Magnesium in PDB 5hmp: Myosin Vc Pre-Powerstroke State

The structure of Myosin Vc Pre-Powerstroke State, PDB code: 5hmp was solved by V.Ropars, O.Pylypenko, H.L.Sweeney, A.Houdusse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.50 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	103.780, 66.740, 131.260, 90.00, 104.45, 90.00
R / Rfree (%)	20.5 / 22.7

The structure of Myosin Vc Pre-Powerstroke State also contains other interesting chemical elements:

Vanadium

(V)

2 atoms

The binding sites of Magnesium atom in the Myosin Vc Pre-Powerstroke State (pdb code 5hmp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Myosin Vc Pre-Powerstroke State, PDB code: 5hmp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Myosin Vc Pre-Powerstroke State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Myosin Vc Pre-Powerstroke State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:43.1 occ:1.00 OG1 A:THR168 2.0 43.0 1.0 O A:HOH983 2.0 44.8 1.0 O A:HOH903 2.1 41.6 1.0 O1 A:VO4802 2.1 44.2 1.0 O1B A:ADP803 2.1 40.2 1.0 OG A:SER216 2.1 43.3 1.0 HB2 A:SER216 3.0 52.1 1.0 H A:SER216 3.0 56.1 1.0 HB A:THR168 3.1 51.7 1.0 CB A:THR168 3.1 43.1 1.0 CB A:SER216 3.1 43.4 1.0 PB A:ADP803 3.3 43.8 1.0 H A:THR168 3.4 55.6 1.0 V A:VO4802 3.6 45.4 1.0 O3B A:ADP803 3.6 45.5 1.0 O2A A:ADP803 3.7 42.4 1.0 N A:SER216 3.7 46.8 1.0 HB3 A:SER216 3.8 52.1 1.0 HG21 A:THR168 3.9 45.9 1.0 N A:THR168 4.0 46.3 1.0 CA A:SER216 4.0 44.4 1.0 CA A:THR168 4.1 45.4 1.0 CG2 A:THR168 4.1 38.3 1.0 HB2 A:LYS167 4.2 50.4 1.0 OD2 A:ASP435 4.2 64.6 1.0 HD21 A:ASN206 4.2 52.5 1.0 OD1 A:ASP435 4.2 65.2 1.0 O3A A:ADP803 4.3 45.4 1.0 HA A:THR168 4.4 54.5 1.0 PA A:ADP803 4.4 42.0 1.0 O3 A:VO4802 4.4 33.0 1.0 O2B A:ADP803 4.4 44.6 1.0 O4 A:VO4802 4.4 45.5 1.0 HG23 A:THR168 4.5 45.9 1.0 HA A:SER215 4.5 55.7 1.0 O A:HOH993 4.5 48.4 1.0 HE2 A:LYS167 4.5 49.6 1.0 O A:ASN214 4.5 46.3 1.0 HD21 A:ASN212 4.5 56.9 1.0 HA A:SER216 4.5 53.2 1.0 HD22 A:ASN212 4.6 56.9 1.0 CG A:ASP435 4.7 64.3 1.0 O1A A:ADP803 4.7 43.2 1.0 C A:SER215 4.8 47.6 1.0 ND2 A:ASN206 4.8 43.8 1.0 O2 A:VO4802 4.8 53.6 1.0 HA A:TYR437 4.8 53.9 1.0 HG22 A:THR168 4.9 45.9 1.0 ND2 A:ASN212 4.9 47.4 1.0 O A:HOH950 5.0 56.6 1.0

Magnesium binding site 2 out of 2 in the Myosin Vc Pre-Powerstroke State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Myosin Vc Pre-Powerstroke State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:58.5 occ:1.00 O1 B:VO4802 2.0 64.5 1.0 OG1 B:THR168 2.0 61.0 1.0 O B:HOH938 2.1 57.9 1.0 O B:HOH902 2.1 43.4 1.0 O1B B:ADP803 2.1 53.1 1.0 OG B:SER216 2.1 59.9 1.0 H B:SER216 3.1 69.8 1.0 HB B:THR168 3.1 73.5 1.0 HB2 B:SER216 3.1 71.0 1.0 CB B:THR168 3.1 61.3 1.0 CB B:SER216 3.1 59.2 1.0 PB B:ADP803 3.3 54.4 1.0 H B:THR168 3.4 74.8 1.0 V B:VO4802 3.5 52.1 1.0 O3B B:ADP803 3.5 53.6 1.0 O1A B:ADP803 3.7 64.2 1.0 N B:SER216 3.8 58.2 1.0 HB3 B:SER216 3.8 71.0 1.0 N B:THR168 4.0 62.3 1.0 HG21 B:THR168 4.0 73.8 1.0 OD2 B:ASP435 4.0 75.5 1.0 CA B:SER216 4.1 58.3 1.0 CA B:THR168 4.1 63.5 1.0 OD1 B:ASP435 4.1 76.7 1.0 CG2 B:THR168 4.2 61.5 1.0 HB2 B:LYS167 4.2 66.8 1.0 O3A B:ADP803 4.3 47.4 1.0 HD21 B:ASN206 4.3 74.0 1.0 O3 B:VO4802 4.3 62.0 1.0 PA B:ADP803 4.3 62.9 1.0 HA B:THR168 4.3 76.2 1.0 O2B B:ADP803 4.4 55.8 1.0 O4 B:VO4802 4.4 39.5 1.0 HA B:SER215 4.5 65.2 1.0 O B:ASN214 4.5 54.4 1.0 HE2 B:LYS167 4.5 65.0 1.0 CG B:ASP435 4.5 76.6 1.0 HG23 B:THR168 4.5 73.8 1.0 HA B:SER216 4.5 70.0 1.0 O2A B:ADP803 4.5 63.2 1.0 HD21 B:ASN212 4.6 61.4 1.0 HD22 B:ASN212 4.6 61.4 1.0 O2 B:VO4802 4.7 55.0 1.0 C B:SER215 4.8 55.9 1.0 ND2 B:ASN206 4.8 61.6 1.0 HA B:TYR437 4.9 73.3 1.0 HZ1 B:LYS167 4.9 59.0 1.0 HG22 B:THR168 4.9 73.8 1.0 ND2 B:ASN212 4.9 51.1 1.0 HD22 B:ASN206 5.0 74.0 1.0

V.Ropars, Z.Yang, T.Isabet, F.Blanc, K.Zhou, T.Lin, X.Liu, P.Hissier, F.Samazan, B.Amigues, E.D.Yang, H.Park, O.Pylypenko, M.Cecchini, C.V.Sindelar, H.L.Sweeney, A.Houdusse. The Myosin X Motor Is Optimized For Movement on Actin Bundles. Nat Commun V. 7 12456 2016.
ISSN: ESSN 2041-1723
PubMed: 27580874
DOI: 10.1038/NCOMMS12456