Magnesium in PDB 3zc0: Structure of AFC3PO - Duplex Rna Complex

The structure of Structure of AFC3PO - Duplex Rna Complex, PDB code: 3zc0 was solved by E.A.Parizotto, E.D.Lowe, J.S.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	83.091 / 2.98
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	183.060, 183.060, 198.120, 90.00, 90.00, 120.00
R / Rfree (%)	20.78 / 25.72

The structure of Structure of AFC3PO - Duplex Rna Complex also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Structure of AFC3PO - Duplex Rna Complex (pdb code 3zc0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Structure of AFC3PO - Duplex Rna Complex, PDB code: 3zc0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Structure of AFC3PO - Duplex Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of AFC3PO - Duplex Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg197 b:43.0 occ:1.00 OE2 A:GLU118 2.0 45.6 1.0 O A:HOH2003 2.0 43.2 1.0 O A:HOH2002 2.1 59.0 1.0 OE2 A:GLU83 2.2 54.8 1.0 OP1 M:G12 2.5 65.8 0.5 OP1 M:C11 2.6 65.8 0.5 CD A:GLU118 3.2 44.5 1.0 CD A:GLU83 3.2 43.1 1.0 OE1 A:GLU83 3.6 63.2 1.0 P M:G12 3.8 90.5 0.5 P M:C11 3.8 90.5 0.5 CG A:GLU118 3.8 37.7 1.0 O3' M:C11 4.1 87.8 0.5 O3' M:U10 4.1 87.8 0.5 OE1 A:GLU118 4.2 39.7 1.0 O5' M:G12 4.5 74.3 0.5 CG A:GLU83 4.6 29.5 1.0 O5' M:C11 4.6 74.1 0.5 NH1 A:ARG121 4.6 56.5 1.0 O A:ALA114 4.8 40.3 1.0 OE1 A:GLU80 4.9 84.2 1.0 CD1 A:ILE35 4.9 32.7 1.0

Magnesium binding site 2 out of 12 in the Structure of AFC3PO - Duplex Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of AFC3PO - Duplex Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg197 b:30.3 occ:1.00 O B:HOH2002 2.1 39.9 1.0 O B:HOH2001 2.1 36.9 1.0 OE2 B:GLU83 2.2 39.0 1.0 OE1 B:GLU118 2.3 41.2 1.0 CD B:GLU83 3.2 43.9 1.0 OE1 B:GLU83 3.4 52.5 1.0 CD B:GLU118 3.5 34.2 1.0 OE2 B:GLU118 4.2 53.9 1.0 CG B:GLU118 4.5 30.2 1.0 CG B:GLU83 4.6 27.1 1.0 O B:ALA114 4.7 31.4 1.0 OE2 B:GLU80 4.7 73.6 1.0 CB B:GLU118 5.0 25.3 1.0

Magnesium binding site 3 out of 12 in the Structure of AFC3PO - Duplex Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of AFC3PO - Duplex Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg197 b:50.9 occ:1.00 O C:HOH2004 2.0 34.5 1.0 O C:HOH2003 2.1 48.4 1.0 O C:HOH2002 2.1 57.2 1.0 OE2 C:GLU118 2.1 38.7 1.0 OE2 C:GLU83 2.3 44.2 1.0 CD C:GLU83 3.2 41.0 1.0 CD C:GLU118 3.3 38.5 1.0 OE1 C:GLU83 3.4 49.7 1.0 CG C:GLU118 3.8 34.5 1.0 OE2 C:GLU80 4.3 71.1 1.0 OE1 C:GLU118 4.3 22.7 1.0 CD1 C:ILE35 4.4 32.4 1.0 CG C:GLU83 4.6 33.0 1.0 O C:HOH2008 4.8 43.6 1.0 O C:ALA114 4.8 40.8 1.0

Magnesium binding site 4 out of 12 in the Structure of AFC3PO - Duplex Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of AFC3PO - Duplex Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg197 b:64.1 occ:1.00 OE1 D:GLU118 2.0 52.2 1.0 O D:HOH2003 2.1 55.4 1.0 O D:HOH2002 2.1 66.2 1.0 OE2 D:GLU83 2.3 55.6 1.0 CD D:GLU118 3.2 44.8 1.0 CD D:GLU83 3.4 50.7 1.0 OE2 D:GLU118 3.7 39.5 1.0 OE1 D:GLU83 3.9 49.4 1.0 CG D:GLU118 4.3 44.8 1.0 CD1 D:ILE35 4.7 32.5 1.0 CG D:GLU83 4.7 38.1 1.0 CB D:GLU118 4.9 39.3 1.0 O D:ALA114 4.9 44.3 1.0

Magnesium binding site 5 out of 12 in the Structure of AFC3PO - Duplex Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of AFC3PO - Duplex Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg197 b:46.0 occ:1.00 O E:HOH2003 2.1 47.4 1.0 OE2 E:GLU118 2.1 49.4 1.0 OE2 E:GLU83 2.2 57.3 1.0 OP1 N:G12 2.5 61.8 0.5 OP1 N:C11 2.5 61.8 0.5 CD E:GLU83 3.2 45.8 1.0 CD E:GLU118 3.3 47.3 1.0 OE1 E:GLU83 3.5 65.0 1.0 P N:G12 3.7 93.7 0.5 P N:C11 3.8 93.6 0.5 CG E:GLU118 3.9 37.2 1.0 O3' N:C11 3.9 92.2 0.5 O3' N:U10 3.9 92.2 0.5 OE1 E:GLU118 4.3 48.2 1.0 O5' N:G12 4.3 72.6 0.5 O5' N:C11 4.4 72.4 0.5 CG E:GLU83 4.6 33.3 1.0 NH1 E:ARG121 4.7 54.2 1.0 O E:ALA114 4.8 44.3 1.0 OE1 E:GLU80 5.0 65.6 1.0 CD1 E:ILE35 5.0 33.5 1.0 OP2 N:G12 5.0 87.5 0.5

Magnesium binding site 6 out of 12 in the Structure of AFC3PO - Duplex Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of AFC3PO - Duplex Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg197 b:34.8 occ:1.00 O F:HOH2005 2.1 45.4 1.0 O F:HOH2004 2.1 46.4 1.0 OE2 F:GLU83 2.2 41.8 1.0 OE1 F:GLU118 2.3 45.7 1.0 O F:HOH2003 3.1 44.3 1.0 CD F:GLU83 3.1 47.0 1.0 OE1 F:GLU83 3.3 57.5 1.0 CD F:GLU118 3.6 40.2 1.0 OE2 F:GLU118 4.3 51.2 1.0 CG F:GLU83 4.5 30.4 1.0 CG F:GLU118 4.6 35.1 1.0 O F:ALA114 4.6 30.6 1.0 OE2 F:GLU80 4.7 70.2 1.0

Magnesium binding site 7 out of 12 in the Structure of AFC3PO - Duplex Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of AFC3PO - Duplex Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg197 b:53.9 occ:1.00 O G:HOH2004 2.0 30.3 1.0 O G:HOH2003 2.1 51.2 1.0 OE2 G:GLU83 2.2 49.2 1.0 OE2 G:GLU118 2.2 42.9 1.0 CD G:GLU83 3.1 44.7 1.0 CD G:GLU118 3.4 38.1 1.0 OE1 G:GLU83 3.4 51.0 1.0 CG G:GLU118 3.9 39.8 1.0 OE2 G:GLU80 4.2 72.4 1.0 OE1 G:GLU118 4.4 21.5 1.0 CD1 G:ILE35 4.5 37.7 1.0 CG G:GLU83 4.5 29.9 1.0 O G:ALA114 4.8 41.5 1.0 O G:HOH2009 4.8 44.4 1.0

Magnesium binding site 8 out of 12 in the Structure of AFC3PO - Duplex Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of AFC3PO - Duplex Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg197 b:59.6 occ:1.00 O H:HOH2002 2.0 46.3 1.0 OE1 H:GLU118 2.1 57.3 1.0 OE2 H:GLU83 2.2 55.6 1.0 CD H:GLU118 3.2 48.1 1.0 CD H:GLU83 3.4 55.1 1.0 OE2 H:GLU118 3.9 32.0 1.0 OE1 H:GLU83 3.9 57.5 1.0 CG H:GLU118 4.3 52.6 1.0 CG H:GLU83 4.6 42.7 1.0 O E:HOH2004 4.7 44.8 1.0 CD1 H:ILE35 4.7 32.4 1.0 O H:ALA114 4.9 46.0 1.0 CB H:GLU118 4.9 44.3 1.0

Magnesium binding site 9 out of 12 in the Structure of AFC3PO - Duplex Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of AFC3PO - Duplex Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg197 b:44.8 occ:1.00 O I:HOH2002 2.1 48.5 1.0 OE2 I:GLU118 2.1 51.8 1.0 OE2 I:GLU83 2.1 54.6 1.0 OP1 O:C11 2.9 76.7 0.5 OP1 O:G12 2.9 76.7 0.5 CD I:GLU83 3.2 48.4 1.0 CD I:GLU118 3.3 39.9 1.0 OE1 I:GLU83 3.5 63.4 1.0 P O:G12 3.9 99.6 0.5 P O:C11 3.9 99.6 0.5 CG I:GLU118 3.9 34.7 1.0 O3' O:C11 4.0 89.8 0.5 O3' O:U10 4.0 90.3 0.5 O5' O:G12 4.0 87.2 0.5 O5' O:C11 4.2 86.3 0.5 OE1 I:GLU118 4.3 42.6 1.0 CG I:GLU83 4.5 34.1 1.0 NH1 I:ARG121 4.7 56.9 1.0 O I:ALA114 4.8 43.5 1.0 OE1 I:GLU80 4.9 79.8 1.0 CD1 I:ILE35 4.9 39.4 1.0

Magnesium binding site 10 out of 12 in the Structure of AFC3PO - Duplex Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of AFC3PO - Duplex Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg197 b:36.0 occ:1.00 O J:HOH2003 2.1 40.5 1.0 O J:HOH2002 2.1 40.9 1.0 OE2 J:GLU83 2.2 38.3 1.0 OE1 J:GLU118 2.4 38.8 1.0 CD J:GLU83 3.1 46.2 1.0 OE1 J:GLU83 3.3 50.4 1.0 O J:HOH2001 3.4 45.2 1.0 CD J:GLU118 3.6 35.5 1.0 OE2 J:GLU118 4.3 54.4 1.0 CG J:GLU83 4.5 28.8 1.0 CG J:GLU118 4.6 35.5 1.0 O J:ALA114 4.7 35.0 1.0 OE2 J:GLU80 4.7 70.8 1.0

E.A.Parizotto, E.D.Lowe, J.S.Parker. Structural Basis For Duplex Rna Recognition and Cleavage By Archaeoglobus Fulgidus C3PO. Nat.Struct.Mol.Biol. V. 20 380 2013.
ISSN: ISSN 1545-9993
PubMed: 23353787
DOI: 10.1038/NSMB.2487