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

Protein crystallography data

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

Other elements in 5hmp:

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

Magnesium (Mg) 2 atoms

Vanadium Binding Sites:

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

Vanadium binding site 1 out of 2 in 5hmp

Go back to Vanadium Binding Sites List in 5hmp
Vanadium binding site 1 out of 2 in the Myosin Vc Pre-Powerstroke State


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Myosin Vc Pre-Powerstroke State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V802

b:45.4
occ:1.00
V A:VO4802 0.0 45.4 1.0
O3 A:VO4802 1.7 33.0 1.0
O1 A:VO4802 1.7 44.2 1.0
O2 A:VO4802 1.7 53.6 1.0
O4 A:VO4802 1.9 45.5 1.0
O3B A:ADP803 2.1 45.5 1.0
H A:SER216 3.0 56.1 1.0
HG A:SER163 3.0 52.9 1.0
HG A:SER215 3.1 57.8 1.0
HD22 A:ASN212 3.2 56.9 1.0
H A:GLY164 3.2 55.1 1.0
HA A:SER163 3.2 52.4 1.0
PB A:ADP803 3.2 43.8 1.0
HZ1 A:LYS167 3.3 48.4 1.0
H A:GLY438 3.4 54.4 1.0
HA A:SER215 3.4 55.7 1.0
MG A:MG801 3.6 43.1 1.0
O1B A:ADP803 3.6 40.2 1.0
HA A:TYR437 3.7 53.9 1.0
N A:SER216 3.8 46.8 1.0
OG A:SER163 3.8 44.1 1.0
HB2 A:SER216 3.9 52.1 1.0
OG A:SER215 3.9 48.1 1.0
O A:HOH983 3.9 44.8 1.0
N A:GLY164 3.9 45.9 1.0
ND2 A:ASN212 4.0 47.4 1.0
O2B A:ADP803 4.0 44.6 1.0
CA A:SER163 4.1 43.7 1.0
O A:HOH976 4.1 47.8 1.0
NZ A:LYS167 4.1 40.3 1.0
HZ3 A:LYS167 4.1 48.4 1.0
CA A:SER215 4.2 46.4 1.0
HD21 A:ASN212 4.2 56.9 1.0
N A:GLY438 4.3 45.3 1.0
HB2 A:SER163 4.3 52.5 1.0
CB A:SER163 4.3 43.7 1.0
O A:HOH903 4.4 41.6 1.0
HE2 A:LYS167 4.4 49.6 1.0
O A:SER216 4.5 43.1 1.0
O3A A:ADP803 4.5 45.4 1.0
CB A:SER216 4.5 43.4 1.0
CB A:SER215 4.5 47.2 1.0
C A:SER215 4.5 47.6 1.0
C A:SER163 4.5 45.0 1.0
OG A:SER216 4.6 43.3 1.0
HB3 A:ASN212 4.6 57.0 1.0
HB2 A:SER215 4.6 56.7 1.0
CA A:TYR437 4.6 44.9 1.0
CA A:SER216 4.7 44.4 1.0
HA2 A:GLY164 4.7 56.0 1.0
HB3 A:TYR437 4.7 52.5 1.0
HZ2 A:LYS167 4.7 48.4 1.0
CE A:LYS167 4.8 41.4 1.0
HA3 A:GLY438 4.8 55.1 1.0
HB2 A:ASN212 4.9 57.0 1.0
CA A:GLY164 5.0 46.7 1.0

Vanadium binding site 2 out of 2 in 5hmp

Go back to Vanadium Binding Sites List in 5hmp
Vanadium binding site 2 out of 2 in the Myosin Vc Pre-Powerstroke State


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Myosin Vc Pre-Powerstroke State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V802

b:52.1
occ:1.00
V B:VO4802 0.0 52.1 1.0
O3 B:VO4802 1.7 62.0 1.0
O1 B:VO4802 1.7 64.5 1.0
O2 B:VO4802 1.7 55.0 1.0
O4 B:VO4802 1.9 39.5 1.0
O3B B:ADP803 1.9 53.6 1.0
H B:SER216 3.0 69.8 1.0
PB B:ADP803 3.2 54.4 1.0
HZ1 B:LYS167 3.2 59.0 1.0
HA B:SER163 3.2 62.0 1.0
HG B:SER163 3.2 62.2 1.0
H B:GLY164 3.2 61.9 1.0
HD22 B:ASN212 3.2 61.4 1.0
HG B:SER215 3.3 62.7 1.0
H B:GLY438 3.3 70.8 1.0
HA B:SER215 3.5 65.2 1.0
MG B:MG801 3.5 58.5 1.0
O1B B:ADP803 3.6 53.1 1.0
HA B:TYR437 3.7 73.3 1.0
N B:SER216 3.8 58.2 1.0
O B:HOH938 3.8 57.9 1.0
HB2 B:SER216 3.8 71.0 1.0
NZ B:LYS167 4.0 49.1 1.0
N B:GLY164 4.0 51.6 1.0
O2B B:ADP803 4.0 55.8 1.0
OG B:SER163 4.0 51.8 1.0
HZ3 B:LYS167 4.0 59.0 1.0
ND2 B:ASN212 4.0 51.1 1.0
CA B:SER163 4.1 51.6 1.0
OG B:SER215 4.1 52.3 1.0
N B:GLY438 4.1 59.0 1.0
O B:HOH936 4.1 53.8 1.0
CA B:SER215 4.3 54.4 1.0
O B:HOH902 4.3 43.4 1.0
HD21 B:ASN212 4.3 61.4 1.0
HB2 B:SER163 4.3 61.5 1.0
O3A B:ADP803 4.4 47.4 1.0
CB B:SER163 4.4 51.3 1.0
HE2 B:LYS167 4.4 65.0 1.0
CB B:SER216 4.5 59.2 1.0
OG B:SER216 4.5 59.9 1.0
O B:SER216 4.5 55.8 1.0
HZ2 B:LYS167 4.5 59.0 1.0
CA B:TYR437 4.6 61.1 1.0
C B:SER215 4.6 55.9 1.0
C B:SER163 4.6 51.7 1.0
CB B:SER215 4.6 52.5 1.0
HB2 B:SER215 4.6 63.0 1.0
CA B:SER216 4.6 58.3 1.0
HA3 B:GLY438 4.7 70.2 1.0
HB3 B:ASN212 4.7 58.5 1.0
HB3 B:TYR437 4.7 69.9 1.0
CE B:LYS167 4.7 54.2 1.0
HA2 B:GLY164 4.8 61.8 1.0
C B:TYR437 4.9 60.7 1.0
O1A B:ADP803 4.9 64.2 1.0
HE3 B:LYS167 5.0 65.0 1.0

Reference:

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
Page generated: Thu Oct 29 07:05:54 2020

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