Magnesium in PDB 6z7t: Nucleotide-Free Myosin-II Motor Domain

The structure of Nucleotide-Free Myosin-II Motor Domain, PDB code: 6z7t was solved by W.Ewert, M.Preller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.36 / 1.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.681, 174.395, 100.252, 90.00, 106.38, 90.00
R / Rfree (%)	19.1 / 21.7

The binding sites of Magnesium atom in the Nucleotide-Free Myosin-II Motor Domain (pdb code 6z7t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Nucleotide-Free Myosin-II Motor Domain, PDB code: 6z7t:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Nucleotide-Free Myosin-II Motor Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Nucleotide-Free Myosin-II Motor Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:62.7 occ:1.00 HG A:SER181 2.2 64.0 1.0 HA A:SER181 2.7 71.7 1.0 H11 A:GOL817 2.9 56.9 1.0 O A:HOH1108 3.0 44.0 1.0 OG A:SER181 3.0 53.4 1.0 O A:HOH935 3.2 47.0 1.0 HG1 A:THR186 3.3 44.8 1.0 HB2 A:SER181 3.4 59.0 1.0 CA A:SER181 3.5 59.8 1.0 HE2 A:LYS185 3.5 44.2 1.0 OG1 A:THR186 3.5 37.4 1.0 H31 A:GOL817 3.5 53.7 1.0 CB A:SER181 3.5 49.2 1.0 C1 A:GOL817 3.7 47.5 1.0 O1 A:GOL817 3.7 57.2 1.0 HO1 A:GOL817 3.7 68.6 1.0 HO2 A:GOL817 3.8 57.9 1.0 HD22 A:ASN235 3.9 47.5 1.0 N A:SER181 4.0 46.0 1.0 HB3 A:LYS185 4.1 33.7 1.0 HZ3 A:LYS185 4.2 54.6 1.0 H A:THR186 4.2 31.9 1.0 H A:GLY182 4.3 62.9 1.0 OE2 A:GLU223 4.3 54.3 1.0 CE A:LYS185 4.3 36.9 1.0 ND2 A:ASN235 4.3 39.6 1.0 HD21 A:ASN235 4.3 47.5 1.0 H A:SER181 4.3 55.1 1.0 C3 A:GOL817 4.4 44.8 1.0 HE3 A:LYS185 4.4 44.2 1.0 H12 A:GOL817 4.4 56.9 1.0 C2 A:GOL817 4.4 43.0 1.0 O2 A:GOL817 4.5 48.3 1.0 C A:GLU180 4.5 49.3 1.0 O A:GLU180 4.5 59.6 1.0 HB3 A:SER181 4.5 59.0 1.0 NZ A:LYS185 4.6 45.6 1.0 HZ1 A:LYS185 4.6 54.6 1.0 H32 A:GOL817 4.7 53.7 1.0 CB A:THR186 4.7 39.4 1.0 C A:SER181 4.7 58.7 1.0 HB A:THR186 4.7 47.2 1.0 N A:GLY182 4.8 52.5 1.0 O A:ASN235 4.8 31.5 1.0 HD21 A:ASN227 4.8 41.4 1.0 N A:THR186 4.9 26.6 1.0 HB3 A:ASN235 4.9 39.3 1.0 O A:GLY179 5.0 32.7 1.0

Magnesium binding site 2 out of 4 in the Nucleotide-Free Myosin-II Motor Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Nucleotide-Free Myosin-II Motor Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:45.6 occ:1.00 O A:ALA183 2.2 34.5 1.0 O A:ALA125 2.5 22.7 1.0 HB3 A:CYS655 2.7 25.3 1.0 H A:ILE656 2.9 26.8 1.0 HA A:CYS655 3.2 20.6 1.0 H12 A:EDO804 3.2 58.0 1.0 C A:ALA125 3.2 25.1 1.0 HA3 A:GLY184 3.3 38.8 1.0 HB3 A:ALA125 3.3 28.5 1.0 H A:ASN127 3.3 29.6 1.0 O2 A:EDO804 3.4 47.8 1.0 HB2 A:ASN127 3.4 29.8 1.0 N A:ASN127 3.4 24.7 1.0 C A:ALA183 3.4 36.3 1.0 N A:ILE656 3.5 22.4 1.0 CB A:CYS655 3.5 21.1 1.0 O A:ILE656 3.5 23.4 1.0 HA A:VAL126 3.5 30.1 1.0 HB1 A:ALA125 3.6 28.5 1.0 HA A:ASN127 3.6 28.5 1.0 C A:VAL126 3.6 30.5 1.0 CA A:CYS655 3.7 17.2 1.0 CB A:ALA125 3.8 23.8 1.0 N A:VAL126 3.8 20.2 1.0 CA A:ASN127 3.9 23.8 1.0 CA A:VAL126 3.9 25.1 1.0 C A:CYS655 3.9 25.2 1.0 HO2 A:EDO804 4.0 57.3 1.0 HD21 A:ASN188 4.0 31.6 1.0 CB A:ASN127 4.1 24.9 1.0 CA A:GLY184 4.1 32.4 1.0 HB1 A:ALA183 4.1 39.8 1.0 CA A:ALA125 4.1 23.1 1.0 C1 A:EDO804 4.2 48.4 1.0 N A:GLY184 4.2 34.3 1.0 HG A:CYS655 4.2 29.5 1.0 HB2 A:CYS655 4.3 25.3 1.0 SG A:CYS655 4.3 24.6 1.0 C A:ILE656 4.3 23.3 1.0 HD22 A:ASN188 4.3 31.6 1.0 O A:VAL126 4.3 31.7 1.0 C2 A:EDO804 4.4 50.2 1.0 HA A:ALA183 4.4 44.6 1.0 ND2 A:ASN188 4.4 26.4 1.0 CA A:ALA183 4.4 37.2 1.0 CA A:ILE656 4.5 21.4 1.0 H A:VAL126 4.5 24.2 1.0 H11 A:EDO804 4.7 58.0 1.0 C A:GLY184 4.7 32.6 1.0 HB2 A:ALA125 4.7 28.5 1.0 CB A:ALA183 4.8 33.2 1.0 HA A:ALA125 4.8 27.7 1.0 HB3 A:ASN127 4.8 29.8 1.0 HA2 A:GLY184 4.8 38.8 1.0 H A:ALA125 4.8 23.7 1.0 HD22 A:ASN127 4.8 39.4 1.0 CG A:ASN127 4.8 32.5 1.0 HA A:ILE656 4.9 25.6 1.0 H21 A:EDO804 4.9 60.2 1.0

Magnesium binding site 3 out of 4 in the Nucleotide-Free Myosin-II Motor Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Nucleotide-Free Myosin-II Motor Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:53.1 occ:1.00 O B:GLU180 2.2 55.4 1.0 H B:LYS185 2.3 26.5 1.0 H B:ALA183 2.5 44.9 1.0 H12 B:EDO812 2.6 44.0 1.0 HB3 B:ALA183 2.7 40.7 1.0 HA B:SER181 2.7 74.5 1.0 HB3 B:LYS185 2.8 32.2 1.0 H B:GLY184 2.9 42.3 1.0 C B:GLU180 3.1 48.0 1.0 N B:LYS185 3.2 22.1 1.0 HB2 B:LYS185 3.2 32.2 1.0 N B:ALA183 3.2 37.5 1.0 O1 B:EDO812 3.3 48.0 1.0 CB B:LYS185 3.4 26.9 1.0 N B:GLY184 3.4 35.3 1.0 C1 B:EDO812 3.4 36.7 1.0 CB B:ALA183 3.5 34.0 1.0 CA B:SER181 3.5 62.1 1.0 HE2 B:LYS185 3.6 46.5 1.0 CA B:ALA183 3.6 34.4 1.0 H B:GLY182 3.7 74.2 1.0 N B:SER181 3.7 54.0 1.0 O B:GLY179 3.7 30.0 1.0 H B:THR186 3.8 32.9 1.0 C B:GLY179 3.8 33.7 1.0 C B:ALA183 3.8 35.4 1.0 N B:GLY182 3.9 61.8 1.0 HB2 B:ALA183 3.9 40.7 1.0 HO1 B:EDO812 3.9 57.5 1.0 CA B:LYS185 3.9 28.3 1.0 HA3 B:GLY179 3.9 30.3 1.0 C B:SER181 4.0 54.8 1.0 O B:HOH1297 4.0 51.7 1.0 H11 B:EDO812 4.0 44.0 1.0 N B:GLU180 4.0 45.5 1.0 CA B:GLU180 4.1 55.7 1.0 C B:GLY184 4.2 34.9 1.0 HB1 B:ALA183 4.2 40.7 1.0 CA B:GLY184 4.3 33.2 1.0 C B:GLY182 4.3 42.9 1.0 HA B:GLU180 4.4 66.8 1.0 CA B:GLY179 4.4 25.3 1.0 H B:GLU180 4.5 54.5 1.0 H B:SER181 4.5 64.7 1.0 N B:THR186 4.5 27.5 1.0 CE B:LYS185 4.5 38.8 1.0 C2 B:EDO812 4.5 38.4 1.0 O2 B:EDO812 4.5 37.0 1.0 HA B:ALA183 4.6 41.2 1.0 HA B:LYS185 4.6 33.9 1.0 CA B:GLY182 4.7 46.7 1.0 CG B:LYS185 4.7 30.7 1.0 HA2 B:GLY184 4.7 39.8 1.0 CB B:SER181 4.7 52.0 1.0 C B:LYS185 4.8 24.8 1.0 HD3 B:LYS185 4.8 42.5 1.0 HB2 B:SER181 4.8 62.4 1.0 HZ3 B:LYS185 4.8 62.6 1.0 HB2 B:CYS655 4.8 27.6 1.0 H22 B:EDO812 4.8 46.0 1.0 O B:SER181 4.9 59.9 1.0 O B:ALA183 4.9 36.3 1.0 CD B:LYS185 4.9 35.4 1.0 HA2 B:GLY179 5.0 30.3 1.0

Magnesium binding site 4 out of 4 in the Nucleotide-Free Myosin-II Motor Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Nucleotide-Free Myosin-II Motor Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:42.3 occ:1.00 O B:ALA183 2.2 36.3 1.0 H21 B:EDO804 2.4 52.8 1.0 HB3 B:CYS655 2.8 27.6 1.0 O B:ALA125 2.8 20.9 1.0 HA3 B:GLY184 2.9 39.8 1.0 C2 B:EDO804 3.2 44.0 1.0 HB3 B:ALA125 3.2 25.0 1.0 H B:ILE656 3.2 25.2 1.0 HB2 B:ASN127 3.4 27.9 1.0 O2 B:EDO804 3.4 38.0 1.0 C B:ALA183 3.4 35.4 1.0 H B:ASN127 3.4 27.4 1.0 HA B:CYS655 3.4 22.3 1.0 N B:ASN127 3.5 22.9 1.0 C B:ALA125 3.5 21.4 1.0 CB B:CYS655 3.6 23.0 1.0 H22 B:EDO804 3.6 52.8 1.0 HA B:ASN127 3.6 31.2 1.0 HO2 B:EDO804 3.6 45.5 1.0 HB1 B:ALA125 3.7 25.0 1.0 O B:ILE656 3.8 22.6 1.0 N B:ILE656 3.8 21.1 1.0 CA B:GLY184 3.8 33.2 1.0 HD21 B:ASN188 3.8 33.1 1.0 CB B:ALA125 3.8 20.9 1.0 HA B:VAL126 3.9 24.1 1.0 C B:VAL126 3.9 27.5 1.0 CA B:CYS655 3.9 18.6 1.0 CA B:ASN127 3.9 26.1 1.0 N B:GLY184 4.0 35.3 1.0 CB B:ASN127 4.0 23.3 1.0 N B:VAL126 4.1 19.9 1.0 HG B:CYS655 4.1 29.1 1.0 HD22 B:ASN188 4.1 33.1 1.0 CA B:VAL126 4.2 20.2 1.0 SG B:CYS655 4.2 24.3 1.0 C B:CYS655 4.2 21.8 1.0 ND2 B:ASN188 4.2 27.6 1.0 HB2 B:CYS655 4.3 27.6 1.0 CA B:ALA125 4.3 17.5 1.0 HB1 B:ALA183 4.4 40.7 1.0 C B:GLY184 4.4 34.9 1.0 C1 B:EDO804 4.5 48.9 1.0 HA B:ALA183 4.5 41.2 1.0 HA2 B:GLY184 4.5 39.8 1.0 O1 B:EDO804 4.5 47.5 1.0 CA B:ALA183 4.5 34.4 1.0 C B:ILE656 4.6 23.7 1.0 O B:VAL126 4.6 30.4 1.0 HD22 B:ASN127 4.6 30.7 1.0 O B:GLY184 4.7 29.0 1.0 HB2 B:ALA125 4.7 25.0 1.0 H B:VAL126 4.7 23.8 1.0 CG B:ASN127 4.7 34.9 1.0 CA B:ILE656 4.8 24.0 1.0 HB3 B:ASN127 4.8 27.9 1.0 H B:GLY184 4.9 42.3 1.0 ND2 B:ASN127 4.9 25.6 1.0 CB B:ALA183 4.9 34.0 1.0 HA B:ALA125 5.0 20.9 1.0

W.Ewert, P.Franz, G.Tsiavaliaris, M.Preller. Structural and Computational Insights Into A Blebbistatin-Bound Myosin•Adp Complex with Characteristics of An Adp-Release Conformation Along the Two-Step Myosin Power Stoke. Int J Mol Sci V. 21 2020.
ISSN: ESSN 1422-0067
PubMed: 33049993
DOI: 10.3390/IJMS21197417