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Magnesium in PDB 1lkx: Motor Domain of Myoe, A Class-I Myosin

Protein crystallography data

The structure of Motor Domain of Myoe, A Class-I Myosin, PDB code: 1lkx was solved by M.Kollmar, U.Durrwang, W.Kliche, D.J.Manstein, F.J.Kull, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.818, 143.667, 236.050, 90.00, 94.86, 90.00
R / Rfree (%) 22.8 / 27.3

Other elements in 1lkx:

The structure of Motor Domain of Myoe, A Class-I Myosin also contains other interesting chemical elements:

Vanadium (V) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Motor Domain of Myoe, A Class-I Myosin (pdb code 1lkx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Motor Domain of Myoe, A Class-I Myosin, PDB code: 1lkx:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1lkx

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Magnesium binding site 1 out of 4 in the Motor Domain of Myoe, A Class-I Myosin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Motor Domain of Myoe, A Class-I Myosin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg790

b:22.2
occ:1.00
OG1 A:THR108 2.1 25.4 1.0
OG A:SER158 2.4 33.5 1.0
O1B A:ADP791 2.4 28.4 1.0
O2 A:VO4792 2.4 27.9 1.0
O A:HOH805 2.6 14.3 1.0
CB A:THR108 2.9 28.9 1.0
O A:HOH808 3.1 10.9 1.0
O2A A:ADP791 3.1 28.1 1.0
PB A:ADP791 3.2 29.4 1.0
O2B A:ADP791 3.2 29.4 1.0
N A:SER158 3.5 33.9 1.0
CB A:SER158 3.5 34.5 1.0
V A:VO4792 3.6 30.3 1.0
CG2 A:THR108 3.8 27.6 1.0
O3A A:ADP791 3.9 28.5 1.0
PA A:ADP791 3.9 28.1 1.0
CA A:SER158 4.1 34.2 1.0
CA A:THR108 4.1 30.6 1.0
N A:THR108 4.1 29.9 1.0
ND2 A:ASN148 4.3 32.9 1.0
O1A A:ADP791 4.3 27.1 1.0
C A:SER157 4.4 34.1 1.0
O A:HOH798 4.4 38.6 1.0
CA A:SER157 4.5 35.0 1.0
ND2 A:ASN154 4.5 38.2 1.0
O3B A:ADP791 4.5 28.9 1.0
O3 A:VO4792 4.6 29.9 1.0
O4 A:VO4792 4.7 33.2 1.0
N A:SER157 4.7 37.5 1.0
OD1 A:ASP386 4.8 51.4 1.0
O1 A:VO4792 4.9 31.4 1.0

Magnesium binding site 2 out of 4 in 1lkx

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Magnesium binding site 2 out of 4 in the Motor Domain of Myoe, A Class-I Myosin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Motor Domain of Myoe, A Class-I Myosin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg793

b:22.8
occ:1.00
OG1 B:THR108 2.3 30.6 1.0
O3 B:VO4795 2.4 41.1 1.0
O1B B:ADP794 2.5 40.9 1.0
OG B:SER158 2.6 37.7 1.0
O B:HOH797 2.6 19.7 1.0
O B:HOH796 2.8 14.6 1.0
O2A B:ADP794 2.9 38.3 1.0
CB B:THR108 3.0 32.3 1.0
PB B:ADP794 3.1 40.2 1.0
O3A B:ADP794 3.3 39.3 1.0
O2B B:ADP794 3.3 40.1 1.0
V B:VO4795 3.5 43.2 1.0
N B:SER158 3.5 38.0 1.0
PA B:ADP794 3.5 38.9 1.0
CB B:SER158 3.7 37.8 1.0
CG2 B:THR108 3.9 32.8 1.0
O1A B:ADP794 4.0 36.8 1.0
O1 B:VO4795 4.0 39.9 1.0
CA B:THR108 4.2 33.5 1.0
N B:THR108 4.2 33.4 1.0
CA B:SER158 4.2 37.4 1.0
ND2 B:ASN154 4.2 44.4 1.0
CA B:SER157 4.3 38.8 1.0
C B:SER157 4.4 38.5 1.0
ND2 B:ASN148 4.4 38.9 1.0
O4 B:VO4795 4.4 41.8 1.0
O3B B:ADP794 4.6 38.1 1.0
N B:SER157 4.6 40.4 1.0
OD1 B:ASP386 4.9 53.0 1.0
O2 B:VO4795 4.9 38.8 1.0
O5' B:ADP794 5.0 39.2 1.0

Magnesium binding site 3 out of 4 in 1lkx

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Magnesium binding site 3 out of 4 in the Motor Domain of Myoe, A Class-I Myosin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Motor Domain of Myoe, A Class-I Myosin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg890

b:8.4
occ:1.00
OG1 C:THR108 2.1 29.4 1.0
O C:HOH909 2.2 39.4 1.0
OG C:SER158 2.5 34.6 1.0
O2 C:VO4892 2.5 26.0 1.0
O1B C:ADP891 2.6 19.0 1.0
O2B C:ADP891 2.7 15.8 1.0
O C:HOH897 2.9 28.6 1.0
PB C:ADP891 3.0 15.0 1.0
CB C:THR108 3.0 31.8 1.0
V C:VO4892 3.4 27.7 1.0
CB C:SER158 3.5 35.0 1.0
O2A C:ADP891 3.6 19.2 1.0
N C:SER158 3.6 35.8 1.0
O3A C:ADP891 3.6 19.2 1.0
N C:THR108 4.0 31.1 1.0
PA C:ADP891 4.0 20.2 1.0
CG2 C:THR108 4.1 32.9 1.0
CA C:THR108 4.1 32.6 1.0
CA C:SER158 4.2 35.0 1.0
OD1 C:ASP386 4.3 53.0 1.0
O1A C:ADP891 4.4 22.1 1.0
O1 C:VO4892 4.4 28.6 1.0
O3B C:ADP891 4.4 14.2 1.0
C C:SER157 4.5 36.1 1.0
ND2 C:ASN154 4.5 41.8 1.0
CA C:SER157 4.6 36.6 1.0
O3 C:VO4892 4.6 29.2 1.0
O4 C:VO4892 4.6 27.9 1.0
OD2 C:ASP386 4.7 53.0 1.0
ND2 C:ASN148 4.8 30.3 1.0
N C:SER157 4.9 38.6 1.0
CG C:ASP386 5.0 51.0 1.0

Magnesium binding site 4 out of 4 in 1lkx

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Magnesium binding site 4 out of 4 in the Motor Domain of Myoe, A Class-I Myosin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Motor Domain of Myoe, A Class-I Myosin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg893

b:5.4
occ:1.00
O D:HOH906 2.3 14.2 1.0
OG1 D:THR108 2.3 33.3 1.0
O3 D:VO4895 2.4 35.5 1.0
OG D:SER158 2.4 38.6 1.0
O3B D:ADP894 2.6 35.8 1.0
O2B D:ADP894 2.9 40.6 1.0
PB D:ADP894 3.0 37.3 1.0
O D:HOH905 3.2 30.2 1.0
CB D:THR108 3.2 34.7 1.0
O3A D:ADP894 3.2 38.1 1.0
V D:VO4895 3.2 36.6 1.0
CB D:SER158 3.4 37.2 1.0
N D:SER158 3.4 38.0 1.0
O2A D:ADP894 3.6 37.6 1.0
PA D:ADP894 3.9 37.3 1.0
CA D:SER158 4.0 37.7 1.0
O1 D:VO4895 4.0 38.1 1.0
N D:THR108 4.2 32.1 1.0
CG2 D:THR108 4.2 35.3 1.0
CA D:THR108 4.3 34.5 1.0
C D:SER157 4.3 37.2 1.0
CA D:SER157 4.4 38.1 1.0
O1A D:ADP894 4.4 38.4 1.0
O1B D:ADP894 4.5 39.1 1.0
O4 D:VO4895 4.5 36.5 1.0
ND2 D:ASN154 4.5 43.2 1.0
O2 D:VO4895 4.6 36.5 1.0
ND2 D:ASN148 4.6 33.6 1.0
OD1 D:ASP386 4.6 55.5 1.0
N D:SER157 4.8 41.0 1.0
OD2 D:ASP386 4.9 55.6 1.0

Reference:

M.Kollmar, U.Durrwang, W.Kliche, D.J.Manstein, F.J.Kull. Crystal Structure of the Motor Domain of A Class-I Myosin. Embo J. V. 21 2517 2002.
ISSN: ISSN 0261-4189
PubMed: 12032065
DOI: 10.1093/EMBOJ/21.11.2517
Page generated: Mon Dec 14 06:23:28 2020

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