1.0 CA A:SER39 4.5 34.5 1.0 CD A:LYS43 4.5 46.9 1.0 CG A:ARG40 4.5 49.6 1.0 CG A:LYS43 4.6 36.2 1.0 C A:SER39 4.6 36.6 1.0 CB A:SER39 4.8 35.9 1.0 CA A:ARG40 4.8 38.8 1.0 NH2 A:ARG40 4.9 61.7 1.0 CZ A:ARG40 5.0 60.1 1.0 CA A:VAL796 5.0 51.9 1.0

Iodine binding site 8 out of 23 in the Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1508 b:87.0 occ:0.59 O A:HOH1681 3.2 29.1 1.0 O A:HOH2066 3.3 36.0 1.0 N A:PHE524 3.5 28.3 1.0 O A:SER522 3.7 30.7 1.0 CB A:PHE524 4.0 31.2 1.0 OD1 A:ASP523 4.1 29.9 1.0 CA A:ASP523 4.1 30.7 1.0 CA A:HIS1248 4.3 30.6 1.0 O A:HIS1248 4.3 28.1 1.0 C A:ASP523 4.4 31.4 1.0 O A:GLU1247 4.4 27.9 1.0 CA A:PHE524 4.4 30.0 1.0 CD1 A:LEU517 4.5 32.3 1.0 C A:HIS1248 4.6 29.3 1.0 C A:SER522 4.7 33.4 1.0 O A:HOH1740 4.7 36.5 1.0 OG A:SER511 4.9 36.5 1.0 CB A:HIS1248 4.9 30.1 1.0 N A:ASP523 4.9 32.6 1.0 CD1 A:PHE1249 4.9 25.1 1.0 CG A:ASP523 4.9 28.8 1.0 CA A:ARG508 5.0 24.3 1.0

Iodine binding site 9 out of 23 in the Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1509 b:75.4 occ:0.52 O A:HOH2054 3.6 44.1 1.0 N A:LYS615 3.6 50.2 1.0 O A:HOH2126 3.7 41.1 1.0 CA A:GLY614 3.9 49.1 1.0 CZ3 A:TRP616 4.1 33.3 1.0 CB A:SER598 4.1 30.0 1.0 CE A:LYS1199 4.1 52.9 1.0 C A:GLY614 4.2 50.9 1.0 CB A:LYS615 4.3 52.0 1.0 O A:ASN613 4.3 57.8 1.0 NZ A:LYS1199 4.4 56.0 1.0 CD A:LYS1199 4.4 45.3 1.0 O A:HOH2230 4.5 42.3 1.0 CA A:LYS615 4.6 46.9 1.0 CE3 A:TRP616 4.6 34.3 1.0 N A:GLY614 4.9 52.7 1.0 OG A:SER598 4.9 28.7 1.0 CH2 A:TRP616 5.0 33.4 1.0 C A:ASN613 5.0 56.9 1.0

Iodine binding site 10 out of 23 in the Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of LBACAS13A (C2C2) Bound to Mature Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1510 b:84.0 occ:0.48 NZ A:LYS321 3.3 58.0 1.0 O A:HOH2099 3.4 38.7 1.0 CD A:ARG290 4.0 32.9 1.0 CE A:LYS321 4.2 55.1 1.0 O A:HOH2012 4.3 43.6 1.0 CG A:ARG290 4.4 29.4 1.0 CB A:ARG290 4.6 29.9 1.0 CD A:LYS321 4.8 51.7 1.0

G.J.Knott, A.East-Seletsky, J.C.Cofsky, J.M.Holton, E.Charles, M.R.O'connell, J.A.Doudna. Guide-Bound Structures of An Rna-Targeting A-Cleaving Crispr-CAS13A Enzyme. Nat. Struct. Mol. Biol. V. 24 825 2017.
ISSN: ESSN 1545-9985
PubMed: 28892041
DOI: 10.1038/NSMB.3466