Magnesium in PDB 6ut3: X-Ray Structure of Thermococcus Gammatolerans Mcrb Aaa+ Domain Hexamer in P21 Symmetry

The structure of X-Ray Structure of Thermococcus Gammatolerans Mcrb Aaa+ Domain Hexamer in P21 Symmetry, PDB code: 6ut3 was solved by Y.Niu, C.J.Hosford, J.S.Chappie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	114.65 / 2.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	102.474, 109.619, 120.782, 90.00, 108.34, 90.00
R / Rfree (%)	34.5 / 36.3

The binding sites of Magnesium atom in the X-Ray Structure of Thermococcus Gammatolerans Mcrb Aaa+ Domain Hexamer in P21 Symmetry (pdb code 6ut3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the X-Ray Structure of Thermococcus Gammatolerans Mcrb Aaa+ Domain Hexamer in P21 Symmetry, PDB code: 6ut3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the X-Ray Structure of Thermococcus Gammatolerans Mcrb Aaa+ Domain Hexamer in P21 Symmetry


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Thermococcus Gammatolerans Mcrb Aaa+ Domain Hexamer in P21 Symmetry within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:0.1 occ:1.00 OG1 B:THR222 2.1 0.5 1.0 O2B C:GSP701 2.1 0.0 1.0 O2G C:GSP701 2.1 0.0 1.0 O1B C:GSP701 2.3 0.0 1.0 PB C:GSP701 2.4 0.0 1.0 PG C:GSP701 3.1 0.0 1.0 O3B C:GSP701 3.2 0.0 1.0 OE1 B:GLU357 3.2 0.9 1.0 CB B:THR222 3.3 0.5 1.0 OD1 B:ASP356 3.4 1.0 1.0 O3G C:GSP701 3.4 0.0 1.0 OD2 B:ASP356 3.7 1.0 1.0 O3A C:GSP701 3.9 0.0 1.0 CG B:ASP356 3.9 1.0 1.0 NH2 C:ARG426 3.9 92.0 1.0 CG2 B:THR222 4.1 0.5 1.0 OG1 B:THR408 4.2 0.0 1.0 N B:THR222 4.3 0.5 1.0 CD B:GLU357 4.3 0.9 1.0 CA B:THR222 4.4 0.5 1.0 CB B:THR408 4.8 0.0 1.0 O1A C:GSP701 4.8 0.0 1.0 S1G C:GSP701 4.9 0.0 1.0 NH2 C:ARG425 4.9 98.9 1.0

Magnesium binding site 2 out of 4 in the X-Ray Structure of Thermococcus Gammatolerans Mcrb Aaa+ Domain Hexamer in P21 Symmetry


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of Thermococcus Gammatolerans Mcrb Aaa+ Domain Hexamer in P21 Symmetry within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg703 b:80.5 occ:1.00 OG1 C:THR222 2.1 90.5 1.0 O1B C:GSP702 2.1 0.9 1.0 O3G C:GSP702 2.5 0.9 1.0 PB C:GSP702 3.2 0.9 1.0 CB C:THR222 3.3 90.5 1.0 NH2 D:ARG426 3.3 90.1 1.0 OD2 C:ASP356 3.4 78.1 1.0 OE2 C:GLU357 3.5 78.8 1.0 O2B C:GSP702 3.6 0.9 1.0 PG C:GSP702 3.7 0.9 1.0 CG2 C:THR222 3.8 90.5 1.0 OD1 C:ASP356 3.9 78.1 1.0 O3B C:GSP702 3.9 0.9 1.0 CG C:ASP356 4.0 78.1 1.0 S1G C:GSP702 4.3 0.9 1.0 O1A C:GSP702 4.4 0.9 1.0 O3A C:GSP702 4.5 0.9 1.0 CA C:THR222 4.5 90.5 1.0 CZ D:ARG426 4.6 90.1 1.0 CD C:GLU357 4.6 78.8 1.0 N C:THR222 4.6 90.5 1.0 CG C:GLU357 4.8 78.8 1.0 OG1 C:THR408 4.9 70.4 1.0 O2G C:GSP702 4.9 0.9 1.0 PA C:GSP702 4.9 0.9 1.0 OG1 D:THR372 5.0 84.1 1.0

Magnesium binding site 3 out of 4 in the X-Ray Structure of Thermococcus Gammatolerans Mcrb Aaa+ Domain Hexamer in P21 Symmetry


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure of Thermococcus Gammatolerans Mcrb Aaa+ Domain Hexamer in P21 Symmetry within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:84.7 occ:1.00 OG1 D:THR222 2.1 96.3 1.0 O3G D:GSP700 2.4 0.9 1.0 OD2 D:ASP356 2.6 90.1 1.0 O1B D:GSP700 2.7 0.9 1.0 OE2 D:GLU357 3.0 86.7 1.0 OD1 D:ASP356 3.2 90.1 1.0 CG D:ASP356 3.3 90.1 1.0 CB D:THR222 3.3 96.3 1.0 NH2 E:ARG426 3.6 84.2 1.0 CG2 D:THR222 3.7 96.3 1.0 PG D:GSP700 3.8 0.9 1.0 PB D:GSP700 4.1 0.9 1.0 CD D:GLU357 4.1 86.7 1.0 O3B D:GSP700 4.3 0.9 1.0 OG1 D:THR408 4.3 85.8 1.0 CA D:THR222 4.5 96.3 1.0 CG2 E:THR372 4.6 87.8 1.0 CG D:GLU357 4.6 86.7 1.0 S1G D:GSP700 4.7 0.9 1.0 N D:THR222 4.7 96.3 1.0 CB D:ASP356 4.7 90.1 1.0 O2A D:GSP700 4.8 0.9 1.0 O2G D:GSP700 4.8 0.9 1.0 CZ E:ARG426 4.9 84.2 1.0 CA E:THR372 5.0 87.8 1.0 OG1 E:THR372 5.0 87.8 1.0

Magnesium binding site 4 out of 4 in the X-Ray Structure of Thermococcus Gammatolerans Mcrb Aaa+ Domain Hexamer in P21 Symmetry


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Structure of Thermococcus Gammatolerans Mcrb Aaa+ Domain Hexamer in P21 Symmetry within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg701 b:0.5 occ:1.00 OG1 E:THR222 2.1 99.7 1.0 O2B E:GSP700 2.1 0.8 1.0 O2G E:GSP700 2.2 0.8 1.0 PB E:GSP700 2.6 0.8 1.0 O1B E:GSP700 2.7 0.8 1.0 OD2 E:ASP356 2.9 92.1 1.0 OE2 E:GLU357 3.0 91.3 1.0 PG E:GSP700 3.2 0.8 1.0 O3B E:GSP700 3.3 0.8 1.0 CB E:THR222 3.4 99.7 1.0 CG2 E:THR408 3.5 87.2 1.0 CG E:ASP356 3.7 92.1 1.0 OD1 E:ASP356 3.9 92.1 1.0 S1G E:GSP700 3.9 0.8 1.0 O3A E:GSP700 4.1 0.8 1.0 CD E:GLU357 4.2 91.3 1.0 CG2 E:THR222 4.2 99.7 1.0 N E:THR222 4.3 99.7 1.0 CA E:THR222 4.4 99.7 1.0 NH1 F:ARG426 4.4 97.8 1.0 CB E:THR408 4.5 87.2 1.0 O3G E:GSP700 4.5 0.8 1.0 O2A E:GSP700 4.7 0.8 1.0 NZ E:LYS221 4.8 93.4 1.0 OE1 E:GLU357 4.9 91.3 1.0 CE E:LYS221 4.9 93.4 1.0 OG1 E:THR408 4.9 87.2 1.0 PA E:GSP700 4.9 0.8 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. Nat Commun V. 11 5907 2020.
ISSN: ESSN 2041-1723
PubMed: 33219217
DOI: 10.1038/S41467-020-19735-4