Magnesium 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:

Chlorine

(Cl)

5 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Uvrb Bound to Duplex Dna with Adp, PDB code: 6o8e:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Uvrb Bound to Duplex Dna with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg603 b:63.9 occ:1.00 O1B A:ADP601 2.2 79.8 1.0 PB A:ADP601 3.5 73.8 1.0 O1 A:PO4602 3.6 59.9 1.0 O3B A:ADP601 4.1 70.1 1.0 O2B A:ADP601 4.2 63.9 1.0 O1A A:ADP601 4.3 67.2 1.0 OG1 A:THR46 4.5 61.2 1.0 O3A A:ADP601 4.7 68.8 1.0 PA A:ADP601 4.8 69.9 1.0 OE1 A:GLU76 4.8 75.9 1.0 O2A A:ADP601 4.8 64.2 1.0 OE2 A:GLU76 4.8 84.4 1.0 CE A:LYS45 5.0 61.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Uvrb Bound to Duplex Dna with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg604 b:51.7 occ:1.00 OD1 A:ASP16 3.5 84.0 1.0 OD2 A:ASP16 3.5 77.8 1.0 CG A:ASP16 3.8 73.0 1.0 NE2 A:GLN19 4.3 67.1 1.0 CB A:GLU409 4.3 69.3 1.0 CG A:GLU409 4.4 76.3 1.0 O A:GLU409 4.6 67.3 1.0 CG1 A:ILE411 4.6 82.4 1.0 C A:GLU409 4.8 62.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Uvrb Bound to Duplex Dna with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 B:Mg603 b:64.7 occ:1.00 O3B B:ADP601 2.5 92.4 1.0 O2A B:ADP601 2.8 94.4 1.0 OD2 B:ASP510 3.2 92.1 1.0 OD1 B:ASP510 3.5 99.0 1.0 PB B:ADP601 3.7 93.0 1.0 CG B:ASP510 3.8 96.1 1.0 PA B:ADP601 3.8 88.8 1.0 O2B B:ADP601 3.9 81.5 1.0 O4 B:PO4602 3.9 72.0 1.0 O1A B:ADP601 4.0 82.7 1.0 O3A B:ADP601 4.3 85.3 1.0 OE1 B:GLN72 4.4 90.9 1.0 NH2 B:ARG543 4.5 94.3 1.0 CA B:GLY508 4.7 63.1 1.0 O1B B:ADP601 4.9 73.5 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg604 b:54.2 occ:1.00 OE1 B:GLU380 3.6 82.1 1.0 OD1 B:ASN352 3.7 58.2 1.0 O B:ARG348 4.1 58.1 1.0 N B:PHE379 4.1 63.4 1.0 OE2 B:GLU380 4.1 85.5 1.0 CB B:THR378 4.2 56.9 1.0 CG2 B:THR378 4.2 57.7 1.0 CD B:GLU380 4.3 78.3 1.0 CD2 B:TYR351 4.3 58.5 1.0 CG B:ARG348 4.4 69.6 1.0 CG B:ASN352 4.5 54.8 1.0 CA B:THR378 4.6 56.5 1.0 CB B:PHE379 4.6 58.8 1.0 ND2 B:ASN352 4.6 58.2 1.0 C B:THR378 4.9 62.3 1.0 CE2 B:TYR351 4.9 61.8 1.0 CA B:PHE379 5.0 58.9 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