Chlorine in PDB 6o8e: Crystal Structure of Uvrb Bound to Duplex Dna with Adp

The structure of Crystal Structure of Uvrb Bound to Duplex Dna with Adp, PDB code: 6o8e was solved by S.-J.Lee, G.L.Verdine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.51 / 2.61
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.269, 115.719, 266.795, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 27

The structure of Crystal Structure of Uvrb Bound to Duplex Dna with Adp also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Chlorine atom in the Crystal Structure of Uvrb Bound to Duplex Dna with Adp (pdb code 6o8e). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Uvrb Bound to Duplex Dna with Adp, PDB code: 6o8e:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Crystal Structure of Uvrb Bound to Duplex Dna with Adp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Uvrb Bound to Duplex Dna with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl605 b:88.9 occ:1.00 CD1 A:ILE431 3.8 97.5 1.0 CE A:MET457 4.2 83.9 1.0 CD1 A:LEU520 4.6 71.7 1.0 CG1 A:ILE431 4.7 90.2 1.0 NE2 A:GLN430 4.8 75.2 1.0 CL A:CL606 4.9 86.4 1.0

Chlorine binding site 2 out of 5 in the Crystal Structure of Uvrb Bound to Duplex Dna with Adp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Uvrb Bound to Duplex Dna with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl606 b:86.4 occ:1.00 CD2 A:TYR464 3.5 0.9 1.0 CD1 A:ILE431 3.5 97.5 1.0 CE2 A:TYR464 4.1 1.0 1.0 CG A:TYR464 4.2 0.4 1.0 CB A:TYR464 4.3 94.9 1.0 CG1 A:ILE431 4.8 90.2 1.0 CG2 A:ILE431 4.8 78.1 1.0 CL A:CL605 4.9 88.9 1.0

Chlorine binding site 3 out of 5 in the Crystal Structure of Uvrb Bound to Duplex Dna with Adp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Uvrb Bound to Duplex Dna with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl607 b:76.8 occ:1.00 O A:HOH712 2.9 47.9 1.0 NZ A:LYS385 3.0 74.8 1.0 CG2 A:THR321 3.5 71.9 1.0 OD2 A:ASP327 3.8 55.9 1.0 OD1 A:ASP327 3.8 59.1 1.0 CD1 A:TYR323 3.9 66.7 1.0 O A:PRO322 4.0 56.7 1.0 CE A:LYS385 4.0 74.5 1.0 CG A:ASP327 4.1 54.7 1.0 O A:THR321 4.1 57.2 1.0 CE1 A:TYR323 4.2 65.0 1.0 CA A:TYR323 4.3 56.4 1.0 C A:PRO322 4.3 60.8 1.0 N A:TYR323 4.3 56.2 1.0 CG A:TYR323 4.5 63.5 1.0 CB A:THR321 4.6 67.7 1.0 C A:THR321 4.7 61.8 1.0 NH2 A:ARG316 4.7 77.8 1.0 CB A:TYR323 4.9 59.7 1.0

Chlorine binding site 4 out of 5 in the Crystal Structure of Uvrb Bound to Duplex Dna with Adp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Uvrb Bound to Duplex Dna with Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl605 b:82.0 occ:1.00 NZ B:LYS385 3.1 76.9 1.0 CE1 B:TYR323 3.9 82.8 1.0 O B:THR321 3.9 68.3 1.0 CD1 B:TYR323 4.0 85.7 1.0 O B:PRO322 4.2 64.6 1.0 OD2 B:ASP327 4.3 70.4 1.0 CE B:LYS385 4.3 74.3 1.0 CB B:THR321 4.5 71.8 1.0 NH2 B:ARG316 4.6 86.9 1.0 C B:THR321 4.6 64.9 1.0 C B:PRO322 4.7 64.6 1.0 CG2 B:THR321 4.7 76.3 1.0 OD1 B:ASP327 4.8 69.0 1.0 CG B:ASP327 4.8 67.2 1.0 CZ B:TYR323 4.8 83.0 1.0 N B:TYR323 5.0 66.6 1.0 CG B:TYR323 5.0 76.5 1.0

Chlorine binding site 5 out of 5 in the Crystal Structure of Uvrb Bound to Duplex Dna with Adp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Uvrb Bound to Duplex Dna with Adp within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl101 b:93.5 occ:1.00 CD1 B:TYR95 2.9 0.2 1.0 CE1 B:TYR95 3.0 0.0 1.0 N3 F:DC9 3.3 0.7 1.0 N7 F:DG8 3.3 0.1 1.0 C2 F:DC9 3.4 0.4 1.0 C8 F:DG8 3.5 0.2 1.0 O2 F:DC9 3.6 1.0 1.0 CG B:TYR95 3.7 0.2 1.0 C4 F:DC9 3.8 0.9 1.0 CZ B:TYR95 3.8 0.0 1.0 N1 F:DC9 4.0 0.8 1.0 C5 F:DC9 4.3 0.6 1.0 N4 F:DC9 4.3 0.6 1.0 CD2 B:TYR95 4.3 0.9 1.0 C6 F:DC9 4.4 0.7 1.0 CE2 B:TYR95 4.4 0.4 1.0 CB B:TYR95 4.4 82.8 1.0 C5 F:DG8 4.5 0.1 1.0 OH B:TYR95 4.5 0.2 1.0 N9 F:DG8 4.7 0.8 1.0 C1' F:DC9 4.7 0.8 1.0

S.J.Lee, R.J.Sung, G.L.Verdine. Mechanism of Dna Lesion Homing and Recognition By the Uvr Nucleotide Excision Repair System. Res V.2019 41746 2019.
ISSN: ESSN 2639-5274
PubMed: 31549070
DOI: 10.34133/2019/5641746