Magnesium in PDB 8u72: Cryo-Em Structure of the Sparta Oligomer with Guide Rna and Target Dna

The binding sites of Magnesium atom in the Cryo-Em Structure of the Sparta Oligomer with Guide Rna and Target Dna (pdb code 8u72). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryo-Em Structure of the Sparta Oligomer with Guide Rna and Target Dna, PDB code: 8u72:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of the Sparta Oligomer with Guide Rna and Target Dna


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 Sparta Oligomer with Guide Rna and Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg601 b:53.5 occ:1.00 OP1 S:A3 2.2 65.0 1.0 OD1 I:ASN468 2.4 53.0 1.0 OP1 S:U1 2.4 72.4 1.0 CG I:ASN468 3.2 53.0 1.0 ND2 I:ASN468 3.3 53.0 1.0 O I:ILE507 3.4 69.3 1.0 P S:A3 3.6 65.0 1.0 P S:U1 3.7 72.4 1.0 NZ I:LYS263 3.9 47.5 1.0 O3' S:G2 4.0 65.0 1.0 OP2 S:U1 4.2 72.4 1.0 C I:ILE507 4.2 69.3 1.0 O5' S:A3 4.3 65.0 1.0 O5' S:U1 4.6 72.4 1.0 CB I:ASN468 4.6 53.0 1.0 O I:ASN468 4.7 53.0 1.0 OP2 S:A3 4.7 65.0 1.0 C5' S:U1 4.7 72.4 1.0 OE1 I:GLN222 4.8 51.9 1.0 CB I:ILE507 4.8 69.3 1.0 CA I:ILE507 4.9 69.3 1.0 CE I:LYS263 4.9 47.5 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of the Sparta Oligomer with Guide Rna and Target Dna


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 Sparta Oligomer with Guide Rna and Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg601 b:49.1 occ:1.00 OP1 M:A3 2.2 65.0 1.0 OD1 E:ASN468 2.4 46.5 1.0 OP2 M:U1 3.0 66.5 1.0 CG E:ASN468 3.3 46.5 1.0 ND2 E:ASN468 3.5 46.5 1.0 P M:A3 3.5 65.0 1.0 OP1 M:U1 3.7 66.5 1.0 P M:U1 3.8 66.5 1.0 O3' M:G2 3.9 65.0 1.0 O5' M:A3 4.3 65.0 1.0 C E:ILE507 4.5 55.0 1.0 CG2 E:ILE507 4.5 55.0 1.0 O5' M:U1 4.6 66.5 1.0 C5' M:U1 4.6 66.5 1.0 OP2 M:A3 4.7 65.0 1.0 CB E:ASN468 4.7 46.5 1.0 O E:ASN468 4.8 46.5 1.0 OE1 E:GLN222 4.9 53.5 1.0 CE E:LYS263 5.0 37.6 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of the Sparta Oligomer with Guide Rna and Target Dna


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 Sparta Oligomer with Guide Rna and Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:72.9 occ:1.00 OP1 U:U1 2.2 75.6 1.0 OP1 U:A3 2.2 65.0 1.0 OD1 C:ASN468 2.7 58.5 1.0 O C:ILE507 3.2 73.4 1.0 ND2 C:ASN468 3.3 58.5 1.0 CG C:ASN468 3.4 58.5 1.0 P U:A3 3.5 65.0 1.0 P U:U1 3.5 75.6 1.0 NZ C:LYS263 3.8 49.3 1.0 O3' U:G2 3.9 65.0 1.0 O5' U:A3 4.1 65.0 1.0 C C:ILE507 4.2 73.4 1.0 OP2 U:U1 4.5 75.6 1.0 O5' U:U1 4.5 75.6 1.0 C5' U:U1 4.7 75.6 1.0 OE1 C:GLN222 4.7 62.1 1.0 OP2 U:A3 4.7 65.0 1.0 O C:ASN468 4.8 58.5 1.0 CB C:ASN468 4.8 58.5 1.0 C5' U:A3 4.9 65.0 1.0 CE C:LYS263 4.9 49.3 1.0 CA C:ILE507 4.9 73.4 1.0 CB C:ILE507 4.9 73.4 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of the Sparta Oligomer with Guide Rna and Target Dna


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 Sparta Oligomer with Guide Rna and Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg601 b:74.8 occ:1.00 OP1 X:U1 2.1 75.8 1.0 OP1 X:A3 2.2 65.0 1.0 OD1 G:ASN468 2.3 56.2 1.0 O G:ILE507 3.1 72.7 1.0 CG G:ASN468 3.3 56.2 1.0 P X:U1 3.4 75.8 1.0 ND2 G:ASN468 3.5 56.2 1.0 P X:A3 3.5 65.0 1.0 O3' X:G2 3.9 65.0 1.0 NZ G:LYS263 3.9 51.9 1.0 O5' X:A3 4.1 65.0 1.0 C G:ILE507 4.2 72.7 1.0 OP2 X:U1 4.3 75.8 1.0 O5' X:U1 4.5 75.8 1.0 O G:ASN468 4.7 56.2 1.0 CB G:ASN468 4.7 56.2 1.0 C5' X:U1 4.7 75.8 1.0 OP2 X:A3 4.8 65.0 1.0 OE1 G:GLN222 4.8 57.4 1.0 C5' X:A3 4.9 65.0 1.0 CE G:LYS263 4.9 51.9 1.0 CA G:ILE507 5.0 72.7 1.0

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