Magnesium in PDB 4e8v: Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+, PDB code: 4e8v was solved by M.Marcia, A.M.Pyle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.91 / 4.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.727, 96.548, 227.673, 90.00, 90.00, 90.00
R / Rfree (%)	29.7 / 34.5

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+ also contains other interesting chemical elements:

Barium	(Ba)	42 atoms
Potassium	(K)	4 atoms

The binding sites of Magnesium atom in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+ (pdb code 4e8v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+, PDB code: 4e8v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:0.1 occ:1.00 OP2 A:A105 1.9 0.9 1.0 P A:A105 2.9 0.8 1.0 OP1 A:A105 3.1 0.7 1.0 O5' A:A105 3.7 0.8 1.0 O6 A:G111 4.1 0.8 1.0 O3' A:G104 4.2 0.1 1.0 OP2 A:A106 4.5 0.1 1.0 O A:HOH529 4.8 0.4 1.0 C5' A:A105 4.8 0.9 1.0 N7 A:G111 4.9 0.3 1.0

Magnesium binding site 2 out of 5 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:76.9 occ:1.00 OP1 A:C190 3.8 0.1 1.0 OP1 A:C53 4.4 0.3 1.0 OP2 A:C190 4.6 0.5 1.0 P A:C190 4.8 0.2 1.0 OP1 A:G170 4.9 0.0 1.0

Magnesium binding site 3 out of 5 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:0.7 occ:1.00 OP2 A:U66 2.6 0.1 1.0 P A:U66 3.4 0.5 1.0 OP1 A:A67 3.4 0.9 1.0 OP1 A:U66 3.7 0.6 1.0 O5' A:U66 3.7 0.1 1.0 O3' A:U66 3.7 0.8 1.0 P A:A67 4.3 0.3 1.0 C5' A:U66 4.7 0.9 1.0 C4' A:U66 4.7 0.0 1.0 OP1 A:A27 4.7 0.1 1.0 C3' A:U66 4.8 0.7 1.0 O3' A:U65 4.9 0.1 1.0

Magnesium binding site 4 out of 5 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:80.5 occ:1.00 O A:HOH516 2.4 78.9 1.0 OP1 A:A95 3.2 0.2 1.0 OP1 A:G284 3.3 0.6 1.0 O3' A:A283 3.8 0.9 1.0 P A:G284 4.0 0.5 1.0 P A:A95 4.5 0.4 1.0 O5' A:A95 4.5 0.4 1.0 OP2 A:U96 4.6 0.7 1.0 OP2 A:G284 4.7 0.6 1.0 OP1 A:G81 4.8 1.0 1.0 C3' A:A283 5.0 0.5 1.0

Magnesium binding site 5 out of 5 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:96.3 occ:1.00 O4 A:U384 3.0 0.9 1.0 N3 A:G288 3.6 0.4 1.0 N2 A:G288 3.8 0.1 1.0 O6 A:G383 3.9 0.8 1.0 C2 A:G288 4.1 0.0 1.0 C4 A:U384 4.1 0.6 1.0 O2' A:G288 4.3 0.9 1.0 O4' A:C289 4.6 0.0 1.0 C4 A:G288 4.7 0.5 1.0 C5 A:U384 4.8 0.3 1.0 C6 A:G383 4.8 0.8 1.0 C2' A:G288 5.0 0.1 1.0

M.Marcia, A.M.Pyle. Visualizing Group II Intron Catalysis Through the Stages of Splicing. Cell(Cambridge,Mass.) V. 151 497 2012.
ISSN: ISSN 0092-8674
PubMed: 23101623
DOI: 10.1016/J.CELL.2012.09.033