Magnesium in PDB 6ut5: Cryo-Em Structure of the Thermococcus Gammatolerans Mcrbc Complex

The binding sites of Magnesium atom in the Cryo-Em Structure of the Thermococcus Gammatolerans Mcrbc Complex (pdb code 6ut5). 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 the Thermococcus Gammatolerans Mcrbc Complex, PDB code: 6ut5:
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 the Thermococcus Gammatolerans Mcrbc 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 Thermococcus Gammatolerans Mcrbc Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:48.8 occ:1.00 OG1 A:THR222 2.1 46.8 1.0 O A:HOH802 2.1 49.4 1.0 O A:HOH801 2.2 48.4 1.0 O3G A:GSP701 2.5 54.8 1.0 O2B A:GSP701 2.7 54.8 1.0 OD1 A:ASP356 2.9 44.8 1.0 OE2 A:GLU357 3.4 47.0 1.0 OD2 A:ASP356 3.4 44.8 1.0 CB A:THR222 3.5 46.8 1.0 CG A:ASP356 3.5 44.8 1.0 CG2 A:THR408 3.6 42.8 1.0 PG A:GSP701 3.7 54.8 1.0 O2G A:GSP701 3.9 54.8 1.0 PB A:GSP701 4.0 54.8 1.0 CD A:GLU357 4.0 47.0 1.0 CG2 A:THR222 4.1 46.8 1.0 O3B A:GSP701 4.3 54.8 1.0 N A:THR222 4.4 46.8 1.0 OE1 A:GLU357 4.4 47.0 1.0 CA A:THR222 4.5 46.8 1.0 O2A A:GSP701 4.6 54.8 1.0 CB A:THR408 4.7 42.8 1.0 O1B A:GSP701 4.8 54.8 1.0 CG A:GLU357 4.9 47.0 1.0 CB A:ASP356 4.9 44.8 1.0

Magnesium binding site 2 out of 6 in the Cryo-Em Structure of the Thermococcus Gammatolerans Mcrbc 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 Thermococcus Gammatolerans Mcrbc Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:39.6 occ:1.00 OG1 B:THR222 2.1 38.3 1.0 O2G B:GSP701 2.1 40.6 1.0 O B:HOH804 2.2 39.5 1.0 O B:HOH801 2.2 37.3 1.0 OD1 B:ASP356 2.7 43.7 1.0 O1B B:GSP701 2.8 40.6 1.0 OD2 B:ASP356 3.3 43.7 1.0 PG B:GSP701 3.4 40.6 1.0 CG B:ASP356 3.4 43.7 1.0 CB B:THR222 3.5 38.3 1.0 OE2 B:GLU357 3.6 45.6 1.0 O3G B:GSP701 3.6 40.6 1.0 OG1 B:THR408 3.7 42.9 1.0 PB B:GSP701 4.0 40.6 1.0 CG2 B:THR222 4.2 38.3 1.0 O3B B:GSP701 4.2 40.6 1.0 CD B:GLU357 4.3 45.6 1.0 NH2 C:ARG426 4.3 36.5 1.0 N B:THR222 4.3 38.3 1.0 CA B:THR222 4.4 38.3 1.0 CB B:THR408 4.5 42.9 1.0 S1G B:GSP701 4.7 40.6 1.0 O2A B:GSP701 4.7 40.6 1.0 CG B:GLU357 4.8 45.6 1.0 CB B:ASP356 4.8 43.7 1.0 O2B B:GSP701 4.9 40.6 1.0

Magnesium binding site 3 out of 6 in the Cryo-Em Structure of the Thermococcus Gammatolerans Mcrbc 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 Thermococcus Gammatolerans Mcrbc Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:30.1 occ:1.00 O2G C:GSP701 2.1 27.8 1.0 O C:HOH901 2.1 31.7 1.0 OG1 C:THR222 2.1 29.8 1.0 O C:HOH905 2.1 33.6 1.0 OD2 C:ASP356 2.9 32.0 1.0 O2B C:GSP701 2.9 27.8 1.0 OE2 C:GLU357 3.1 33.3 1.0 OD1 C:ASP356 3.4 32.0 1.0 CB C:THR222 3.4 29.8 1.0 CG C:ASP356 3.5 32.0 1.0 NH2 D:ARG426 3.5 34.7 1.0 PG C:GSP701 3.6 27.8 1.0 CG2 C:THR222 4.0 29.8 1.0 CD C:GLU357 4.1 33.3 1.0 O3G C:GSP701 4.1 27.8 1.0 PB C:GSP701 4.2 27.8 1.0 OG1 C:THR408 4.2 30.8 1.0 O3B C:GSP701 4.3 27.8 1.0 O2A C:GSP701 4.4 27.8 1.0 CG C:GLU357 4.5 33.3 1.0 CA C:THR222 4.5 29.8 1.0 N C:THR222 4.6 29.8 1.0 S1G C:GSP701 4.7 27.8 1.0 OG1 D:THR372 4.7 34.0 1.0 CZ D:ARG426 4.8 34.7 1.0 CB C:ASP356 5.0 32.0 1.0

Magnesium binding site 4 out of 6 in the Cryo-Em Structure of the Thermococcus Gammatolerans Mcrbc 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 Thermococcus Gammatolerans Mcrbc Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg702 b:32.4 occ:1.00 OG1 D:THR222 2.1 31.7 1.0 O D:HOH803 2.1 30.7 1.0 O2G D:GSP701 2.1 28.1 1.0 O D:HOH807 2.1 30.2 1.0 O1B D:GSP701 2.2 28.1 1.0 O D:HOH805 2.7 27.0 1.0 PG D:GSP701 3.1 28.1 1.0 PB D:GSP701 3.4 28.1 1.0 CB D:THR222 3.4 31.7 1.0 OE1 D:GLU357 3.5 31.6 1.0 S1G D:GSP701 3.5 28.1 1.0 OD1 D:ASP356 3.6 29.4 1.0 O3B D:GSP701 3.6 28.1 1.0 OD2 D:ASP356 3.7 29.4 1.0 OE2 D:GLU357 3.8 31.6 1.0 OG1 D:THR408 3.9 28.9 1.0 CD D:GLU357 4.0 31.6 1.0 NH1 E:ARG426 4.0 29.0 1.0 CG D:ASP356 4.0 29.4 1.0 N D:THR222 4.1 31.7 1.0 O2B D:GSP701 4.2 28.1 1.0 CG2 D:THR222 4.3 31.7 1.0 O2A D:GSP701 4.3 28.1 1.0 CA D:THR222 4.3 31.7 1.0 O D:HOH804 4.5 32.4 1.0 O3G D:GSP701 4.5 28.1 1.0 CB D:THR408 4.5 28.9 1.0 O3A D:GSP701 4.5 28.1 1.0 PA D:GSP701 4.7 28.1 1.0 O1A D:GSP701 4.8 28.1 1.0 CE D:LYS221 4.9 30.9 1.0

Magnesium binding site 5 out of 6 in the Cryo-Em Structure of the Thermococcus Gammatolerans Mcrbc 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 Thermococcus Gammatolerans Mcrbc Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg702 b:33.4 occ:1.00 OG1 E:THR222 2.0 31.2 1.0 O3G E:GSP701 2.1 41.8 1.0 O E:HOH803 2.1 33.7 1.0 O E:HOH801 2.1 33.3 1.0 O1B E:GSP701 2.1 41.8 1.0 O E:HOH804 2.2 29.1 1.0 CB E:THR222 3.2 31.2 1.0 OD2 E:ASP356 3.3 28.3 1.0 NH2 F:ARG426 3.4 30.7 1.0 PG E:GSP701 3.5 41.8 1.0 OE2 E:GLU357 3.5 30.9 1.0 PB E:GSP701 3.5 41.8 1.0 OD1 E:ASP356 3.6 28.3 1.0 CG E:ASP356 3.9 28.3 1.0 CG2 E:THR222 3.9 31.2 1.0 O3B E:GSP701 3.9 41.8 1.0 O1A E:GSP701 4.0 41.8 1.0 S1G E:GSP701 4.2 41.8 1.0 CA E:THR222 4.4 31.2 1.0 N E:THR222 4.4 31.2 1.0 O3A E:GSP701 4.4 41.8 1.0 O2B E:GSP701 4.5 41.8 1.0 OG1 E:THR408 4.5 27.3 1.0 O2G E:GSP701 4.5 41.8 1.0 NZ F:LYS378 4.6 33.5 1.0 PA E:GSP701 4.6 41.8 1.0 CD E:GLU357 4.6 30.9 1.0 CZ F:ARG426 4.7 30.7 1.0 O2A E:GSP701 4.7 41.8 1.0 OG1 F:THR372 4.9 32.5 1.0 NH1 F:ARG425 4.9 30.6 1.0

Magnesium binding site 6 out of 6 in the Cryo-Em Structure of the Thermococcus Gammatolerans Mcrbc 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 the Thermococcus Gammatolerans Mcrbc Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg702 b:38.7 occ:1.00 O1B F:GDP701 2.1 43.1 1.0 O F:HOH802 2.2 38.7 1.0 OG1 F:THR222 2.2 38.1 1.0 O F:HOH803 2.4 37.9 1.0 PB F:GDP701 3.3 43.1 1.0 CB F:THR222 3.4 38.1 1.0 O2B F:GDP701 3.5 43.1 1.0 OD1 F:ASP356 3.5 35.7 1.0 OE2 F:GLU357 3.7 41.0 1.0 OD2 F:ASP356 3.7 35.7 1.0 O2A F:GDP701 4.0 43.1 1.0 CG F:ASP356 4.0 35.7 1.0 N F:THR222 4.2 38.1 1.0 O3A F:GDP701 4.3 43.1 1.0 CG2 F:THR222 4.3 38.1 1.0 O3B F:GDP701 4.4 43.1 1.0 ND2 F:ASN410 4.4 41.7 1.0 CA F:THR222 4.4 38.1 1.0 OD1 F:ASN410 4.4 41.7 1.0 OG1 F:THR408 4.4 34.9 1.0 PA F:GDP701 4.5 43.1 1.0 O1A F:GDP701 4.7 43.1 1.0 CD F:GLU357 4.8 41.0 1.0 CG F:ASN410 4.8 41.7 1.0

Y.Niu, H.Suzuki, C.J.Hosford, T.Walz, J.S.Chappie. Structural Asymmetry Governs the Assembly and Gtpase Activity of Mcrbc Restriction Complexes To Be Published.