Iodine in PDB 5wlh: Crystal Structure of LBACAS13A H328A (C2C2) Bound to Pre-Crrna (24-Nt Spacer)

The structure of Crystal Structure of LBACAS13A H328A (C2C2) Bound to Pre-Crrna (24-Nt Spacer), PDB code: 5wlh 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 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	150.842, 92.213, 115.858, 90.00, 92.43, 90.00
R / Rfree (%)	18.4 / 21.7

Pages:

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

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of LBACAS13A H328A (C2C2) Bound to Pre-Crrna (24-Nt Spacer) (pdb code 5wlh). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 20 binding sites of Iodine where determined in the Crystal Structure of LBACAS13A H328A (C2C2) Bound to Pre-Crrna (24-Nt Spacer), PDB code: 5wlh:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 20 in the Crystal Structure of LBACAS13A H328A (C2C2) Bound to Pre-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 H328A (C2C2) Bound to Pre-Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1501 b:38.5 occ:0.63 O A:HOH1978 3.5 47.0 1.0 N A:ASP210 3.6 25.5 1.0 CA A:PRO211 3.7 34.4 1.0 N A:PRO211 3.7 35.0 1.0 CA A:SER209 3.8 32.3 1.0 C A:ASP210 3.9 29.8 1.0 NZ A:LYS198 3.9 27.3 1.0 CD A:PRO211 4.1 31.4 1.0 CB A:PRO211 4.1 33.9 1.0 CB A:SER209 4.1 36.9 1.0 O A:ASP210 4.2 31.1 1.0 C A:SER209 4.2 25.8 1.0 CE A:LYS198 4.2 27.7 1.0 O A:HOH1760 4.3 36.8 1.0 OG A:SER209 4.3 34.0 1.0 CA A:ASP210 4.4 29.3 1.0 O A:TYR208 4.6 33.0 1.0 CG A:PRO211 4.6 33.1 1.0 C A:PRO211 5.0 32.7 1.0

Iodine binding site 2 out of 20 in the Crystal Structure of LBACAS13A H328A (C2C2) Bound to Pre-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 H328A (C2C2) Bound to Pre-Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1502 b:47.0 occ:0.72 O A:HOH1871 3.2 41.5 1.0 CA A:PHE854 4.0 30.6 1.0 CG2 A:VAL735 4.3 30.6 1.0 CG A:GLU857 4.3 58.0 1.0 N A:PHE854 4.3 30.9 1.0 CB A:ASN734 4.3 47.8 1.0 CG A:GLU853 4.4 59.1 1.0 ND2 A:ASN858 4.4 38.1 1.0 CD1 A:PHE854 4.4 30.9 1.0 CB A:GLU857 4.4 47.3 1.0 N A:VAL735 4.4 40.2 1.0 CB A:PHE854 4.5 26.5 1.0 OE2 A:GLU853 4.5 75.8 1.0 O A:GLU853 4.5 32.6 1.0 C A:ASN734 4.6 43.6 1.0 C A:GLU853 4.6 37.8 1.0 CA A:VAL735 4.6 35.9 1.0 O A:ASN734 4.8 39.4 1.0 CD A:GLU853 4.8 71.2 1.0 OD2 A:ASP732 4.8 37.0 1.0 CD A:ARG738 4.9 66.1 1.0 CG A:PHE854 5.0 27.8 1.0 CG A:ARG738 5.0 58.5 1.0

Iodine binding site 3 out of 20 in the Crystal Structure of LBACAS13A H328A (C2C2) Bound to Pre-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 H328A (C2C2) Bound to Pre-Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1503 b:33.4 occ:0.75 NH1 A:ARG1126 3.6 23.4 1.0 O A:HOH2164 3.8 43.6 1.0 NH1 A:ARG1243 3.9 31.3 1.0 CA A:GLU1127 4.0 17.4 1.0 N A:GLU1127 4.1 17.0 1.0 CD A:ARG1126 4.1 22.2 1.0 CG A:ARG1126 4.1 19.6 1.0 CB A:GLU1127 4.2 23.2 1.0 CB A:ARG1126 4.3 16.9 1.0 C A:ARG1126 4.4 15.6 1.0 O A:ILE1123 4.4 17.2 1.0 CD2 A:LEU1130 4.5 21.7 1.0 CG A:GLU1127 4.6 23.0 1.0 CZ A:ARG1126 4.7 25.3 1.0 CG A:ARG1243 4.7 29.2 1.0 O A:ARG1126 4.7 18.4 1.0 CZ A:PHE1270 4.7 19.8 1.0 NE A:ARG1126 4.8 24.2 1.0 OE2 A:GLU1127 4.9 33.0 1.0

Iodine binding site 4 out of 20 in the Crystal Structure of LBACAS13A H328A (C2C2) Bound to Pre-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 H328A (C2C2) Bound to Pre-Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1504 b:42.5 occ:0.53 O A:HOH1843 3.5 38.3 1.0 N A:TYR887 3.7 27.9 1.0 CA A:LYS885 3.8 42.5 1.0 CD A:PRO886 3.9 37.3 1.0 C A:LYS885 3.9 37.2 1.0 N A:PRO886 4.0 35.9 1.0 CB A:TYR887 4.0 25.6 1.0 CD2 A:TYR887 4.1 30.5 1.0 CA A:TYR887 4.4 27.9 1.0 CD A:LYS885 4.4 51.0 1.0 CB A:LYS885 4.4 43.0 1.0 O A:THR629 4.5 30.6 1.0 CG A:PRO886 4.5 32.3 1.0 CG A:TYR887 4.6 28.8 1.0 O A:LYS885 4.6 32.4 1.0 O A:VAL884 4.7 49.2 1.0 C A:PRO886 4.8 31.0 1.0 N A:ALA888 4.8 35.2 1.0 C A:TYR887 4.8 34.4 1.0 CA A:PRO886 4.9 32.5 1.0 N A:LYS885 4.9 46.3 1.0 CG2 A:THR633 4.9 41.2 1.0

Iodine binding site 5 out of 20 in the Crystal Structure of LBACAS13A H328A (C2C2) Bound to Pre-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 H328A (C2C2) Bound to Pre-Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1505 b:43.6 occ:0.55 N A:SER1201 3.4 24.2 1.0 NZ A:LYS528 3.6 53.7 1.0 OG A:SER1201 3.7 30.1 1.0 CB A:SER1201 3.8 27.1 1.0 CE A:LYS528 4.0 51.9 1.0 CA A:GLU1200 4.1 22.4 1.0 CB A:GLU1200 4.2 22.2 1.0 CA A:SER1201 4.2 27.1 1.0 C A:GLU1200 4.3 26.1 1.0 CB A:ALA1204 4.4 29.8 1.0 CD2 A:LEU526 4.6 23.0 1.0

Iodine binding site 6 out of 20 in the Crystal Structure of LBACAS13A H328A (C2C2) Bound to Pre-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 H328A (C2C2) Bound to Pre-Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1506 b:46.5 occ:0.45 O A:HOH1968 3.7 42.6 1.0 N A:LYS615 3.7 50.5 1.0 O A:HOH2050 3.8 31.9 1.0 CE A:LYS1199 3.9 46.0 1.0 CZ3 A:TRP616 3.9 30.4 1.0 O A:ASN613 3.9 63.9 1.0 CA A:GLY614 4.0 52.3 1.0 CB A:SER598 4.1 27.7 1.0 O A:HOH2246 4.3 40.0 1.0 CD A:LYS1199 4.3 43.0 1.0 CB A:LYS615 4.3 55.2 1.0 C A:GLY614 4.3 51.2 1.0 CG A:LYS615 4.4 60.2 1.0 NZ A:LYS1199 4.4 49.2 1.0 CE3 A:TRP616 4.5 29.8 1.0 CD A:LYS615 4.5 63.2 1.0 CA A:LYS615 4.6 52.3 1.0 C A:ASN613 4.7 64.0 1.0 N A:GLY614 4.8 56.7 1.0 CH2 A:TRP616 4.8 26.3 1.0 OG A:SER598 5.0 29.1 1.0

Iodine binding site 7 out of 20 in the Crystal Structure of LBACAS13A H328A (C2C2) Bound to Pre-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 H328A (C2C2) Bound to Pre-Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1507 b:54.3 occ:0.45 NE A:ARG40 3.4 74.4 1.0 NH2 A:ARG40 3.5 80.1 1.0 N A:ARG40 3.7 37.0 1.0 OG A:SER39 3.7 44.0 1.0 CZ A:ARG40 3.9 79.6 1.0 CB A:ARG40 4.1 49.5 1.0 CG2 A:VAL796 4.1 40.8 1.0 CB A:LYS43 4.2 26.2 1.0 CA A:SER39 4.3 25.4 1.0 C A:SER39 4.4 31.4 1.0 CG A:LYS43 4.4 34.6 1.0 CA A:ARG40 4.5 43.2 1.0 CD A:ARG40 4.5 66.1 1.0 CD A:LYS43 4.6 46.4 1.0 CB A:SER39 4.6 33.1 1.0 CG A:ARG40 4.7 58.2 1.0

Iodine binding site 8 out of 20 in the Crystal Structure of LBACAS13A H328A (C2C2) Bound to Pre-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 H328A (C2C2) Bound to Pre-Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1508 b:53.8 occ:0.46 O A:LYS193 4.0 28.3 1.0 CD A:LYS197 4.1 40.5 1.0 C A:LYS193 4.2 27.3 1.0 CG A:ARG194 4.2 30.8 1.0 N A:ARG194 4.2 27.2 1.0 CA A:ARG194 4.3 28.1 1.0 CB A:LYS197 4.3 31.4 1.0 CB A:LYS193 4.3 33.3 1.0 O A:HOH2227 4.5 48.4 1.0 O A:HOH2210 4.6 60.3 1.0 CE A:LYS193 4.8 45.7 1.0 CG A:LYS197 4.8 34.8 1.0 CB A:ARG194 4.9 28.7 1.0 O A:HOH1833 4.9 39.2 1.0 CA A:LYS193 4.9 28.9 1.0

Iodine binding site 9 out of 20 in the Crystal Structure of LBACAS13A H328A (C2C2) Bound to Pre-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 H328A (C2C2) Bound to Pre-Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1509 b:71.5 occ:0.52 O A:HOH2214 3.4 41.6 1.0 O A:ASP1113 3.6 20.8 1.0 NE2 A:GLN914 3.9 29.9 1.0 CG A:GLN914 3.9 22.3 1.0 C A:ASP1113 4.0 18.7 1.0 CB A:ASP1113 4.2 21.8 1.0 N A:GLU1114 4.3 18.3 1.0 CA A:GLU1114 4.3 18.7 1.0 CG A:GLU1114 4.4 23.1 1.0 CD A:GLN914 4.5 24.0 1.0 CE1 A:TYR502 4.5 29.6 1.0 CD2 A:HIS917 4.6 29.9 1.0 CE2 A:PHE505 4.6 23.1 1.0 CA A:ASP1113 4.7 19.6 1.0 OH A:TYR502 4.7 38.1 1.0 O A:HOH1826 4.9 29.7 1.0 CZ A:PHE505 4.9 24.5 1.0 O A:HOH1664 4.9 31.2 1.0 CB A:GLN914 5.0 20.5 1.0 CB A:GLU1114 5.0 21.0 1.0

Iodine binding site 10 out of 20 in the Crystal Structure of LBACAS13A H328A (C2C2) Bound to Pre-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 H328A (C2C2) Bound to Pre-Crrna (24-Nt Spacer) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1510 b:57.3 occ:0.50 O A:HOH2005 3.5 35.0 1.0 NE A:ARG848 3.5 52.1 1.0 N A:VAL680 3.7 28.1 1.0 O A:VAL678 3.8 33.5 1.0 NH2 A:ARG848 3.8 53.6 1.0 ND2 A:ASN683 3.8 36.3 1.0 CZ A:ARG848 3.9 53.4 1.0 CB A:ASN683 4.0 32.4 1.0 CD1 A:LEU687 4.0 47.2 1.0 CB A:VAL680 4.1 30.8 1.0 CG2 A:VAL680 4.2 32.8 1.0 CD A:ARG848 4.4 47.9 1.0 CA A:PHE679 4.4 27.6 1.0 CG A:ASN683 4.5 40.1 1.0 CA A:VAL680 4.5 30.3 1.0 C A:PHE679 4.6 28.2 1.0 C A:VAL678 4.7 30.2 1.0 O A:VAL680 4.7 35.9 1.0 N A:PHE679 5.0 26.7 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