Iodine in PDB 8syj: Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)

The structure of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form), PDB code: 8syj was solved by B.E.Eckenroth, A.F.Gardner, S.Doublie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.49 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.554, 89.116, 128.043, 90, 90, 90
R / Rfree (%)	22.5 / 26

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 51;

Binding sites:

The binding sites of Iodine atom in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) (pdb code 8syj). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 51 binding sites of Iodine where determined in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form), PDB code: 8syj:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:41.4 occ:0.50 I A:IOD201 0.0 41.4 0.5 I A:IOD201 2.2 43.0 0.5 OG1 A:THR104 3.3 44.7 1.0 N A:ILE101 3.5 31.8 1.0 CG2 A:THR104 3.7 39.1 1.0 CG1 A:ILE101 3.8 31.3 1.0 N A:THR104 4.1 35.1 1.0 O A:ILE101 4.1 31.9 1.0 CA A:VAL100 4.1 32.2 1.0 CB A:THR104 4.1 35.8 1.0 CB A:PHE103 4.2 45.0 1.0 CE A:MET32 4.2 43.1 1.0 C A:VAL100 4.3 32.1 1.0 CA A:ILE101 4.3 30.0 1.0 C A:ILE101 4.4 37.5 1.0 CB A:VAL100 4.6 37.2 1.0 CB A:ILE101 4.6 34.9 1.0 O A:CYS99 4.7 34.2 1.0 CA A:THR104 4.7 43.5 1.0 C A:PHE103 4.8 43.7 1.0 CD1 A:ILE101 4.8 32.8 1.0 N A:PHE103 4.8 32.6 1.0 CA A:PHE103 4.8 41.1 1.0

Iodine binding site 2 out of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:43.0 occ:0.50 I A:IOD201 0.0 43.0 0.5 I A:IOD201 2.2 41.4 0.5 CE A:MET32 3.6 43.1 1.0 CB A:PHE103 4.3 45.0 1.0 CB A:ALA21 4.4 36.0 1.0 CG1 A:ILE101 4.4 31.3 1.0 CB A:MET32 4.5 37.8 1.0 CD2 A:PHE103 4.5 45.5 1.0 SD A:MET23 4.5 59.6 1.0 CE A:MET23 4.8 54.4 1.0 CD1 A:ILE101 4.8 32.8 1.0 SD A:MET32 4.8 49.6 1.0 CG A:PHE103 4.8 42.8 1.0 CG A:MET32 4.8 46.0 1.0 CG2 A:THR104 4.9 39.1 1.0

Iodine binding site 3 out of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:52.2 occ:1.00 N A:PRO16 3.7 39.5 1.0 C A:LYS15 3.8 46.9 1.0 CA A:LYS15 3.9 45.6 1.0 CD A:PRO16 3.9 39.4 1.0 OG A:SER3 4.0 59.2 1.0 N A:LYS15 4.2 44.3 1.0 O A:ASP14 4.2 48.6 1.0 C A:ASP14 4.2 47.4 1.0 O A:LYS15 4.2 43.9 1.0 CB A:ASP14 4.3 47.8 1.0 CA A:PRO16 4.3 43.3 1.0 CG A:PRO16 4.6 42.9 1.0 CB A:SER3 4.9 48.4 1.0 CA A:ASP14 4.9 45.2 1.0

Iodine binding site 4 out of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:60.6 occ:1.00 OG A:SER7 3.4 59.5 1.0 O A:GLY10 3.6 58.5 1.0 C A:GLY10 3.9 54.5 1.0 O A:LYS5 3.9 54.2 1.0 O A:HOH318 4.0 43.7 1.0 CD1 A:ILE12 4.0 43.6 1.0 N A:SER7 4.1 61.5 1.0 CB A:SER7 4.1 63.6 1.0 CG1 A:ILE12 4.1 46.6 1.0 CG A:LYS5 4.2 63.7 1.0 CE A:LYS5 4.3 66.4 1.0 N A:TYR11 4.3 50.2 1.0 CD A:LYS5 4.3 62.6 1.0 N A:GLY10 4.4 57.9 1.0 C A:LYS5 4.4 54.5 1.0 C A:LYS6 4.4 60.5 1.0 CA A:TYR11 4.5 50.9 1.0 C A:TYR11 4.6 46.9 1.0 CA A:GLY10 4.6 55.2 1.0 CA A:LYS6 4.6 63.3 1.0 N A:LYS6 4.6 60.2 1.0 CA A:SER7 4.7 65.2 1.0 N A:ILE12 4.7 42.2 1.0 CB A:LYS5 4.9 51.4 1.0 CB A:ILE12 4.9 47.7 1.0 CB A:SER9 5.0 71.8 1.0 NZ A:LYS5 5.0 62.2 1.0 O A:TYR11 5.0 45.1 1.0

Iodine binding site 5 out of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:I204 b:68.9 occ:0.50 C A:SER7 3.8 65.2 1.0 CA A:SER7 3.9 65.2 1.0 N A:LYS8 4.0 56.5 1.0 CG A:LYS6 4.1 60.3 1.0 O A:SER7 4.2 66.2 1.0 N A:SER7 4.3 61.5 1.0 C A:LYS6 4.5 60.5 1.0 CD A:LYS6 4.5 64.6 1.0 O A:LYS6 4.6 68.8 1.0 CE A:LYS6 4.6 72.1 1.0 CA A:LYS8 4.7 61.9 1.0

Iodine binding site 6 out of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:I205 b:98.7 occ:1.00 CG A:LYS67 3.7 57.4 1.0 CD A:LYS70 3.8 54.3 1.0 CG A:PRO62 3.9 53.3 1.0 CD A:PRO62 4.2 57.5 1.0 CB A:LYS67 4.2 51.2 1.0 CE A:LYS70 4.2 61.1 1.0 CA A:LYS67 4.2 52.4 1.0 CD A:LYS67 4.4 65.0 1.0 CE A:LYS67 4.5 72.8 1.0 CB A:PRO62 4.9 51.3 1.0 CB A:LYS70 4.9 55.5 1.0 CG A:LYS70 5.0 49.0 1.0

Iodine binding site 7 out of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:I206 b:65.7 occ:1.00 O A:HOH324 3.2 27.9 1.0 N A:GLY89 3.8 40.0 1.0 CA A:GLY89 4.0 43.4 1.0 CD2 A:LEU162 4.1 48.5 1.0 CD1 A:LEU162 4.1 53.6 1.0 NE A:ARG158 4.3 88.0 1.0 CG A:ARG158 4.3 66.5 1.0 CD A:ARG158 4.3 69.6 1.0 CB A:LYS88 4.4 49.7 1.0 CG A:LYS88 4.4 55.9 1.0 CG A:LEU162 4.5 54.3 1.0 C A:LYS88 4.5 40.9 1.0 CD A:LYS88 4.8 61.2 1.0 CA A:LYS88 5.0 46.5 1.0 CZ A:ARG158 5.0 93.1 1.0

Iodine binding site 8 out of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:I207 b:87.1 occ:1.00 CG A:GLU159 3.8 92.5 1.0 CD1 A:LEU162 4.0 53.6 1.0 CA A:GLU159 4.1 65.1 1.0 CB B:PRO154 4.2 65.1 1.0 CB A:GLU159 4.3 76.9 1.0 N A:GLU159 4.4 63.9 1.0 CD A:GLU159 4.5 86.9 1.0 CA B:PRO154 4.6 58.2 1.0 CG A:ARG158 4.6 66.5 1.0 OE2 A:GLU159 4.8 93.2 1.0 CD A:ARG158 4.9 69.6 1.0 C A:ARG158 4.9 61.4 1.0

Iodine binding site 9 out of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:I208 b:67.9 occ:0.50 I A:IOD208 0.0 67.9 0.5 I A:IOD208 2.0 57.4 0.5 CE1 A:PHE136 3.9 42.9 1.0 NZ A:LYS148 4.4 58.2 1.0 CE A:LYS148 4.4 58.6 1.0 CD A:LYS148 4.4 56.8 1.0 CG1 A:VAL144 4.6 44.3 1.0 CD1 A:PHE136 4.6 42.0 1.0 CZ A:PHE136 4.8 49.8 1.0

Iodine binding site 10 out of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:I208 b:57.4 occ:0.50 I A:IOD208 0.0 57.4 0.5 I A:IOD208 2.0 67.9 0.5 CE1 A:PHE136 4.2 42.9 1.0 CG1 A:VAL144 4.3 44.3 1.0 CZ A:PHE136 4.6 49.8 1.0

P.J.Caffrey, B.E.Eckenroth, B.W.Burkhart, K.M.Zatopek, C.M.Mcclung, T.J.Santangelo, S.Doublie, A.F.Gardner. Thermococcus Kodakarensis TK0353 Is A Novel Ap Lyase with A New Fold. J.Biol.Chem. 05503 2023.
ISSN: ESSN 1083-351X
PubMed: 38013090
DOI: 10.1016/J.JBC.2023.105503