Magnesium in PDB 1ipp: Homing Endonuclease/Dna Complex

The structure of Homing Endonuclease/Dna Complex, PDB code: 1ipp was solved by K.E.Flick, M.S.Jurica, R.J.Monnat Jr., B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.900, 113.900, 88.500, 90.00, 90.00, 120.00
R / Rfree (%)	21.2 / 31.6

The structure of Homing Endonuclease/Dna Complex also contains other interesting chemical elements:

Cadmium

(Cd)

4 atoms

The binding sites of Magnesium atom in the Homing Endonuclease/Dna Complex (pdb code 1ipp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Homing Endonuclease/Dna Complex, PDB code: 1ipp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Homing Endonuclease/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:34.1 occ:1.00 O A:HOH306 2.2 33.9 1.0 OD1 A:ASN119 2.2 27.1 1.0 O A:HOH308 2.2 33.1 1.0 O A:HOH307 2.2 32.6 1.0 O D:HOH222 2.3 36.5 1.0 O3' D:DA213 2.3 27.9 1.0 CG A:ASN119 3.4 23.8 1.0 C3' D:DA213 3.5 25.2 1.0 N A:HIS98 3.8 27.8 1.0 C4' D:DA213 3.9 26.8 1.0 O A:ASN119 4.1 28.0 1.0 ND2 A:ASN119 4.1 24.5 1.0 CA A:SER97 4.2 26.0 1.0 OG A:SER97 4.3 29.6 1.0 C A:ASN119 4.3 25.5 1.0 C2' D:DA213 4.3 30.5 1.0 C5' D:DA213 4.5 26.9 1.0 C A:SER97 4.5 25.6 1.0 O5' D:DG214 4.5 29.8 1.0 CB A:ASN119 4.5 19.7 1.0 OD1 A:ASN123 4.6 26.7 1.0 O A:HIS98 4.6 30.8 1.0 CA A:ASN119 4.6 22.2 1.0 O A:HOH448 4.7 46.9 1.0 CB A:SER97 4.7 26.4 1.0 CA A:HIS98 4.7 28.8 1.0 CB A:HIS98 4.7 27.5 1.0 O A:ALA96 4.7 30.7 1.0 C5' D:DG214 4.8 22.5 1.0

Magnesium binding site 2 out of 2 in the Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Homing Endonuclease/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg306 b:36.4 occ:1.00 OD1 B:ASN119 2.2 25.0 1.0 O C:HOH222 2.2 22.0 1.0 O B:HOH308 2.2 25.8 1.0 O B:HOH309 2.2 33.2 1.0 O B:HOH307 2.3 28.7 1.0 O3' C:DA213 2.3 32.9 1.0 CG B:ASN119 3.4 22.7 1.0 C3' C:DA213 3.7 27.2 1.0 O B:ASN119 3.8 29.3 1.0 N B:HIS98 3.9 28.1 1.0 ND2 B:ASN119 4.0 22.9 1.0 C4' C:DA213 4.1 28.3 1.0 C B:ASN119 4.2 26.3 1.0 CD2 B:HIS101 4.4 24.2 1.0 C2' C:DA213 4.5 29.4 1.0 CA B:SER97 4.5 24.3 1.0 OD1 B:ASN123 4.5 34.7 1.0 CB B:HIS98 4.6 25.8 1.0 CB B:ASN119 4.6 22.4 1.0 O B:HIS98 4.6 30.1 1.0 O5' C:DG214 4.6 35.7 1.0 OG B:SER97 4.6 23.9 1.0 CA B:ASN119 4.7 23.3 1.0 CA B:HIS98 4.7 27.6 1.0 C5' C:DA213 4.7 25.3 1.0 C B:SER97 4.7 27.0 1.0 O B:HOH417 4.9 40.7 1.0 C5' C:DG214 4.9 31.7 1.0 NE2 B:HIS101 4.9 32.2 1.0 N B:LYS120 4.9 26.6 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