Magnesium in PDB 1p8k: The Structure and Dna Recognition of A Bifunctional Homing Endonuclease and Group I Intron Splicing Factor

The structure of The Structure and Dna Recognition of A Bifunctional Homing Endonuclease and Group I Intron Splicing Factor, PDB code: 1p8k was solved by B.L.Stoddard, J.M.Bolduc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.462, 72.841, 65.231, 90.00, 108.21, 90.00
R / Rfree (%)	23.9 / 26.4

The binding sites of Magnesium atom in the The Structure and Dna Recognition of A Bifunctional Homing Endonuclease and Group I Intron Splicing Factor (pdb code 1p8k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Structure and Dna Recognition of A Bifunctional Homing Endonuclease and Group I Intron Splicing Factor, PDB code: 1p8k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Structure and Dna Recognition of A Bifunctional Homing Endonuclease and Group I Intron Splicing Factor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure and Dna Recognition of A Bifunctional Homing Endonuclease and Group I Intron Splicing Factor within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg601 b:60.1 occ:1.00 O Z:GLY15 2.0 60.3 1.0 OP1 A:DC416 2.3 69.8 1.0 OE2 Z:GLU148 2.4 60.9 1.0 OP2 D:DC517 2.6 97.4 1.0 OE1 Z:GLU148 2.7 62.9 1.0 CD Z:GLU148 2.8 61.3 1.0 OP3 D:DC517 2.9 98.4 1.0 C Z:GLY15 3.0 59.7 1.0 P D:DC517 3.2 98.0 1.0 CA Z:GLY15 3.4 59.0 1.0 P A:DC416 3.7 69.0 1.0 OE1 Z:GLN171 3.7 53.4 1.0 O5' D:DC517 3.8 91.2 1.0 O Z:GLU14 4.0 59.1 1.0 N Z:ASP16 4.1 59.6 1.0 CG Z:GLU148 4.1 59.8 1.0 O3' A:DT415 4.1 69.1 1.0 O5' A:DC416 4.3 69.6 1.0 NE2 Z:GLN171 4.3 54.0 1.0 CD Z:GLN171 4.4 54.4 1.0 C5' D:DC517 4.5 78.8 1.0 CA Z:ASP16 4.5 59.2 1.0 N Z:GLY15 4.6 58.7 1.0 OD2 Z:ASP16 4.6 64.2 1.0 O3' C:DA516 4.6 63.1 1.0 OP1 D:DC517 4.7 96.9 1.0 C Z:GLU14 4.7 58.6 1.0 C4' A:DC416 4.8 74.4 1.0 OP2 A:DC416 4.9 69.6 1.0

Magnesium binding site 2 out of 2 in the The Structure and Dna Recognition of A Bifunctional Homing Endonuclease and Group I Intron Splicing Factor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure and Dna Recognition of A Bifunctional Homing Endonuclease and Group I Intron Splicing Factor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:77.7 occ:1.00 OP2 B:DT417 2.5 81.5 0.5 O Z:ALA147 2.5 56.7 1.0 OP1 C:DA516 2.5 60.4 1.0 OP1 B:DT417 2.8 81.5 0.5 OD1 Z:ASP16 2.9 62.3 1.0 P B:DT417 3.2 82.0 0.5 C Z:ALA147 3.4 57.0 1.0 O Z:GLU146 3.6 56.9 1.0 CA Z:ALA147 3.8 56.8 1.0 P C:DA516 3.9 61.2 1.0 CG Z:ASP16 4.0 62.0 1.0 OP3 B:DT417 4.3 83.7 1.0 OD2 Z:ASP16 4.3 64.2 1.0 O5' B:DT417 4.3 80.3 1.0 CE Z:LYS227 4.4 59.6 1.0 C Z:GLU146 4.5 57.6 1.0 O3' C:DA515 4.5 63.2 1.0 N Z:ALA147 4.6 57.1 1.0 NZ Z:LYS227 4.6 59.0 1.0 N Z:GLU148 4.6 56.6 1.0 OP2 C:DA516 4.6 60.8 1.0 C5' B:DT417 4.7 73.0 1.0 CB Z:ALA147 4.9 56.2 1.0

J.M.Bolduc, P.C.Spiegel, P.Chatterjee, K.L.Brady, M.E.Downing, M.G.Caprara, R.B.Waring, B.L.Stoddard. Structural and Biochemical Analyses of Dna and Rna Binding By A Bifunctional Homing Endonuclease and Group I Intron Splicing Factor. Genes Dev. V. 17 2875 2003.
ISSN: ISSN 0890-9369
PubMed: 14633971
DOI: 10.1101/GAD.1109003