Magnesium in PDB 1cyq: Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex

The structure of Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex, PDB code: 1cyq was solved by E.A.Galburt, B.Chevalier, M.S.Jurica, K.E.Flick, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.93
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.866, 113.866, 89.040, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 23.5

The structure of Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Magnesium atom in the Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex (pdb code 1cyq). 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 Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex, PDB code: 1cyq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg606 b:18.5 occ:1.00 OD1 B:ASN319 2.3 11.1 1.0 O B:HOH620 2.4 14.5 1.0 O B:HOH608 2.5 13.4 1.0 O B:HOH618 2.5 18.5 1.0 O3' C:DA413 2.6 15.8 1.0 OP1 C:DG414 2.6 16.2 1.0 P C:DG414 3.2 15.6 1.0 CG B:ASN319 3.4 10.5 1.0 O B:ASN319 3.7 13.0 1.0 N B:ALA298 3.8 9.3 1.0 C3' C:DA413 3.8 14.5 1.0 ND2 B:ASN319 4.0 10.1 1.0 O5' C:DG414 4.0 16.5 1.0 C4' C:DA413 4.1 13.1 1.0 OG B:SER297 4.2 12.0 1.0 O B:ALA298 4.2 11.8 1.0 C B:ASN319 4.2 12.8 1.0 O B:HOH703 4.3 28.0 1.0 O C:HOH278 4.4 28.6 1.0 OP2 C:DG414 4.4 13.9 1.0 C2' C:DA413 4.5 12.6 1.0 CA B:SER297 4.5 10.4 1.0 OD1 B:ASN323 4.6 13.6 1.0 CA B:ALA298 4.6 11.4 1.0 C B:SER297 4.6 10.7 1.0 CB B:ALA298 4.6 10.8 1.0 CB B:ASN319 4.7 11.5 1.0 C B:ALA298 4.7 12.4 1.0 CA B:ASN319 4.7 11.5 1.0 C5' C:DA413 4.8 13.0 1.0 ND1 B:HIS301 4.8 11.2 1.0 CB B:SER297 4.9 10.3 1.0 N B:LYS320 5.0 10.9 1.0 O C:HOH271 5.0 37.0 1.0 CE1 B:HIS301 5.0 11.4 1.0

Magnesium binding site 2 out of 2 in the Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg605 b:17.2 occ:1.00 OD1 A:ASN119 2.3 10.6 1.0 O A:HOH604 2.5 12.2 1.0 O A:HOH623 2.5 16.6 1.0 O A:HOH629 2.5 16.7 1.0 OP1 D:DG514 2.5 15.9 1.0 O3' D:DA513 2.5 12.4 1.0 P D:DG514 3.1 13.9 1.0 CG A:ASN119 3.5 10.1 1.0 O A:ASN119 3.7 11.7 1.0 C3' D:DA513 3.8 13.1 1.0 N A:ALA98 3.9 9.6 1.0 O5' D:DG514 4.0 13.0 1.0 ND2 A:ASN119 4.1 9.3 1.0 C4' D:DA513 4.1 13.6 1.0 OG A:SER97 4.2 9.0 1.0 C A:ASN119 4.2 10.9 1.0 O A:ALA98 4.2 11.9 1.0 O A:HOH717 4.3 26.2 1.0 OP2 D:DG514 4.3 13.9 1.0 O A:HOH699 4.4 36.5 1.0 CA A:SER97 4.5 9.1 1.0 C2' D:DA513 4.5 12.3 1.0 OD1 A:ASN123 4.5 14.8 1.0 C A:SER97 4.5 9.4 1.0 CA A:ALA98 4.6 9.5 1.0 CB A:ASN119 4.6 8.6 1.0 CB A:ALA98 4.7 9.6 1.0 CA A:ASN119 4.7 9.9 1.0 C5' D:DA513 4.7 14.2 1.0 C A:ALA98 4.7 11.9 1.0 CB A:SER97 4.9 7.4 1.0 N A:LYS120 4.9 9.5 1.0 ND1 A:HIS101 4.9 11.7 1.0 CE1 A:HIS101 5.0 11.6 1.0

E.A.Galburt, B.Chevalier, W.Tang, M.S.Jurica, K.E.Flick, R.J.Monnat Jr., B.L.Stoddard. A Novel Endonuclease Mechanism Directly Visualized For I-Ppoi. Nat.Struct.Biol. V. 6 1096 1999.
ISSN: ISSN 1072-8368
PubMed: 10581547
DOI: 10.1038/70027