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Magnesium in PDB 5n69: Cardiac Muscle Myosin S1 Fragment in the Pre-Powerstroke State Co- Crystallized with the Activator Omecamtiv Mecarbil

Protein crystallography data

The structure of Cardiac Muscle Myosin S1 Fragment in the Pre-Powerstroke State Co- Crystallized with the Activator Omecamtiv Mecarbil, PDB code: 5n69 was solved by V.J.Planelles-Herrero, J.J.Hartman, J.Robert-Paganin, F.I.Malik, A.Houdusse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.22 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.320, 122.450, 187.430, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 22.4

Other elements in 5n69:

The structure of Cardiac Muscle Myosin S1 Fragment in the Pre-Powerstroke State Co- Crystallized with the Activator Omecamtiv Mecarbil also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Vanadium (V) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cardiac Muscle Myosin S1 Fragment in the Pre-Powerstroke State Co- Crystallized with the Activator Omecamtiv Mecarbil (pdb code 5n69). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cardiac Muscle Myosin S1 Fragment in the Pre-Powerstroke State Co- Crystallized with the Activator Omecamtiv Mecarbil, PDB code: 5n69:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5n69

Go back to Magnesium Binding Sites List in 5n69
Magnesium binding site 1 out of 2 in the Cardiac Muscle Myosin S1 Fragment in the Pre-Powerstroke State Co- Crystallized with the Activator Omecamtiv Mecarbil


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cardiac Muscle Myosin S1 Fragment in the Pre-Powerstroke State Co- Crystallized with the Activator Omecamtiv Mecarbil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:38.3
occ:1.00
OG1 A:THR185 1.9 37.6 1.0
OG A:SER242 2.0 42.3 1.0
O A:HOH1020 2.0 26.9 1.0
O2 A:VO4902 2.1 38.5 1.0
O2B A:ADP901 2.1 36.2 1.0
O A:HOH1003 2.2 35.5 1.0
CB A:SER242 3.1 37.0 1.0
CB A:THR185 3.1 38.0 1.0
PB A:ADP901 3.5 36.8 1.0
V A:VO4902 3.7 41.7 1.0
N A:SER242 3.8 35.7 1.0
O3B A:ADP901 3.8 37.0 1.0
N A:THR185 4.0 31.8 1.0
OD1 A:ASP461 4.0 54.1 1.0
CA A:SER242 4.0 35.3 1.0
CG2 A:THR185 4.1 29.8 1.0
O2A A:ADP901 4.1 38.3 1.0
CA A:THR185 4.1 30.8 1.0
OD2 A:ASP461 4.2 61.6 1.0
O1 A:VO4902 4.4 38.7 1.0
O3A A:ADP901 4.4 35.9 1.0
O A:HOH1032 4.5 49.6 1.0
O3 A:VO4902 4.5 45.9 1.0
CG A:ASP461 4.5 55.2 1.0
O1B A:ADP901 4.6 35.5 1.0
O4 A:VO4902 4.6 38.7 1.0
O1A A:ADP901 4.6 32.2 1.0
PA A:ADP901 4.6 35.2 1.0
O A:ASN240 4.7 40.9 1.0
O A:ILE462 4.7 42.2 1.0
ND2 A:ASN238 4.9 29.3 1.0
C A:SER241 4.9 40.2 1.0

Magnesium binding site 2 out of 2 in 5n69

Go back to Magnesium Binding Sites List in 5n69
Magnesium binding site 2 out of 2 in the Cardiac Muscle Myosin S1 Fragment in the Pre-Powerstroke State Co- Crystallized with the Activator Omecamtiv Mecarbil


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cardiac Muscle Myosin S1 Fragment in the Pre-Powerstroke State Co- Crystallized with the Activator Omecamtiv Mecarbil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg903

b:43.1
occ:1.00
OG B:SER242 1.9 36.7 1.0
OG1 B:THR185 2.0 40.5 1.0
O3 B:VO4902 2.1 41.0 1.0
O3B B:ADP901 2.1 36.7 1.0
O B:HOH1010 2.2 38.4 1.0
O B:HOH1001 2.2 24.4 1.0
CB B:THR185 3.1 39.9 1.0
CB B:SER242 3.1 36.6 1.0
PB B:ADP901 3.4 37.2 1.0
O1B B:ADP901 3.6 35.5 1.0
V B:VO4902 3.6 45.1 1.0
N B:SER242 3.8 35.7 1.0
N B:THR185 4.0 32.7 1.0
O1A B:ADP901 4.0 37.5 1.0
OD1 B:ASP461 4.1 54.3 1.0
CG2 B:THR185 4.1 33.9 1.0
CA B:SER242 4.1 33.9 1.0
CA B:THR185 4.1 31.7 1.0
OD2 B:ASP461 4.2 51.5 1.0
O B:HOH1050 4.2 46.1 1.0
O3A B:ADP901 4.3 37.7 1.0
O4 B:VO4902 4.3 44.6 1.0
O2 B:VO4902 4.5 47.2 1.0
O2B B:ADP901 4.5 37.1 1.0
CG B:ASP461 4.5 52.3 1.0
O1 B:VO4902 4.6 39.6 1.0
PA B:ADP901 4.6 38.7 1.0
O B:ASN240 4.6 41.6 1.0
O B:ILE462 4.7 43.0 1.0
O2A B:ADP901 4.8 37.5 1.0
ND2 B:ASN238 4.9 36.6 1.0
C B:SER241 4.9 40.4 1.0

Reference:

V.J.Planelles-Herrero, J.J.Hartman, J.Robert-Paganin, F.I.Malik, A.Houdusse. Mechanistic and Structural Basis For Activation of Cardiac Myosin Force Production By Omecamtiv Mecarbil. Nat Commun V. 8 190 2017.
ISSN: ESSN 2041-1723
PubMed: 28775348
DOI: 10.1038/S41467-017-00176-5
Page generated: Mon Dec 14 20:55:03 2020

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