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Magnesium in PDB 1dfl: Scallop Myosin S1 Complexed with Mgadp:Vanadate-Transition State

Protein crystallography data

The structure of Scallop Myosin S1 Complexed with Mgadp:Vanadate-Transition State, PDB code: 1dfl was solved by A.Houdusse, A.G.Szent-Gyorgyi, C.Cohen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 4.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.032, 243.475, 124.650, 90.00, 100.20, 90.00
R / Rfree (%) 39.4 / 40

Other elements in 1dfl:

The structure of Scallop Myosin S1 Complexed with Mgadp:Vanadate-Transition State also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Vanadium (V) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Scallop Myosin S1 Complexed with Mgadp:Vanadate-Transition State (pdb code 1dfl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Scallop Myosin S1 Complexed with Mgadp:Vanadate-Transition State, PDB code: 1dfl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1dfl

Go back to Magnesium Binding Sites List in 1dfl
Magnesium binding site 1 out of 4 in the Scallop Myosin S1 Complexed with Mgadp:Vanadate-Transition State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Scallop Myosin S1 Complexed with Mgadp:Vanadate-Transition State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1997

b:30.0
occ:1.00
O1 A:VO41998 1.9 30.0 1.0
O1B A:ADP1999 2.2 30.0 1.0
CB A:THR183 2.8 30.0 1.0
PB A:ADP1999 3.4 30.0 1.0
V A:VO41998 3.4 30.0 1.0
CB A:SER241 3.4 30.0 1.0
O3B A:ADP1999 3.7 30.0 1.0
N A:THR183 3.8 30.0 1.0
CA A:THR183 3.8 30.0 1.0
O2A A:ADP1999 4.1 30.0 1.0
O3A A:ADP1999 4.3 30.0 1.0
N A:SER241 4.3 30.0 1.0
O3 A:VO41998 4.4 30.0 1.0
O2B A:ADP1999 4.5 30.0 1.0
CA A:SER241 4.5 30.0 1.0
PA A:ADP1999 4.6 30.0 1.0
O1A A:ADP1999 4.7 30.0 1.0
O4 A:VO41998 4.7 30.0 1.0
O2 A:VO41998 4.7 30.0 1.0
CB A:LYS182 4.8 30.0 1.0
C A:LYS182 4.9 30.0 1.0

Magnesium binding site 2 out of 4 in 1dfl

Go back to Magnesium Binding Sites List in 1dfl
Magnesium binding site 2 out of 4 in the Scallop Myosin S1 Complexed with Mgadp:Vanadate-Transition State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Scallop Myosin S1 Complexed with Mgadp:Vanadate-Transition State within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg1996

b:30.0
occ:1.00
O Y:PHE34 2.1 30.0 1.0
C Y:PHE34 3.0 30.0 1.0
CA Y:PHE34 3.8 30.0 1.0
N Y:PHE34 3.9 30.0 1.0
N Y:VAL35 3.9 30.0 1.0
CB Y:PHE34 3.9 30.0 1.0
CB Y:ASP32 4.1 30.0 1.0
N Y:SER36 4.1 30.0 1.0
CA Y:VAL35 4.1 30.0 1.0
CB Y:ASP39 4.5 30.0 1.0
C Y:VAL35 4.5 30.0 1.0
N Y:ASP32 4.5 30.0 1.0
CB Y:SER36 4.5 30.0 1.0
CB Y:ASP30 4.5 30.0 1.0
CA Y:ASP32 4.7 30.0 1.0
C Y:ASP32 4.8 30.0 1.0
CA Y:SER36 5.0 30.0 1.0
CB Y:ASP28 5.0 30.0 1.0

Magnesium binding site 3 out of 4 in 1dfl

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Magnesium binding site 3 out of 4 in the Scallop Myosin S1 Complexed with Mgadp:Vanadate-Transition State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Scallop Myosin S1 Complexed with Mgadp:Vanadate-Transition State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2997

b:30.0
occ:1.00
O1 B:VO42998 1.9 30.0 1.0
O1B B:ADP2999 2.2 30.0 1.0
CB B:THR183 2.8 30.0 1.0
PB B:ADP2999 3.4 30.0 1.0
V B:VO42998 3.4 30.0 1.0
O3B B:ADP2999 3.7 30.0 1.0
CB B:SER241 3.7 30.0 1.0
N B:THR183 3.8 30.0 1.0
CA B:THR183 3.8 30.0 1.0
O2A B:ADP2999 4.1 30.0 1.0
O3A B:ADP2999 4.3 30.0 1.0
O3 B:VO42998 4.4 30.0 1.0
O2B B:ADP2999 4.5 30.0 1.0
PA B:ADP2999 4.6 30.0 1.0
N B:SER241 4.6 30.0 1.0
O1A B:ADP2999 4.7 30.0 1.0
O4 B:VO42998 4.7 30.0 1.0
O2 B:VO42998 4.7 30.0 1.0
CB B:LYS182 4.8 30.0 1.0
CA B:SER241 4.8 30.0 1.0
C B:LYS182 4.9 30.0 1.0

Magnesium binding site 4 out of 4 in 1dfl

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Magnesium binding site 4 out of 4 in the Scallop Myosin S1 Complexed with Mgadp:Vanadate-Transition State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Scallop Myosin S1 Complexed with Mgadp:Vanadate-Transition State within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg2996

b:30.0
occ:1.00
O W:PHE34 2.1 30.0 1.0
C W:PHE34 3.1 30.0 1.0
N W:PHE34 3.9 30.0 1.0
CA W:PHE34 3.9 30.0 1.0
N W:VAL35 4.0 30.0 1.0
CB W:ASP32 4.1 30.0 1.0
N W:ASP32 4.2 30.0 1.0
CA W:VAL35 4.2 30.0 1.0
CB W:PHE34 4.2 30.0 1.0
CB W:ASP30 4.3 30.0 1.0
CB W:ASP39 4.3 30.0 1.0
N W:SER36 4.4 30.0 1.0
CB W:ASP28 4.5 30.0 1.0
CA W:ASP32 4.5 30.0 1.0
CA W:ASP28 4.5 30.0 1.0
N W:ASP30 4.6 30.0 1.0
C W:ASP30 4.7 30.0 1.0
C W:ASP32 4.7 30.0 1.0
C W:VAL35 4.7 30.0 1.0
CA W:ASP30 4.8 30.0 1.0
C W:ASP28 4.8 30.0 1.0
O W:ASP30 4.8 30.0 1.0
N W:GLY33 4.8 30.0 1.0
CB W:SER36 4.9 30.0 1.0
N W:ARG31 5.0 30.0 1.0

Reference:

A.Houdusse, A.G.Szent-Gyorgyi, C.Cohen. Three Conformational States of Scallop Myosin S1. Proc.Natl.Acad.Sci.Usa V. 97 11238 2000.
ISSN: ISSN 0027-8424
PubMed: 11016966
DOI: 10.1073/PNAS.200376897
Page generated: Mon Dec 14 05:50:24 2020

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