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Magnesium in PDB 4zg4: Myosin Vc Pre-Powerstroke

Protein crystallography data

The structure of Myosin Vc Pre-Powerstroke, PDB code: 4zg4 was solved by V.Ropars, O.Pylypenko, L.Sweeney, A.Houdusse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.54 / 2.36
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 118.280, 67.320, 133.180, 90.00, 108.48, 90.00
R / Rfree (%) 17.3 / 21.3

Other elements in 4zg4:

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

Vanadium (V) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Myosin Vc Pre-Powerstroke (pdb code 4zg4). 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, PDB code: 4zg4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4zg4

Go back to Magnesium Binding Sites List in 4zg4
Magnesium binding site 1 out of 2 in the Myosin Vc Pre-Powerstroke


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg801

b:44.7
occ:1.00
OG1 B:THR168 2.0 41.7 1.0
O1 B:VO4802 2.0 41.2 1.0
O1B B:ADP803 2.0 35.9 1.0
O B:HOH1011 2.1 42.1 1.0
O B:HOH918 2.1 38.3 1.0
OG B:SER216 2.1 38.8 1.0
H B:SER216 3.0 49.1 1.0
HB B:THR168 3.1 48.5 1.0
CB B:THR168 3.1 40.5 1.0
HB2 B:SER216 3.2 51.3 1.0
CB B:SER216 3.2 42.8 1.0
PB B:ADP803 3.3 47.9 1.0
H B:THR168 3.4 62.3 1.0
V B:VO4802 3.5 42.1 1.0
O3B B:ADP803 3.6 50.2 1.0
N B:SER216 3.7 40.9 1.0
HB3 B:SER216 3.9 51.3 1.0
HG21 B:THR168 4.0 43.9 1.0
N B:THR168 4.0 51.9 1.0
OD1 B:ASP435 4.1 68.9 1.0
CA B:SER216 4.1 42.8 1.0
O2A B:ADP803 4.1 42.6 1.0
CA B:THR168 4.1 38.4 1.0
CG2 B:THR168 4.1 36.6 1.0
O3A B:ADP803 4.2 51.5 1.0
HB2 B:LYS167 4.2 45.5 1.0
HD21 B:ASN206 4.2 57.3 1.0
OD2 B:ASP435 4.3 71.8 1.0
O B:HOH980 4.3 69.1 1.0
O3 B:VO4802 4.3 54.6 1.0
HA B:THR168 4.4 46.1 1.0
HA B:SER215 4.4 66.0 1.0
O4 B:VO4802 4.4 42.1 1.0
O2B B:ADP803 4.4 41.7 1.0
HE2 B:LYS167 4.4 49.1 1.0
HD21 B:ASN212 4.5 49.4 1.0
HG23 B:THR168 4.5 43.9 1.0
O B:ASN214 4.5 39.1 1.0
PA B:ADP803 4.5 47.1 1.0
HD22 B:ASN212 4.5 49.4 1.0
CG B:ASP435 4.6 85.2 1.0
HA B:SER216 4.6 51.3 1.0
O1A B:ADP803 4.6 46.9 1.0
O2 B:VO4802 4.8 47.5 1.0
HA B:TYR437 4.8 56.1 1.0
C B:SER215 4.8 54.1 1.0
ND2 B:ASN206 4.8 47.7 1.0
ND2 B:ASN212 4.9 41.1 1.0
HG22 B:THR168 4.9 43.9 1.0
HD22 B:ASN206 5.0 57.3 1.0

Magnesium binding site 2 out of 2 in 4zg4

Go back to Magnesium Binding Sites List in 4zg4
Magnesium binding site 2 out of 2 in the Myosin Vc Pre-Powerstroke


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg801

b:53.6
occ:1.00
O1 E:VO4802 2.0 50.7 1.0
OG1 E:THR168 2.1 55.0 1.0
O1B E:ADP803 2.1 46.2 1.0
O E:HOH1007 2.1 58.6 1.0
O E:HOH952 2.1 49.1 1.0
OG E:SER216 2.1 47.1 1.0
H E:SER216 3.0 56.3 1.0
HB2 E:SER216 3.1 52.7 1.0
HB E:THR168 3.1 51.2 1.0
CB E:THR168 3.1 42.7 1.0
CB E:SER216 3.2 43.9 1.0
PB E:ADP803 3.3 54.1 1.0
V E:VO4802 3.5 51.9 1.0
H E:THR168 3.5 63.5 1.0
O3B E:ADP803 3.5 57.6 1.0
N E:SER216 3.7 46.9 1.0
HB3 E:SER216 3.9 52.7 1.0
HG21 E:THR168 4.0 51.6 1.0
CA E:SER216 4.0 50.4 1.0
N E:THR168 4.1 52.9 1.0
OD2 E:ASP435 4.1 73.0 1.0
CA E:THR168 4.1 58.9 1.0
OD1 E:ASP435 4.1 80.1 1.0
CG2 E:THR168 4.2 43.0 1.0
O3A E:ADP803 4.2 48.3 1.0
O1A E:ADP803 4.2 54.9 1.0
HB2 E:LYS167 4.2 58.2 1.0
HD21 E:ASN206 4.2 60.0 1.0
O E:HOH945 4.3 65.0 1.0
O3 E:VO4802 4.3 45.7 1.0
HA E:THR168 4.4 70.6 1.0
O4 E:VO4802 4.4 51.2 1.0
HA E:SER215 4.4 60.5 1.0
O2B E:ADP803 4.4 48.9 1.0
HE2 E:LYS167 4.5 53.4 1.0
HG23 E:THR168 4.5 51.6 1.0
HA E:SER216 4.6 60.5 1.0
CG E:ASP435 4.6 83.0 1.0
PA E:ADP803 4.6 55.8 1.0
O E:ASN214 4.6 47.6 1.0
HD21 E:ASN212 4.6 52.2 1.0
HD22 E:ASN212 4.7 52.2 1.0
O2A E:ADP803 4.7 56.5 1.0
HA E:TYR437 4.7 58.7 1.0
O2 E:VO4802 4.8 55.2 1.0
C E:SER215 4.8 59.0 1.0
ND2 E:ASN206 4.8 50.0 1.0
HZ1 E:LYS167 4.9 53.7 1.0
HG22 E:THR168 4.9 51.6 1.0
HZ3 E:LYS167 5.0 53.7 1.0
ND2 E:ASN212 5.0 43.5 1.0

Reference:

S.F.Wulf, V.Ropars, S.Fujita-Becker, M.Oster, G.Hofhaus, L.G.Trabuco, O.Pylypenko, H.L.Sweeney, A.M.Houdusse, R.R.Schroder. Force-Producing Adp State of Myosin Bound to Actin. Proc.Natl.Acad.Sci.Usa V. 113 E1844 2016.
ISSN: ESSN 1091-6490
PubMed: 26976594
DOI: 10.1073/PNAS.1516598113
Page generated: Mon Dec 14 19:57:01 2020

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