Magnesium in PDB 7dvq: Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)

Enzymatic activity of Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)

Other elements in 7dvq:

Magnesium Binding Sites:

Magnesium binding site 1 out of 5 in 7dvq

Magnesium Binding Sites List in 7dvq

Magnesium binding site 1 out of 5 in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)


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 the Activated Human Minor Spliceosome (Minor Bact Complex) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1501 b:40.0 occ:1.00 O2B C:GTP1500 2.1 23.7 1.0 O1G C:GTP1500 2.1 23.7 1.0 OG1 C:THR143 2.1 27.7 1.0 O C:HOH1602 2.1 46.7 1.0 O C:HOH1601 2.1 33.4 1.0 O C:HOH1603 2.1 30.2 1.0 CB C:THR143 3.1 27.7 1.0 PG C:GTP1500 3.3 23.7 1.0 PB C:GTP1500 3.3 23.7 1.0 O3B C:GTP1500 3.7 23.7 1.0 O2G C:GTP1500 3.8 23.7 1.0 N C:THR143 3.9 27.7 1.0 CG2 C:THR143 4.1 27.7 1.0 CA C:THR143 4.1 27.7 1.0 OD1 C:ASP169 4.1 38.4 1.0 O1B C:GTP1500 4.2 23.7 1.0 OD2 C:ASP204 4.2 38.1 1.0 O2A C:GTP1500 4.2 23.7 1.0 OD1 C:ASP204 4.3 38.1 1.0 O3A C:GTP1500 4.3 23.7 1.0 O3G C:GTP1500 4.4 23.7 1.0 CA C:GLY180 4.5 31.3 1.0 OD2 C:ASP169 4.5 38.4 1.0 CG C:ASP204 4.6 38.1 1.0 CG C:ASP169 4.7 38.4 1.0 O C:THR205 4.7 31.5 1.0 CE C:LYS142 4.8 20.8 1.0 PA C:GTP1500 4.8 23.7 1.0 N C:GLY180 4.8 31.3 1.0 CB C:LYS142 4.8 20.8 1.0 C C:LYS142 5.0 20.8 1.0

Magnesium binding site 2 out of 5 in 7dvq

Magnesium Binding Sites List in 7dvq

Magnesium binding site 2 out of 5 in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)


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 the Activated Human Minor Spliceosome (Minor Bact Complex) within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg201 b:31.4 occ:1.00 OP1 F:G44 2.7 36.9 1.0 OP2 F:U46 2.8 34.9 1.0 O2' G:A0 3.1 34.5 1.0 O3' G:A0 3.4 34.5 1.0 OP1 F:G27 3.6 36.9 1.0 OP2 G:A1 3.7 28.7 1.0 O5' F:G27 3.8 36.9 1.0 P F:U46 3.8 34.9 1.0 P F:G44 3.9 36.9 1.0 O5' F:U46 4.1 34.9 1.0 C3' G:A0 4.2 34.5 1.0 C2' G:A0 4.2 34.5 1.0 P F:G27 4.2 36.9 1.0 P G:A1 4.2 28.7 1.0 OP1 F:U46 4.3 34.9 1.0 OP2 F:G44 4.4 36.9 1.0 C4' G:A0 4.5 34.5 1.0 MG F:MG202 4.5 24.5 1.0 C5' F:U46 4.5 34.9 1.0 O3' F:G43 4.6 37.0 1.0 C5' F:G27 4.7 36.9 1.0 OP2 F:G27 4.7 36.9 1.0 O5' G:A1 4.9 28.7 1.0

Magnesium binding site 3 out of 5 in 7dvq

Magnesium Binding Sites List in 7dvq

Magnesium binding site 3 out of 5 in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)


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 the Activated Human Minor Spliceosome (Minor Bact Complex) within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg202 b:24.5 occ:1.00 OP1 F:U46 2.1 34.9 1.0 OP1 F:A26 2.2 39.6 1.0 OP2 F:G27 3.0 36.9 1.0 OP1 F:G27 3.3 36.9 1.0 P F:U46 3.4 34.9 1.0 P F:A26 3.6 39.6 1.0 P F:G27 3.6 36.9 1.0 OP2 F:U46 3.8 34.9 1.0 OP2 G:A1 3.9 28.7 1.0 O5' F:A26 4.2 39.6 1.0 NZ v:LYS4 4.2 24.0 1.0 C5' F:A26 4.3 39.6 1.0 O5' F:U46 4.3 34.9 1.0 K F:K205 4.4 25.9 1.0 O3' F:A45 4.5 37.4 1.0 MG F:MG201 4.5 31.4 1.0 OP2 F:A26 4.5 39.6 1.0 O3' F:U25 4.6 38.0 1.0 O5' F:G27 4.7 36.9 1.0 O3' F:A26 4.8 39.6 1.0

Magnesium binding site 4 out of 5 in 7dvq

Magnesium Binding Sites List in 7dvq

Magnesium binding site 4 out of 5 in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)


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 the Activated Human Minor Spliceosome (Minor Bact Complex) within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg203 b:35.1 occ:1.00 OP2 F:G47 2.3 37.7 1.0 P F:G47 3.7 37.7 1.0 OP2 F:G43 3.8 37.0 1.0 O5' F:G47 4.1 37.7 1.0 OP2 F:A29 4.3 35.1 1.0 O3' F:U46 4.3 34.9 1.0 OP2 F:G44 4.4 36.9 1.0 N7 F:G43 4.6 37.0 1.0 C8 F:G43 4.6 37.0 1.0 OP2 F:C28 4.7 36.8 1.0 OP1 F:C28 4.7 36.8 1.0 C5' F:G43 4.8 37.0 1.0 OP1 F:G47 4.9 37.7 1.0 P F:G43 4.9 37.0 1.0

Magnesium binding site 5 out of 5 in 7dvq

Magnesium Binding Sites List in 7dvq

Magnesium binding site 5 out of 5 in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)


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 the Activated Human Minor Spliceosome (Minor Bact Complex) within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg204 b:35.1 occ:1.00 OP1 F:G43 2.0 37.0 1.0 OP1 F:C28 2.5 36.8 1.0 P F:G43 3.4 37.0 1.0 P F:C28 3.7 36.8 1.0 O5' F:G43 3.8 37.0 1.0 O3' F:G27 3.9 36.9 1.0 NE2 A:GLN675 3.9 35.1 1.0 C5' F:G43 4.2 37.0 1.0 O3' F:A42 4.3 36.9 1.0 OP2 F:G43 4.4 37.0 1.0 C5' F:C28 4.6 36.8 1.0 O5' F:C28 4.7 36.8 1.0 OP2 F:C28 4.8 36.8 1.0 CD A:GLN675 4.9 35.1 1.0

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