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Vanadium 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
Magnesium (Mg) 2 atoms

Vanadium Binding Sites:

The binding sites of Vanadium 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 Vanadium atom.
In total 2 binding sites of Vanadium 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 Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 5n69

Go back to Vanadium Binding Sites List in 5n69
Vanadium 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 Vanadium with other atoms in the V 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:V902

b:41.7
occ:1.00
V A:VO4902 0.0 41.7 1.0
O2 A:VO4902 1.6 38.5 1.0
O1 A:VO4902 1.6 38.7 1.0
O4 A:VO4902 1.6 38.7 1.0
O3 A:VO4902 1.6 45.9 1.0
O3B A:ADP901 2.5 37.0 1.0
PB A:ADP901 3.6 36.8 1.0
MG A:MG903 3.7 38.3 1.0
OG A:SER241 3.7 41.7 1.0
O2B A:ADP901 3.8 36.2 1.0
OG A:SER180 3.9 45.8 1.0
N A:SER242 3.9 35.7 1.0
O A:HOH1042 3.9 29.0 1.0
N A:GLY464 4.0 37.4 1.0
CA A:SER180 4.0 35.8 1.0
O A:HOH1020 4.1 26.9 1.0
ND2 A:ASN238 4.1 29.3 1.0
N A:GLY181 4.2 36.2 1.0
NZ A:LYS184 4.2 30.0 1.0
CB A:SER180 4.3 37.8 1.0
O A:SER242 4.3 41.3 1.0
CA A:SER241 4.3 35.9 1.0
O1B A:ADP901 4.3 35.5 1.0
O A:HOH1003 4.5 35.5 1.0
OG A:SER242 4.5 42.3 1.0
CB A:SER241 4.5 37.3 1.0
C A:SER241 4.6 40.2 1.0
CE A:LYS184 4.6 26.8 1.0
CB A:SER242 4.6 37.0 1.0
CA A:ALA463 4.6 37.1 1.0
C A:SER180 4.7 39.5 1.0
CA A:GLY464 4.7 36.4 1.0
CA A:SER242 4.7 35.3 1.0
C A:ALA463 4.8 41.1 1.0
O3A A:ADP901 4.8 35.9 1.0

Vanadium binding site 2 out of 2 in 5n69

Go back to Vanadium Binding Sites List in 5n69
Vanadium 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 Vanadium with other atoms in the V 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:V902

b:45.1
occ:1.00
V B:VO4902 0.0 45.1 1.0
O3 B:VO4902 1.6 41.0 1.0
O4 B:VO4902 1.6 44.6 1.0
O1 B:VO4902 1.6 39.6 1.0
O2 B:VO4902 1.6 47.2 1.0
O1B B:ADP901 2.5 35.5 1.0
MG B:MG903 3.6 43.1 1.0
PB B:ADP901 3.7 37.2 1.0
OG B:SER241 3.7 50.3 1.0
N B:SER242 3.8 35.7 1.0
O3B B:ADP901 3.9 36.7 1.0
O B:HOH1009 3.9 37.7 1.0
OG B:SER180 3.9 44.2 1.0
N B:GLY464 4.0 37.2 1.0
ND2 B:ASN238 4.1 36.6 1.0
CA B:SER180 4.1 38.1 1.0
N B:GLY181 4.2 36.0 1.0
CA B:SER241 4.2 37.5 1.0
O B:SER242 4.2 35.8 1.0
NZ B:LYS184 4.2 29.8 1.0
O B:HOH1001 4.3 24.4 1.0
CB B:SER180 4.3 40.5 1.0
OG B:SER242 4.4 36.7 1.0
O2B B:ADP901 4.4 37.1 1.0
CB B:SER241 4.5 40.4 1.0
C B:SER241 4.5 40.4 1.0
CB B:SER242 4.5 36.6 1.0
O B:HOH1010 4.5 38.4 1.0
CA B:ALA463 4.6 39.1 1.0
CE B:LYS184 4.6 35.0 1.0
CA B:SER242 4.6 33.9 1.0
C B:SER180 4.7 41.8 1.0
CA B:GLY464 4.8 36.3 1.0
C B:ALA463 4.8 41.3 1.0
O3A B:ADP901 4.8 37.7 1.0
C B:SER242 4.9 37.6 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: Wed Dec 16 02:31:36 2020

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