Magnesium in PDB 8jsi: Cryo-Em Structure of A Dna-Protein Complex

The structure of Cryo-Em Structure of A Dna-Protein Complex also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Cryo-Em Structure of A Dna-Protein Complex (pdb code 8jsi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cryo-Em Structure of A Dna-Protein Complex, PDB code: 8jsi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Cryo-Em Structure of A Dna-Protein 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 A Dna-Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:48.4 occ:1.00 OD2 A:ASP538 1.9 32.6 1.0 OP1 T:DT6 1.9 13.4 1.0 ND1 A:HIS725 2.0 26.2 1.0 CE1 A:HIS725 2.3 26.3 1.0 CG A:ASP538 2.6 35.0 1.0 OD1 A:ASP538 2.8 31.1 1.0 CG A:HIS725 3.1 29.9 1.0 P T:DT6 3.2 14.9 1.0 NE2 A:HIS725 3.4 25.4 1.0 O5' T:DT6 3.8 12.2 1.0 OD2 A:ASP608 3.8 46.7 1.0 CD2 A:HIS725 3.8 26.0 1.0 OP2 T:DT6 3.9 1.3 1.0 MG T:MG101 4.0 33.1 1.0 CB A:HIS725 4.0 26.9 1.0 CB A:ASP538 4.1 28.5 1.0 O A:VAL539 4.1 40.8 1.0 O3' T:DC5 4.4 2.9 1.0 C5' T:DT6 4.4 4.6 1.0 CA A:HIS725 4.5 22.2 1.0 CG A:ASP608 4.5 40.6 1.0 NZ A:LYS637 4.6 22.2 1.0 N A:VAL539 4.8 35.6 1.0 CG1 A:VAL728 5.0 27.5 1.0

Magnesium binding site 2 out of 6 in the Cryo-Em Structure of A Dna-Protein 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 A Dna-Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg101 b:33.1 occ:1.00 OD1 A:ASP538 2.6 31.1 1.0 OP1 T:DT6 2.6 13.4 1.0 O3' T:DC5 2.6 2.9 1.0 O A:ASP608 2.8 32.2 1.0 P T:DT6 3.2 14.9 1.0 OE1 A:GLU576 3.7 49.8 1.0 CG A:ASP538 3.8 35.0 1.0 O A:VAL539 3.8 40.8 1.0 C3' T:DC5 3.9 4.0 1.0 N A:VAL539 3.9 35.6 1.0 O5' T:DT6 3.9 12.2 1.0 C A:ASP608 3.9 23.0 1.0 MG A:MG802 4.0 48.4 1.0 CB A:ASP608 4.0 26.9 1.0 C4' T:DC5 4.1 5.2 1.0 CG A:ASP608 4.2 40.6 1.0 NH1 A:ARG607 4.2 28.2 1.0 OD2 A:ASP538 4.4 32.6 1.0 OD1 A:ASP608 4.4 33.6 1.0 OP2 T:DT6 4.5 1.3 1.0 CA A:ASP538 4.6 17.2 1.0 C5' T:DC5 4.6 7.4 1.0 CA A:ASP608 4.6 19.6 1.0 CA A:VAL539 4.6 32.0 1.0 C A:VAL539 4.6 36.3 1.0 CB A:VAL539 4.6 25.3 1.0 OD2 A:ASP608 4.7 46.7 1.0 CD A:GLU576 4.7 50.9 1.0 C A:ASP538 4.8 21.7 1.0 C2' T:DC5 4.8 3.8 1.0 CB A:ASP538 4.8 28.5 1.0 N A:GLY609 5.0 17.3 1.0

Magnesium binding site 3 out of 6 in the Cryo-Em Structure of A Dna-Protein 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 A Dna-Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg101 b:30.0 occ:1.00 OP1 G:DA3 2.4 20.1 1.0 OP2 G:DG1 2.6 27.4 1.0 P G:DG1 2.9 41.3 1.0 P G:DA3 3.9 27.5 1.0 OP1 G:DG1 3.9 27.7 1.0 O5' G:DG1 4.1 26.9 1.0 C5' G:DG1 4.1 20.0 1.0 NZ A:LYS517 4.2 56.4 1.0 O5' G:DA3 4.5 24.5 1.0 C5' G:DA3 4.6 20.8 1.0 O3' G:DG2 4.7 14.9 1.0 CE A:LYS517 4.7 55.3 1.0 OE1 A:GLN513 4.7 59.4 1.0 OP2 G:DA3 4.9 26.8 1.0

Magnesium binding site 4 out of 6 in the Cryo-Em Structure of A Dna-Protein 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 A Dna-Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:48.4 occ:1.00 OP1 U:DT6 1.8 13.4 1.0 ND1 B:HIS725 2.1 26.2 1.0 OD2 B:ASP538 2.1 32.6 1.0 CE1 B:HIS725 2.2 26.3 1.0 CG B:ASP538 2.9 35.0 1.0 OD1 B:ASP538 3.0 31.1 1.0 P U:DT6 3.0 14.9 1.0 CG B:HIS725 3.2 29.9 1.0 NE2 B:HIS725 3.3 25.4 1.0 O5' U:DT6 3.5 12.2 1.0 OP2 U:DT6 3.7 1.3 1.0 CD2 B:HIS725 3.8 26.0 1.0 MG U:MG101 4.0 33.1 1.0 O B:VAL539 4.0 40.8 1.0 C5' U:DT6 4.1 4.6 1.0 OD2 B:ASP608 4.1 46.7 1.0 CB B:HIS725 4.2 26.9 1.0 O3' U:DC5 4.3 2.9 1.0 CB B:ASP538 4.3 28.5 1.0 CA B:HIS725 4.7 22.2 1.0 NZ B:LYS637 4.7 22.2 1.0 CG B:ASP608 4.7 40.6 1.0 N B:VAL539 4.9 35.6 1.0 C B:VAL539 5.0 36.3 1.0 CG1 B:VAL728 5.0 27.5 1.0

Magnesium binding site 5 out of 6 in the Cryo-Em Structure of A Dna-Protein 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 A Dna-Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ U:Mg101 b:33.1 occ:1.00 OP1 U:DT6 2.6 13.4 1.0 O3' U:DC5 2.6 2.9 1.0 OD1 B:ASP538 2.6 31.1 1.0 O B:ASP608 2.9 32.2 1.0 P U:DT6 3.1 14.9 1.0 OE1 B:GLU576 3.7 49.8 1.0 CG B:ASP538 3.7 35.0 1.0 O B:VAL539 3.8 40.8 1.0 C3' U:DC5 3.8 4.0 1.0 O5' U:DT6 3.8 12.2 1.0 N B:VAL539 3.9 35.6 1.0 MG B:MG801 4.0 48.4 1.0 C B:ASP608 4.0 23.0 1.0 C4' U:DC5 4.0 5.2 1.0 CB B:ASP608 4.1 26.9 1.0 CG B:ASP608 4.2 40.6 1.0 NH1 B:ARG607 4.3 28.2 1.0 OD2 B:ASP538 4.4 32.6 1.0 OP2 U:DT6 4.4 1.3 1.0 OD1 B:ASP608 4.4 33.6 1.0 C5' U:DC5 4.6 7.4 1.0 CA B:ASP538 4.6 17.2 1.0 C B:VAL539 4.6 36.3 1.0 CA B:VAL539 4.6 32.0 1.0 CA B:ASP608 4.7 19.6 1.0 CB B:VAL539 4.7 25.3 1.0 OD2 B:ASP608 4.7 46.7 1.0 C2' U:DC5 4.7 3.8 1.0 CD B:GLU576 4.7 50.9 1.0 C B:ASP538 4.8 21.7 1.0 CB B:ASP538 4.8 28.5 1.0

Magnesium binding site 6 out of 6 in the Cryo-Em Structure of A Dna-Protein Complex


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 Dna-Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg101 b:30.0 occ:1.00 OP1 H:DA3 1.9 20.1 1.0 OP2 H:DG1 2.4 27.4 1.0 P H:DG1 2.8 41.3 1.0 P H:DA3 3.4 27.5 1.0 C5' H:DG1 3.6 20.0 1.0 O5' H:DG1 3.7 26.9 1.0 OP1 H:DG1 4.0 27.7 1.0 O5' H:DA3 4.2 24.5 1.0 OP2 H:DA3 4.2 26.8 1.0 O3' H:DG2 4.3 14.9 1.0 C5' H:DA3 4.5 20.8 1.0 NZ B:LYS517 4.9 56.4 1.0

Z.Li, Z.Li. N/A N/A.