Magnesium in PDB 8jpx: Cryo-Em Structure of Pfago-Guide Dna-Target Dna Complex

The binding sites of Magnesium atom in the Cryo-Em Structure of Pfago-Guide Dna-Target Dna Complex (pdb code 8jpx). 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 Pfago-Guide Dna-Target Dna Complex, PDB code: 8jpx:
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 Pfago-Guide Dna-Target Dna 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 Pfago-Guide Dna-Target Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:27.8 occ:1.00 OP1 U:DT10 1.9 32.7 1.0 OD2 B:ASP558 1.9 44.3 1.0 ND1 B:HIS745 2.0 37.0 1.0 CG B:ASP558 2.8 33.5 1.0 OD2 B:ASP628 2.9 47.2 1.0 CE1 B:HIS745 2.9 30.5 1.0 CG B:HIS745 3.0 30.7 1.0 OD1 B:ASP558 3.1 37.2 1.0 P U:DT10 3.3 47.2 1.0 CB B:HIS745 3.4 17.2 1.0 CA B:HIS745 4.0 12.1 1.0 OP2 U:DT10 4.0 38.1 1.0 CG B:ASP628 4.1 42.8 1.0 NE2 B:HIS745 4.1 30.7 1.0 CD2 B:HIS745 4.1 30.4 1.0 CB B:ASP558 4.2 25.8 1.0 O5' U:DT10 4.2 37.8 1.0 O3' U:DC9 4.3 22.7 1.0 MG B:MG802 4.4 51.5 1.0 C5' U:DT10 4.6 31.9 1.0 NZ B:LYS657 4.8 32.3 1.0 OD1 B:ASP628 4.8 45.4 1.0 N B:HIS745 4.9 24.5 1.0 CB B:ASP628 4.9 28.9 1.0

Magnesium binding site 2 out of 6 in the Cryo-Em Structure of Pfago-Guide Dna-Target Dna 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 Pfago-Guide Dna-Target Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:51.5 occ:1.00 OD1 B:ASP558 2.6 37.2 1.0 O3' U:DC9 2.9 22.7 1.0 OE2 B:GLU596 3.4 54.8 1.0 O B:ASP628 3.4 33.6 1.0 OP1 U:DT10 3.5 32.7 1.0 CG B:ASP558 3.7 33.5 1.0 C4' U:DC9 3.8 28.1 1.0 C3' U:DC9 3.9 27.1 1.0 P U:DT10 3.9 47.2 1.0 O B:VAL559 3.9 45.7 1.0 N B:VAL559 4.0 32.1 1.0 CG B:ASP628 4.0 42.8 1.0 OD2 B:ASP628 4.1 47.2 1.0 CB B:ASP628 4.2 28.9 1.0 NH1 B:ARG627 4.2 31.0 1.0 CD B:GLU596 4.2 60.1 1.0 OD2 B:ASP558 4.3 44.3 1.0 OE1 B:GLU596 4.3 63.2 1.0 C B:ASP628 4.4 22.1 1.0 C5' U:DC9 4.4 32.2 1.0 MG B:MG801 4.4 27.8 1.0 OD1 B:ASP628 4.5 45.4 1.0 C2' U:DC9 4.5 30.7 1.0 C5' U:DT10 4.6 31.9 1.0 CA B:ASP558 4.7 23.8 1.0 CA B:VAL559 4.7 30.9 1.0 C B:VAL559 4.8 32.1 1.0 CB B:VAL559 4.8 25.5 1.0 CB B:ASP558 4.8 25.8 1.0 O5' U:DT10 4.8 37.8 1.0 C B:ASP558 4.9 30.6 1.0 CA B:ASP628 4.9 25.1 1.0 O4' U:DC9 4.9 14.5 1.0 OP2 U:DT10 5.0 38.1 1.0

Magnesium binding site 3 out of 6 in the Cryo-Em Structure of Pfago-Guide Dna-Target Dna 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 Pfago-Guide Dna-Target Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg101 b:29.3 occ:1.00 OP1 H:DT1 2.1 45.5 1.0 OP1 H:DA3 2.3 34.0 1.0 NE2 B:GLN533 2.4 44.4 1.0 O B:VAL770 3.1 54.4 1.0 P H:DT1 3.3 60.1 1.0 OP3 H:DT1 3.3 53.0 1.0 OXT B:VAL770 3.4 57.0 1.0 P H:DA3 3.7 45.7 1.0 CD B:GLN533 3.7 42.6 1.0 C B:VAL770 3.7 57.2 1.0 OE1 B:GLN533 4.3 50.1 1.0 C5' H:DT1 4.3 45.4 1.0 O5' H:DT1 4.3 55.8 1.0 OP2 H:DT1 4.3 50.4 1.0 OP2 H:DA3 4.4 36.3 1.0 NZ B:LYS537 4.4 40.9 1.0 O5' H:DA3 4.5 34.1 1.0 CE B:LYS537 4.6 33.6 1.0 O3' H:DG2 4.6 35.8 1.0 CG B:GLN533 4.8 34.1 1.0 C5' H:DA3 4.8 31.7 1.0

Magnesium binding site 4 out of 6 in the Cryo-Em Structure of Pfago-Guide Dna-Target Dna 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 Pfago-Guide Dna-Target Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:26.5 occ:1.00 OP1 T:DT10 1.9 28.8 1.0 OD2 A:ASP558 1.9 44.8 1.0 ND1 A:HIS745 2.0 37.9 1.0 CG A:ASP558 2.8 34.9 1.0 OD2 A:ASP628 2.9 46.9 1.0 CE1 A:HIS745 2.9 31.8 1.0 CG A:HIS745 3.1 31.6 1.0 OD1 A:ASP558 3.1 39.4 1.0 P T:DT10 3.3 43.6 1.0 CB A:HIS745 3.4 19.3 1.0 OP2 T:DT10 4.0 33.2 1.0 CA A:HIS745 4.0 13.6 1.0 NE2 A:HIS745 4.1 30.1 1.0 CG A:ASP628 4.1 43.0 1.0 CD2 A:HIS745 4.2 31.0 1.0 CB A:ASP558 4.2 26.8 1.0 O5' T:DT10 4.2 33.7 1.0 O3' T:DC9 4.3 22.5 1.0 MG A:MG802 4.4 50.3 1.0 C5' T:DT10 4.6 26.7 1.0 NZ A:LYS657 4.8 32.7 1.0 OD1 A:ASP628 4.9 45.1 1.0 N A:HIS745 4.9 25.3 1.0 CB A:ASP628 5.0 29.1 1.0

Magnesium binding site 5 out of 6 in the Cryo-Em Structure of Pfago-Guide Dna-Target Dna 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 Pfago-Guide Dna-Target Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:50.3 occ:1.00 OD1 A:ASP558 2.6 39.4 1.0 O3' T:DC9 2.9 22.5 1.0 OE2 A:GLU596 3.3 54.6 1.0 O A:ASP628 3.4 35.1 1.0 OP1 T:DT10 3.5 28.8 1.0 CG A:ASP558 3.7 34.9 1.0 C4' T:DC9 3.8 25.4 1.0 C3' T:DC9 3.9 24.2 1.0 P T:DT10 3.9 43.6 1.0 O A:VAL559 3.9 45.4 1.0 N A:VAL559 4.0 33.1 1.0 CG A:ASP628 4.0 43.0 1.0 OD2 A:ASP628 4.1 46.9 1.0 CB A:ASP628 4.2 29.1 1.0 NH1 A:ARG627 4.2 32.3 1.0 CD A:GLU596 4.3 57.0 1.0 OD2 A:ASP558 4.3 44.8 1.0 C A:ASP628 4.4 23.4 1.0 MG A:MG801 4.4 26.5 1.0 C5' T:DC9 4.4 27.9 1.0 OD1 A:ASP628 4.5 45.1 1.0 C2' T:DC9 4.5 26.1 1.0 OE1 A:GLU596 4.5 59.6 1.0 C5' T:DT10 4.6 26.7 1.0 CA A:ASP558 4.7 25.6 1.0 CA A:VAL559 4.8 32.0 1.0 C A:VAL559 4.8 33.4 1.0 CB A:ASP558 4.8 26.8 1.0 CB A:VAL559 4.8 25.8 1.0 O5' T:DT10 4.8 33.7 1.0 C A:ASP558 4.9 32.3 1.0 CA A:ASP628 4.9 25.1 1.0 O4' T:DC9 5.0 13.7 1.0

Magnesium binding site 6 out of 6 in the Cryo-Em Structure of Pfago-Guide Dna-Target Dna 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 Pfago-Guide Dna-Target Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg101 b:28.4 occ:1.00 OP1 G:DT1 2.1 47.4 1.0 OP1 G:DA3 2.3 36.3 1.0 NE2 A:GLN533 2.4 46.2 1.0 O A:VAL770 3.1 56.5 1.0 P G:DT1 3.3 63.5 1.0 OP3 G:DT1 3.3 55.2 1.0 OXT A:VAL770 3.4 58.3 1.0 CD A:GLN533 3.7 43.5 1.0 P G:DA3 3.7 47.9 1.0 C A:VAL770 3.7 59.9 1.0 OE1 A:GLN533 4.3 49.9 1.0 C5' G:DT1 4.3 46.8 1.0 O5' G:DT1 4.3 57.5 1.0 OP2 G:DT1 4.3 52.0 1.0 OP2 G:DA3 4.4 39.0 1.0 NZ A:LYS537 4.4 39.6 1.0 O5' G:DA3 4.5 35.6 1.0 CE A:LYS537 4.6 33.6 1.0 O3' G:DG2 4.6 38.2 1.0 CG A:GLN533 4.8 35.9 1.0 C5' G:DA3 4.8 33.2 1.0

L.Zhuang, L.Zhuang. N/A N/A.
ISSN: ISSN 1097-2765
DOI: 10.1016/J.MOLCEL.2024.01.004