Magnesium in PDB 9esi: Structure of A B-State Intermediate Committed to Discard (Bd-II State)

All present enzymatic activity of Structure of A B-State Intermediate Committed to Discard (Bd-II State):
2.3.2.27; 3.6.4.13; 5.2.1.8;

The structure of Structure of A B-State Intermediate Committed to Discard (Bd-II State) also contains other interesting chemical elements:

Zinc	(Zn)	6 atoms
Potassium	(K)	1 atom

The binding sites of Magnesium atom in the Structure of A B-State Intermediate Committed to Discard (Bd-II State) (pdb code 9esi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of A B-State Intermediate Committed to Discard (Bd-II State), PDB code: 9esi:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of A B-State Intermediate Committed to Discard (Bd-II State)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A B-State Intermediate Committed to Discard (Bd-II State) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:61.2 occ:1.00 OG B:SER192 2.0 35.0 1.0 OG B:SER155 2.0 34.6 1.0 O1G B:GTP1001 2.0 44.1 1.0 O2B B:GTP1001 2.3 44.1 1.0 CB B:SER192 3.0 35.0 1.0 CB B:SER155 3.3 34.6 1.0 PG B:GTP1001 3.3 44.1 1.0 PB B:GTP1001 3.5 44.1 1.0 OD2 B:ASP216 3.8 33.3 1.0 O3B B:GTP1001 3.9 44.1 1.0 O2G B:GTP1001 3.9 44.1 1.0 OD1 B:ASP216 4.0 33.3 1.0 N B:SER155 4.0 34.6 1.0 O1B B:GTP1001 4.1 44.1 1.0 CG B:LYS154 4.1 22.4 1.0 CA B:SER155 4.2 34.6 1.0 O B:THR217 4.2 31.1 1.0 CA B:SER192 4.2 35.0 1.0 N B:SER192 4.3 35.0 1.0 CG B:ASP216 4.3 33.3 1.0 OD1 B:ASP181 4.4 38.5 1.0 O3G B:GTP1001 4.4 44.1 1.0 O3A B:GTP1001 4.8 44.1 1.0 O2A B:GTP1001 4.8 44.1 1.0 CD B:LYS154 4.8 22.4 1.0

Magnesium binding site 2 out of 4 in the Structure of A B-State Intermediate Committed to Discard (Bd-II State)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A B-State Intermediate Committed to Discard (Bd-II State) within 5.0Å range: probe atom residue distance (Å) B Occ 6:Mg101 b:68.0 occ:1.00 OP1 6:G65 2.3 108.3 1.0 OP1 6:C49 3.1 96.7 1.0 P 6:G65 3.6 108.3 1.0 O5' 6:G65 4.0 108.3 1.0 O3' 6:G48 4.1 103.8 1.0 P 6:C49 4.2 96.7 1.0 O3' 6:A64 4.3 100.4 1.0 C5' 6:G65 4.6 108.3 1.0 OE1 A:GLN698 4.7 80.6 1.0 OP2 6:G65 4.8 108.3 1.0 O2' 1:U-1 4.9 104.3 1.0

Magnesium binding site 3 out of 4 in the Structure of A B-State Intermediate Committed to Discard (Bd-II State)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A B-State Intermediate Committed to Discard (Bd-II State) within 5.0Å range: probe atom residue distance (Å) B Occ 6:Mg102 b:116.6 occ:1.00 OP2 6:G69 2.0 157.1 1.0 P 6:G69 3.3 157.1 1.0 O3' 6:U68 3.8 146.8 1.0 OP2 6:G65 3.8 108.3 1.0 OP1 6:G69 4.0 157.1 1.0 OP2 6:G66 4.4 131.3 1.0 O5' 6:G69 4.5 157.1 1.0 N7 6:G66 4.7 131.3 1.0 OP2 6:A50 4.7 99.0 1.0 OP2 6:C49 4.8 96.7 1.0 N7 6:G65 4.8 108.3 1.0 C8 6:G65 4.8 108.3 1.0 OP1 6:C49 4.9 96.7 1.0 C5' 6:G65 4.9 108.3 1.0 C5' 6:G69 4.9 157.1 1.0

Magnesium binding site 4 out of 4 in the Structure of A B-State Intermediate Committed to Discard (Bd-II State)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A B-State Intermediate Committed to Discard (Bd-II State) within 5.0Å range: probe atom residue distance (Å) B Occ 6:Mg104 b:112.2 occ:1.00 OP1 6:G69 2.5 157.1 1.0 P 6:G69 3.9 157.1 1.0 O5' 6:G69 4.2 157.1 1.0 N7 6:G69 4.4 157.1 1.0 OP2 6:A70 4.5 175.8 1.0 N7 6:A70 4.5 175.8 1.0 C8 6:G69 4.6 157.1 1.0 O4 6:U51 4.7 121.5 1.0 OP2 6:G69 4.8 157.1 1.0 C2' 6:U68 4.9 146.8 1.0 O3' 6:U68 5.0 146.8 1.0

K.Soni, K.Wild, I.M.Sinning. Structures of Aberrant Spliceosome Intermediates on Their Way to Disassembly To Be Published.