Magnesium in PDB 6ut4: Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb

The binding sites of Magnesium atom in the Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb (pdb code 6ut4). 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 Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb, PDB code: 6ut4:
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 Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb


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 Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:46.2 occ:1.00 OG1 A:THR222 2.1 45.1 1.0 O2B A:GSP701 2.1 50.0 1.0 O2G A:GSP701 2.5 50.0 1.0 OD2 A:ASP356 2.9 45.4 1.0 OD1 A:ASP356 2.9 45.4 1.0 CB A:THR222 3.2 45.1 1.0 CG A:ASP356 3.3 45.4 1.0 NH1 B:ARG425 3.3 58.7 1.0 PB A:GSP701 3.4 50.0 1.0 PG A:GSP701 3.6 50.0 1.0 OE2 A:GLU357 3.8 49.2 1.0 CG2 A:THR222 3.8 45.1 1.0 O3G A:GSP701 3.9 50.0 1.0 O1B A:GSP701 3.9 50.0 1.0 O3B A:GSP701 3.9 50.0 1.0 OG1 A:THR408 4.3 44.9 1.0 CZ B:ARG425 4.4 58.7 1.0 CA A:THR222 4.5 45.1 1.0 O2A A:GSP701 4.5 50.0 1.0 N A:THR222 4.6 45.1 1.0 O3A A:GSP701 4.7 50.0 1.0 CB A:ASP356 4.7 45.4 1.0 CD A:GLU357 4.9 49.2 1.0 PA A:GSP701 5.0 50.0 1.0

Magnesium binding site 2 out of 6 in the Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb


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 Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:36.6 occ:1.00 O C:HOH802 2.1 35.8 1.0 OG1 B:THR222 2.1 40.0 1.0 O B:HOH902 2.1 35.3 1.0 O2G B:GSP701 2.1 40.4 1.0 O2B B:GSP701 2.2 40.4 1.0 OD1 B:ASP356 2.9 40.1 1.0 OD2 B:ASP356 3.3 40.1 1.0 PG B:GSP701 3.4 40.4 1.0 CB B:THR222 3.5 40.0 1.0 PB B:GSP701 3.5 40.4 1.0 CG B:ASP356 3.5 40.1 1.0 OG1 B:THR408 3.8 41.4 1.0 O3B B:GSP701 3.8 40.4 1.0 O3G B:GSP701 3.9 40.4 1.0 N B:THR222 4.1 40.0 1.0 OE2 B:GLU357 4.1 42.9 1.0 NH2 C:ARG426 4.1 33.4 1.0 O1B B:GSP701 4.2 40.4 1.0 CA B:THR222 4.3 40.0 1.0 CG2 B:THR222 4.4 40.0 1.0 CB B:LYS221 4.6 39.0 1.0 CB B:THR408 4.6 41.4 1.0 O2A B:GSP701 4.6 40.4 1.0 O3A B:GSP701 4.7 40.4 1.0 S1G B:GSP701 4.8 40.4 1.0 CD B:GLU357 5.0 42.9 1.0 CB B:ASP356 5.0 40.1 1.0

Magnesium binding site 3 out of 6 in the Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb


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 Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:21.9 occ:1.00 O C:HOH801 2.1 23.2 1.0 O2B C:GSP701 2.1 27.5 1.0 O D:HOH803 2.2 26.1 1.0 O2G C:GSP701 2.2 27.5 1.0 OG1 C:THR222 2.3 23.1 1.0 OD1 C:ASP356 3.0 23.2 1.0 NH2 D:ARG426 3.2 21.8 1.0 CB C:THR222 3.3 23.1 1.0 PB C:GSP701 3.5 27.5 1.0 PG C:GSP701 3.5 27.5 1.0 CG C:ASP356 3.8 23.2 1.0 O3B C:GSP701 3.9 27.5 1.0 OD2 C:ASP356 3.9 23.2 1.0 CG2 C:THR222 4.0 23.1 1.0 O2A C:GSP701 4.2 27.5 1.0 O3G C:GSP701 4.3 27.5 1.0 O1B C:GSP701 4.3 27.5 1.0 OE1 C:GLU357 4.4 24.8 1.0 NZ D:LYS378 4.5 26.6 1.0 CG2 D:THR372 4.5 23.6 1.0 CZ D:ARG426 4.5 21.8 1.0 O3A C:GSP701 4.5 27.5 1.0 CA C:THR222 4.6 23.1 1.0 N C:THR222 4.7 23.1 1.0 S1G C:GSP701 4.7 27.5 1.0 CD C:GLU357 4.8 24.8 1.0 NH1 D:ARG425 4.8 22.7 1.0 PA C:GSP701 4.8 27.5 1.0 OG1 C:THR408 4.9 21.9 1.0 CG C:GLU357 4.9 24.8 1.0

Magnesium binding site 4 out of 6 in the Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb


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 Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg702 b:29.4 occ:1.00 O2B D:GSP701 2.1 40.5 1.0 O D:HOH802 2.1 23.5 1.0 OG1 D:THR222 2.1 22.8 1.0 O D:HOH801 2.1 30.2 1.0 O2G D:GSP701 2.2 40.5 1.0 OD2 D:ASP356 2.9 21.8 1.0 OD1 D:ASP356 3.0 21.8 1.0 OE2 D:GLU357 3.1 23.2 1.0 CB D:THR222 3.3 22.8 1.0 CG D:ASP356 3.4 21.8 1.0 PB D:GSP701 3.4 40.5 1.0 PG D:GSP701 3.6 40.5 1.0 NH2 E:ARG426 3.6 21.3 1.0 O1B D:GSP701 3.8 40.5 1.0 CG2 D:THR222 3.9 22.8 1.0 O3B D:GSP701 4.0 40.5 1.0 CD D:GLU357 4.2 23.2 1.0 OG1 D:THR408 4.2 19.6 1.0 O3G D:GSP701 4.3 40.5 1.0 CA D:THR222 4.5 22.8 1.0 O1A D:GSP701 4.6 40.5 1.0 N D:THR222 4.6 22.8 1.0 CG D:GLU357 4.6 23.2 1.0 O3A D:GSP701 4.7 40.5 1.0 OG1 E:THR372 4.7 21.9 1.0 S1G D:GSP701 4.7 40.5 1.0 NZ E:LYS378 4.8 28.2 1.0 CZ E:ARG426 4.9 21.3 1.0 CB D:ASP356 4.9 21.8 1.0 O2A D:GSP701 5.0 40.5 1.0 PA D:GSP701 5.0 40.5 1.0

Magnesium binding site 5 out of 6 in the Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb


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 Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg702 b:24.0 occ:1.00 O E:HOH801 2.1 21.0 1.0 OG1 E:THR222 2.1 21.1 1.0 O2G E:GSP701 2.1 27.6 1.0 O F:HOH801 2.2 24.6 1.0 OD2 E:ASP356 2.6 21.5 1.0 O2B E:GSP701 2.8 27.6 1.0 OE2 E:GLU357 3.3 22.7 1.0 CB E:THR222 3.3 21.1 1.0 NH2 F:ARG426 3.4 26.1 1.0 CG E:ASP356 3.6 21.5 1.0 PG E:GSP701 3.6 27.6 1.0 OD1 E:ASP356 3.8 21.5 1.0 CG2 E:THR222 4.0 21.1 1.0 PB E:GSP701 4.1 27.6 1.0 O3G E:GSP701 4.3 27.6 1.0 O3B E:GSP701 4.3 27.6 1.0 CD E:GLU357 4.4 22.7 1.0 O2A E:GSP701 4.5 27.6 1.0 CA E:THR222 4.5 21.1 1.0 N E:THR222 4.5 21.1 1.0 CZ F:ARG426 4.6 26.1 1.0 CG E:GLU357 4.6 22.7 1.0 CG2 F:THR372 4.7 24.4 1.0 OG1 E:THR408 4.7 20.1 1.0 S1G E:GSP701 4.7 27.6 1.0 CB E:ASP356 5.0 21.5 1.0

Magnesium binding site 6 out of 6 in the Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb


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 Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg702 b:32.9 occ:1.00 OG1 F:THR222 2.1 31.8 1.0 O2G F:GSP701 2.1 36.6 1.0 O2B F:GSP701 2.2 36.6 1.0 OD1 F:ASP356 2.8 31.2 1.0 OD2 F:ASP356 3.1 31.2 1.0 CG F:ASP356 3.3 31.2 1.0 CB F:THR222 3.3 31.8 1.0 PG F:GSP701 3.4 36.6 1.0 PB F:GSP701 3.5 36.6 1.0 O3B F:GSP701 3.8 36.6 1.0 O3G F:GSP701 3.8 36.6 1.0 CG2 F:THR222 4.0 31.8 1.0 O2A F:GSP701 4.1 36.6 1.0 O1B F:GSP701 4.3 36.6 1.0 OG1 F:THR408 4.4 29.2 1.0 N F:THR222 4.5 31.8 1.0 CA F:THR222 4.5 31.8 1.0 CG F:GLU357 4.6 34.6 1.0 O3A F:GSP701 4.6 36.6 1.0 PA F:GSP701 4.7 36.6 1.0 S1G F:GSP701 4.7 36.6 1.0 O1A F:GSP701 4.7 36.6 1.0 CB F:ASP356 4.8 31.2 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.