Iodine in PDB 8cpn: Crystal Structure of the POLB16_OARG Intein Variant S1A, N183A

The structure of Crystal Structure of the POLB16_OARG Intein Variant S1A, N183A, PDB code: 8cpn was solved by S.Kattelmann, T.Pasch, H.D.Mootz, D.Kummel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.06 / 1.85
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.425, 69.425, 79.162, 90, 90, 120
R / Rfree (%)	21.1 / 24.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of the POLB16_OARG Intein Variant S1A, N183A (pdb code 8cpn). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 14 binding sites of Iodine where determined in the Crystal Structure of the POLB16_OARG Intein Variant S1A, N183A, PDB code: 8cpn:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 14 in the Crystal Structure of the POLB16_OARG Intein Variant S1A, N183A


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 the POLB16_OARG Intein Variant S1A, N183A within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:46.6 occ:0.23 CD1 A:ILE152 4.0 50.9 1.0 CG A:LYS129 4.3 76.5 1.0 N A:VAL130 4.4 65.2 1.0 CG2 A:VAL130 4.5 63.7 1.0 CA A:LYS129 4.6 69.9 1.0 CB A:ILE152 4.6 44.2 1.0 CG2 A:ILE152 4.7 45.2 1.0 O A:LEU128 4.8 79.0 1.0 CG1 A:ILE152 4.9 46.0 1.0

Iodine binding site 2 out of 14 in the Crystal Structure of the POLB16_OARG Intein Variant S1A, N183A


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 the POLB16_OARG Intein Variant S1A, N183A within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:73.9 occ:0.53 CD A:LYS24 3.8 68.2 1.0 CE1 A:HIS3 3.9 47.1 1.0 O A:HOH332 4.0 62.0 1.0 OD2 A:ASP160 4.0 85.3 1.0 CG A:LYS5 4.0 56.8 1.0 CA A:GLY4 4.2 43.0 1.0 NZ A:LYS5 4.2 74.3 1.0 CE A:LYS5 4.3 69.7 1.0 NE2 A:HIS3 4.3 48.5 1.0 C A:GLY4 4.3 43.4 1.0 N A:LYS5 4.4 42.8 1.0 N A:GLY4 4.5 42.2 1.0 ND1 A:HIS3 4.5 45.0 1.0 CE A:LYS24 4.6 73.1 1.0 CD A:LYS5 4.7 63.5 1.0 CB A:LYS24 4.9 59.4 1.0 O A:GLY4 5.0 42.2 1.0

Iodine binding site 3 out of 14 in the Crystal Structure of the POLB16_OARG Intein Variant S1A, N183A


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 the POLB16_OARG Intein Variant S1A, N183A within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:63.1 occ:0.39 N A:ASP22 3.4 44.9 1.0 OG A:SER25 3.4 56.7 1.0 CG1 A:ILE21 3.7 46.0 1.0 CB A:SER25 3.8 54.6 1.0 CB A:ASP22 4.0 51.8 1.0 CA A:ILE21 4.1 40.6 1.0 CG A:ASP22 4.2 54.8 1.0 C A:ILE21 4.3 42.5 1.0 CA A:ASP22 4.3 46.2 1.0 OD2 A:ASP22 4.5 58.9 1.0 CB A:ILE21 4.5 42.4 1.0 OD1 A:ASP22 4.6 54.9 1.0 CD1 A:ILE21 4.9 49.7 1.0 O A:ASP22 5.0 45.0 1.0

Iodine binding site 4 out of 14 in the Crystal Structure of the POLB16_OARG Intein Variant S1A, N183A


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 the POLB16_OARG Intein Variant S1A, N183A within 5.0Å range: probe atom residue distance (Å) B Occ A:I204 b:71.3 occ:0.35 N A:SER135 3.5 45.5 1.0 CD2 A:LEU180 3.7 50.1 1.0 CG2 A:VAL134 3.8 52.3 1.0 CA A:VAL134 4.0 49.9 1.0 CB A:SER135 4.2 47.4 1.0 C A:VAL134 4.3 47.4 1.0 CB A:VAL134 4.4 51.1 1.0 CA A:SER135 4.5 45.1 1.0 CB A:LEU180 4.7 43.1 1.0 CG A:LEU180 4.8 46.6 1.0 O A:TYR133 4.8 59.9 1.0

Iodine binding site 5 out of 14 in the Crystal Structure of the POLB16_OARG Intein Variant S1A, N183A


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 the POLB16_OARG Intein Variant S1A, N183A within 5.0Å range: probe atom residue distance (Å) B Occ A:I205 b:110.6 occ:0.49 N A:ASP-1 3.3 84.8 1.0 NE2 A:HIS109 3.9 128.9 1.0 NZ A:LYS72 4.0 74.3 1.0 CA A:ASP-1 4.3 81.0 1.0 CB A:ASP-1 4.3 86.7 1.0 CD2 A:HIS109 4.7 122.1 1.0 O A:ASP-1 4.7 73.4 1.0 CE1 A:HIS109 4.9 134.3 1.0 C A:ASP-1 5.0 75.0 1.0

Iodine binding site 6 out of 14 in the Crystal Structure of the POLB16_OARG Intein Variant S1A, N183A


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 the POLB16_OARG Intein Variant S1A, N183A within 5.0Å range: probe atom residue distance (Å) B Occ A:I206 b:74.3 occ:0.32 OD1 A:ASP108 3.1 124.7 1.0 N A:HIS73 3.2 60.1 1.0 O A:THR107 3.7 100.5 1.0 CA A:LYS72 3.8 64.9 1.0 CD2 A:HIS73 3.9 60.8 1.0 CB A:LYS72 3.9 63.7 1.0 CB A:HIS73 4.0 53.7 1.0 C A:LYS72 4.0 63.4 1.0 CG A:HIS73 4.0 57.7 1.0 CA A:HIS73 4.2 55.5 1.0 CG A:ASP108 4.3 126.1 1.0 CG A:LYS72 4.3 68.9 1.0 CA A:ASP108 4.6 114.2 1.0 C A:THR107 4.6 100.0 1.0 O A:HIS73 4.7 53.1 1.0 NE2 A:HIS73 4.7 62.5 1.0 O A:HOH344 4.8 76.0 1.0 ND1 A:HIS73 4.9 57.7 1.0 N A:ASP108 4.9 106.7 1.0 C A:HIS73 4.9 52.4 1.0

Iodine binding site 7 out of 14 in the Crystal Structure of the POLB16_OARG Intein Variant S1A, N183A


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 the POLB16_OARG Intein Variant S1A, N183A within 5.0Å range: probe atom residue distance (Å) B Occ A:I207 b:108.4 occ:0.46 N A:MET157 3.4 64.0 1.0 CA A:GLY156 3.7 61.4 1.0 CG A:MET157 4.1 77.2 1.0 C A:GLY156 4.1 59.3 1.0 CE1 A:HIS73 4.3 60.8 1.0 CB A:MET157 4.3 73.7 1.0 NE2 A:HIS73 4.4 62.5 1.0 CA A:MET157 4.5 66.7 1.0 ND1 A:HIS73 4.8 57.7 1.0 SD A:MET157 4.9 87.1 1.0 CD2 A:HIS73 5.0 60.8 1.0

Iodine binding site 8 out of 14 in the Crystal Structure of the POLB16_OARG Intein Variant S1A, N183A


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 the POLB16_OARG Intein Variant S1A, N183A within 5.0Å range: probe atom residue distance (Å) B Occ A:I208 b:79.1 occ:0.36 CG A:GLU166 3.5 75.5 1.0 N A:VAL167 3.5 62.6 1.0 CA A:GLU166 3.6 64.1 1.0 O A:CYS165 4.0 61.2 1.0 CB A:HIS172 4.0 66.1 1.0 CB A:GLU166 4.1 70.5 1.0 C A:GLU166 4.1 63.8 1.0 CG2 A:VAL167 4.1 59.0 1.0 O A:VAL167 4.1 67.9 1.0 CA A:HIS172 4.1 61.8 1.0 CD2 A:HIS172 4.3 72.5 1.0 O A:HIS172 4.5 61.3 1.0 CG A:HIS172 4.5 71.0 1.0 C A:HIS172 4.5 59.5 1.0 CA A:VAL167 4.6 61.1 1.0 N A:GLU166 4.7 60.9 1.0 CD A:GLU166 4.7 83.3 1.0 C A:CYS165 4.8 60.0 1.0 C A:VAL167 4.8 65.3 1.0 CB A:VAL167 4.9 58.7 1.0 OE2 A:GLU166 4.9 89.0 1.0

Iodine binding site 9 out of 14 in the Crystal Structure of the POLB16_OARG Intein Variant S1A, N183A


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 the POLB16_OARG Intein Variant S1A, N183A within 5.0Å range: probe atom residue distance (Å) B Occ A:I209 b:89.6 occ:0.37 CA A:ALA140 3.8 53.1 1.0 CG A:GLU139 3.8 52.0 1.0 N A:ALA140 3.9 50.9 1.0 CD A:GLU139 4.0 55.4 1.0 CB A:ALA140 4.1 56.5 1.0 C A:GLU139 4.2 49.9 1.0 OE1 A:GLU139 4.2 56.5 1.0 O A:GLU139 4.4 50.3 1.0 CB A:GLU139 4.4 48.3 1.0 OE2 A:GLU139 4.5 55.5 1.0 O A:HOH325 5.0 47.4 1.0

Iodine binding site 10 out of 14 in the Crystal Structure of the POLB16_OARG Intein Variant S1A, N183A


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 the POLB16_OARG Intein Variant S1A, N183A within 5.0Å range: probe atom residue distance (Å) B Occ A:I210 b:166.5 occ:1.00 O A:HOH336 3.2 51.5 1.0 OE1 A:GLU18 3.7 56.2 1.0 OE2 A:GLU18 3.7 57.8 1.0 CD A:GLU18 4.1 53.9 1.0 NH2 A:ARG11 4.2 61.1 1.0 CE2 A:TYR59 4.9 49.7 1.0

T.Pasch, A.Schroeder, S.Kattelmann, M.Eisenstein, S.Pietrokovski, D.Kuemmel, H.D.Mootz. Structural and Biochemical Analysis of A Novel Atypically Split Intein Reveals A Conserved Histidine Specific to the Subgroup of Cysteine-Less Inteins To Be Published.
DOI: 10.1039/D3SC01200J