Magnesium in PDB 6lsm: Tubulin Polymerization Inhibitors

Protein crystallography data

The structure of Tubulin Polymerization Inhibitors, PDB code: 6lsm was solved by L.Gang, Y.X.Wang, J.J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.87 / 2.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.553, 158.081, 182.23, 90, 90, 90
R / Rfree (%) 18.1 / 22.7

Other elements in 6lsm:

The structure of Tubulin Polymerization Inhibitors also contains other interesting chemical elements:

Calcium (Ca) 4 atoms
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tubulin Polymerization Inhibitors (pdb code 6lsm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Tubulin Polymerization Inhibitors, PDB code: 6lsm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6lsm

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Magnesium binding site 1 out of 6 in the Tubulin Polymerization Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin Polymerization Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:44.3
occ:1.00
O A:HOH604 1.9 53.0 1.0
O A:HOH602 2.0 75.8 1.0
O1B A:GTP501 2.2 42.7 1.0
O1G A:GTP501 2.2 44.0 1.0
PG A:GTP501 3.4 42.8 1.0
PB A:GTP501 3.5 35.2 1.0
OD2 A:ASP69 3.7 57.6 1.0
OE1 A:GLU71 3.7 67.6 1.0
O2G A:GTP501 3.7 43.4 1.0
CG A:GLU71 3.8 57.9 1.0
OD1 A:ASP69 3.9 52.7 1.0
O3B A:GTP501 3.9 50.5 1.0
NZ B:LYS254 4.1 61.7 1.0
CB A:GLN11 4.2 44.1 1.0
CG A:ASP69 4.2 57.0 1.0
CD A:GLU71 4.2 65.3 1.0
N A:GLN11 4.3 40.1 1.0
O3A A:GTP501 4.3 41.3 1.0
CB A:ASP98 4.5 46.1 1.0
OD2 A:ASP98 4.6 55.0 1.0
O2B A:GTP501 4.6 54.9 1.0
O1A A:GTP501 4.7 43.4 1.0
CG A:ASP98 4.7 51.0 1.0
O3G A:GTP501 4.7 37.1 1.0
OE1 A:GLN11 4.8 54.4 1.0
CA A:GLN11 4.8 39.7 1.0

Magnesium binding site 2 out of 6 in 6lsm

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Magnesium binding site 2 out of 6 in the Tubulin Polymerization Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin Polymerization Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:36.5
occ:1.00
O B:HOH615 1.9 59.7 1.0
OE1 B:GLN11 2.0 57.3 1.0
O B:HOH601 2.0 67.2 1.0
O B:HOH620 2.1 55.4 1.0
O B:HOH622 2.1 52.8 1.0
O1A B:GDP501 2.2 40.1 1.0
CD B:GLN11 3.2 56.1 1.0
OD2 B:ASP179 3.3 55.7 1.0
PA B:GDP501 3.7 28.1 1.0
NE2 B:GLN11 4.1 51.5 1.0
OD1 B:ASN101 4.2 41.9 1.0
CB B:GLN11 4.2 40.6 1.0
CG B:GLN11 4.2 47.3 1.0
O3A B:GDP501 4.3 40.8 1.0
CG B:ASP179 4.4 51.9 1.0
C5' B:GDP501 4.5 24.7 1.0
OE1 C:GLU254 4.6 59.7 1.0
O5' B:GDP501 4.6 23.5 1.0
O2A B:GDP501 4.7 28.0 1.0
O1B B:GDP501 4.8 35.9 1.0

Magnesium binding site 3 out of 6 in 6lsm

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Magnesium binding site 3 out of 6 in the Tubulin Polymerization Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin Polymerization Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg506

b:87.2
occ:1.00
O B:HOH611 2.1 77.0 1.0
OD2 B:ASP120 4.2 68.6 1.0
OD1 B:ASP120 4.2 67.0 1.0
CB B:ASP116 4.5 41.3 1.0
CG B:ASP120 4.6 67.3 1.0
OD2 B:ASP116 4.7 77.6 1.0
CG B:ASP116 4.9 51.6 1.0

Magnesium binding site 4 out of 6 in 6lsm

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Magnesium binding site 4 out of 6 in the Tubulin Polymerization Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin Polymerization Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:46.6
occ:1.00
O C:HOH601 1.9 59.2 1.0
O1G C:GTP501 1.9 41.4 1.0
O C:HOH606 2.0 51.0 1.0
O1B C:GTP501 2.1 43.6 1.0
O C:HOH614 2.3 42.0 1.0
PG C:GTP501 3.3 34.0 1.0
PB C:GTP501 3.4 31.2 1.0
OE1 C:GLU71 3.5 65.2 1.0
NZ D:LYS254 3.7 50.6 1.0
O3B C:GTP501 3.9 40.8 1.0
O3A C:GTP501 3.9 39.3 1.0
OD2 C:ASP98 4.0 41.4 1.0
O2G C:GTP501 4.0 40.2 1.0
CG C:GLU71 4.1 39.4 1.0
OD2 C:ASP69 4.2 42.8 1.0
OD1 C:ASP69 4.2 40.9 1.0
CD C:GLU71 4.2 58.5 1.0
CB C:ASP98 4.4 31.7 1.0
CB C:GLN11 4.4 32.5 1.0
CG C:ASP98 4.5 34.5 1.0
O3G C:GTP501 4.5 34.2 1.0
CG C:ASP69 4.6 35.9 1.0
O2B C:GTP501 4.7 33.1 1.0
N C:GLN11 4.7 28.7 1.0
OE1 C:GLN11 4.7 50.5 1.0
O1A C:GTP501 4.8 34.2 1.0
CE D:LYS254 4.9 38.7 1.0
PA C:GTP501 5.0 28.2 1.0

Magnesium binding site 5 out of 6 in 6lsm

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Magnesium binding site 5 out of 6 in the Tubulin Polymerization Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin Polymerization Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:65.0
occ:1.00
OE1 D:GLN11 2.4 83.9 1.0
O5' D:GDP600 3.2 67.1 1.0
CD D:GLN11 3.5 87.2 1.0
O3A D:GDP600 3.8 71.3 1.0
OD1 D:ASN101 3.9 70.4 1.0
C5' D:GDP600 4.0 64.9 1.0
NE2 D:GLN11 4.0 78.8 1.0
PA D:GDP600 4.1 58.0 1.0
ND2 D:ASN101 4.4 92.5 1.0
CG D:ASN101 4.5 77.5 1.0
CG D:GLN11 4.7 86.4 1.0
CB D:GLN11 4.7 78.0 1.0
O1A D:GDP600 4.8 59.5 1.0

Magnesium binding site 6 out of 6 in 6lsm

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Magnesium binding site 6 out of 6 in the Tubulin Polymerization Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Tubulin Polymerization Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:94.4
occ:1.00
O2B F:ACP402 2.3 127.8 1.0
O1G F:ACP402 3.1 101.5 1.0
OE1 F:GLU331 3.1 100.9 1.0
NZ F:LYS74 3.2 106.1 1.0
OE2 F:GLU331 3.2 108.1 1.0
CD F:GLU331 3.5 95.4 1.0
PB F:ACP402 3.8 124.3 1.0
OD1 F:ASN333 3.8 107.2 1.0
PG F:ACP402 4.3 132.4 1.0
CE F:LYS74 4.4 97.5 1.0
C3B F:ACP402 4.5 112.9 1.0
O1B F:ACP402 4.6 120.8 1.0
O3A F:ACP402 4.8 109.5 1.0
CG F:ASN333 4.9 96.7 1.0
O2G F:ACP402 5.0 105.8 1.0

Reference:

L.Gang, Y.X.Wang, J.J.Chen. Design, Synthesis, and Bioevaluation of Pyrazolo[1,5-A]Pyrimidine Derivatives As Tubulin Polymerization Inhibitors Targeting the Colchicine Binding Site with Potent Anticancer Activities To Be Published.
Page generated: Mon Jan 25 08:52:31 2021

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