Magnesium in PDB 1a73: Intron-Encoded Endonuclease I-Ppoi Complexed with Dna

The structure of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna, PDB code: 1a73 was solved by K.E.Flick, R.J.Monnat Junior, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.700, 113.700, 88.400, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 29.7

The structure of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Magnesium atom in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna (pdb code 1a73). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna, PDB code: 1a73:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg205 b:26.6 occ:1.00 O3' E:DA13 2.2 14.7 1.0 OD1 A:ASN119 2.4 10.2 1.0 O A:HOH520 2.6 19.0 1.0 O A:HOH519 2.7 17.7 1.0 O A:HOH384 2.7 12.4 1.0 O F:HOH512 2.8 15.0 1.0 C3' E:DA13 3.5 12.8 1.0 CG A:ASN119 3.6 8.6 1.0 C4' E:DA13 3.9 13.5 1.0 N A:HIS98 4.0 9.6 1.0 O A:ASN119 4.1 10.5 1.0 ND2 A:ASN119 4.2 8.9 1.0 O F:HOH646 4.3 26.7 1.0 C2' E:DA13 4.3 11.8 1.0 C5' E:DA13 4.4 13.8 1.0 CA A:SER97 4.4 9.7 1.0 OP3 F:DG14 4.4 14.0 1.0 OG A:SER97 4.5 13.8 1.0 C A:ASN119 4.5 10.0 1.0 O A:HOH562 4.6 20.3 1.0 C A:SER97 4.7 9.6 1.0 CB A:HIS98 4.7 11.0 1.0 O A:HIS98 4.7 12.5 1.0 OD1 A:ASN123 4.7 13.8 1.0 CB A:ASN119 4.8 8.6 1.0 O A:ALA96 4.8 9.6 1.0 CA A:HIS98 4.8 11.2 1.0 CB A:SER97 4.9 10.4 1.0 C5' F:DG14 4.9 10.7 1.0 CA A:ASN119 5.0 9.7 1.0

Magnesium binding site 2 out of 2 in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg206 b:22.9 occ:1.00 OD1 B:ASN119 2.3 11.4 1.0 O3' C:DA13 2.5 15.1 1.0 O B:HOH302 2.6 15.8 1.0 O B:HOH451 2.7 13.0 1.0 O B:HOH509 2.7 17.8 1.0 O B:HOH393 2.7 15.2 1.0 CG B:ASN119 3.4 11.9 1.0 C3' C:DA13 3.7 11.5 1.0 N B:HIS98 3.9 10.6 1.0 O B:ASN119 4.0 11.7 1.0 ND2 B:ASN119 4.0 11.4 1.0 C4' C:DA13 4.1 11.7 1.0 O B:HOH499 4.4 17.0 1.0 OP2 D:DG14 4.4 16.5 1.0 C B:ASN119 4.4 12.1 1.0 CA B:SER97 4.5 12.0 1.0 C2' C:DA13 4.5 11.2 1.0 OG B:SER97 4.6 13.5 1.0 CB B:HIS98 4.6 11.8 1.0 CB B:ASN119 4.7 12.8 1.0 C5' C:DA13 4.7 11.8 1.0 O B:HIS98 4.7 11.1 1.0 C B:SER97 4.7 11.7 1.0 CA B:HIS98 4.8 11.3 1.0 OD1 B:ASN123 4.8 12.6 1.0 C5' D:DG14 4.8 12.7 1.0 CA B:ASN119 4.8 11.9 1.0 O B:ALA96 4.9 11.5 1.0 ND1 B:HIS101 5.0 10.8 1.0

K.E.Flick, M.S.Jurica, R.J.Monnat Jr., B.L.Stoddard. Dna Binding and Cleavage By the Nuclear Intron-Encoded Homing Endonuclease I-Ppoi. Nature V. 394 96 1998.
ISSN: ISSN 0028-0836
PubMed: 9665136
DOI: 10.1038/27952