Magnesium in PDB 5z58: Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom.

Enzymatic activity of Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom.

Other elements in 5z58:

Magnesium Binding Sites:

Magnesium binding site 1 out of 6 in 5z58

Magnesium Binding Sites List in 5z58

Magnesium binding site 1 out of 6 in the Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1501 b:40.6 occ:1.00 O1G C:GTP1500 1.8 0.5 1.0 OG1 C:THR143 1.9 78.9 1.0 O2B C:GTP1500 2.1 81.2 1.0 PG C:GTP1500 3.2 0.7 1.0 CB C:THR143 3.2 69.7 1.0 PB C:GTP1500 3.3 68.0 1.0 O3B C:GTP1500 3.7 90.2 1.0 CG2 C:THR143 3.9 66.8 1.0 O1B C:GTP1500 4.0 61.5 1.0 O2G C:GTP1500 4.0 0.9 1.0 O3G C:GTP1500 4.2 0.7 1.0 CA C:THR143 4.3 63.5 1.0 N C:THR143 4.4 59.5 1.0 O3A C:GTP1500 4.5 59.5 1.0 O2A C:GTP1500 4.5 60.4 1.0 O1A C:GTP1500 4.7 52.8 1.0 PA C:GTP1500 4.8 53.9 1.0 OD2 C:ASP204 4.9 0.5 1.0 OD1 C:ASP204 4.9 0.0 1.0

Magnesium binding site 2 out of 6 in 5z58

Magnesium Binding Sites List in 5z58

Magnesium binding site 2 out of 6 in the Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom. within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg200 b:0.6 occ:1.00 OP2 F:U74 2.1 0.2 1.0 OP1 F:G72 2.4 0.6 1.0 P F:U74 3.3 0.3 1.0 OP1 F:U74 3.6 0.7 1.0 O2' G:G-1 3.8 0.6 1.0 P F:G72 3.9 0.9 1.0 O3' G:G-1 3.9 0.2 1.0 O3' F:A73 4.3 0.3 1.0 OP1 F:G54 4.3 0.7 1.0 O5' F:U74 4.4 0.2 1.0 C3' F:A73 4.5 0.6 1.0 O5' F:G72 4.5 0.0 1.0 C3' G:G-1 4.7 0.6 1.0 C4' G:G-1 4.7 0.5 1.0 OP2 F:G72 4.8 0.1 1.0 O3' F:G71 4.8 0.9 1.0 C4' F:A73 4.8 0.3 1.0 O5' F:G54 4.8 0.3 1.0 C2' G:G-1 4.8 0.1 1.0 C5' F:G72 4.9 0.8 1.0 C5' F:A73 4.9 0.8 1.0 C5' F:U74 4.9 0.2 1.0 P F:G54 4.9 0.3 1.0 OP2 G:G1 5.0 0.9 1.0

Magnesium binding site 3 out of 6 in 5z58

Magnesium Binding Sites List in 5z58

Magnesium binding site 3 out of 6 in the Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom. within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg201 b:0.0 occ:1.00 OP2 F:G54 1.9 0.4 1.0 OP1 F:A53 2.0 0.8 1.0 OP1 F:U74 2.1 0.7 1.0 P F:A53 2.4 0.2 1.0 OP2 F:A53 2.7 1.0 1.0 O5' F:A53 2.8 0.1 1.0 P F:G54 3.2 0.3 1.0 P F:U74 3.6 0.3 1.0 OP1 F:G54 3.6 0.7 1.0 C5' F:A53 3.8 0.3 1.0 O3' F:U52 4.0 0.9 1.0 O3' F:A53 4.2 1.0 1.0 O5' F:U74 4.2 0.2 1.0 O5' F:G54 4.2 0.3 1.0 C3' F:A53 4.4 97.1 1.0 O3' F:A73 4.4 0.3 1.0 OP2 F:U74 4.5 0.2 1.0 C5' F:G54 4.5 0.8 1.0 C4' F:A53 4.7 91.4 1.0 C3' F:U52 5.0 0.4 1.0

Magnesium binding site 4 out of 6 in 5z58

Magnesium Binding Sites List in 5z58

Magnesium binding site 4 out of 6 in the Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom. within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg202 b:97.8 occ:1.00 OP1 F:G75 2.6 0.1 1.0 P F:G75 3.9 0.4 1.0 O5' F:G75 4.2 0.3 1.0 O4 F:U57 4.3 0.2 1.0 N4 F:C77 4.3 0.3 1.0 OP2 F:A76 4.4 0.4 1.0 N7 F:G75 4.4 0.5 1.0 N7 F:A76 4.4 0.6 1.0 C8 F:G75 4.7 0.8 1.0 C2' F:U74 4.8 0.0 1.0 OP2 F:G75 4.9 0.3 1.0 O3' F:U74 4.9 0.5 1.0

Magnesium binding site 5 out of 6 in 5z58

Magnesium Binding Sites List in 5z58

Magnesium binding site 5 out of 6 in the Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom. within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg203 b:0.8 occ:1.00 OP2 F:G75 2.1 0.3 1.0 P F:G75 3.3 0.4 1.0 OP1 F:G75 3.9 0.1 1.0 O3' F:U74 3.9 0.5 1.0 OP2 F:G72 4.2 0.1 1.0 OP2 F:G71 4.4 0.4 1.0 N7 F:G72 4.5 0.4 1.0 OP2 F:A56 4.5 0.4 1.0 O5' F:G75 4.6 0.3 1.0 N7 F:G71 4.8 0.2 1.0 C8 F:G71 4.9 0.5 1.0 C5' F:G75 5.0 0.4 1.0

Magnesium binding site 6 out of 6 in 5z58

Magnesium Binding Sites List in 5z58

Magnesium binding site 6 out of 6 in the Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom. within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg204 b:0.7 occ:1.00 OP1 F:C55 2.1 0.8 1.0 OP1 F:G71 2.1 0.3 1.0 P F:C55 3.2 0.3 1.0 P F:G71 3.5 0.6 1.0 O5' F:C55 3.6 0.8 1.0 O3' F:G54 3.7 0.5 1.0 NE2 A:GLN675 3.9 60.0 1.0 C5' F:C55 4.0 98.2 1.0 O5' F:G71 4.1 1.0 1.0 OP2 F:G71 4.3 0.4 1.0 C5' F:G71 4.5 0.1 1.0 OP2 F:C55 4.6 0.9 1.0 O3' F:A70 4.6 0.2 1.0

Reference: