Magnesium in PDB 6lsn: Crystal Structure of Tubulin-Inhibitor Complex

Protein crystallography data

The structure of Crystal Structure of Tubulin-Inhibitor Complex, PDB code: 6lsn was solved by L.Gang, Y.X.Wang, J.J.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.17 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.296, 158.458, 181.959, 90, 90, 90
R / Rfree (%) 17.7 / 22

Other elements in 6lsn:

The structure of Crystal Structure of Tubulin-Inhibitor Complex also contains other interesting chemical elements:

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

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 6 in 6lsn

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Magnesium binding site 1 out of 6 in the Crystal Structure of Tubulin-Inhibitor Complex


Mono view


Stereo pair view

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

b:37.0
occ:1.00
O1G A:GTP501 2.2 40.9 1.0
O A:HOH619 2.2 32.9 1.0
O A:HOH612 2.2 34.9 1.0
O1B A:GTP501 2.4 32.2 1.0
PG A:GTP501 3.1 43.3 1.0
O2G A:GTP501 3.2 44.7 1.0
PB A:GTP501 3.5 45.2 1.0
O3B A:GTP501 3.6 52.5 1.0
NZ B:LYS254 3.8 45.4 1.0
CG A:GLU71 3.8 72.3 1.0
OD1 A:ASP69 3.9 53.1 1.0
OE1 A:GLU71 3.9 78.2 1.0
OD2 A:ASP69 4.1 55.1 1.0
CB A:ASP98 4.1 38.4 1.0
O3A A:GTP501 4.2 38.1 1.0
CD A:GLU71 4.4 76.8 1.0
OD2 A:ASP98 4.4 62.2 1.0
CG A:ASP69 4.4 54.3 1.0
CG A:ASP98 4.4 49.5 1.0
O3G A:GTP501 4.5 36.9 1.0
CB A:GLN11 4.5 35.2 1.0
N A:GLN11 4.6 38.4 1.0
O2B A:GTP501 4.8 50.5 1.0
OG1 A:THR145 4.8 38.5 1.0
O1A A:GTP501 4.9 40.6 1.0

Magnesium binding site 2 out of 6 in 6lsn

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Magnesium binding site 2 out of 6 in the Crystal Structure of Tubulin-Inhibitor Complex


Mono view


Stereo pair view

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

b:43.8
occ:1.00
OE1 B:GLN11 2.0 49.3 1.0
O B:HOH646 2.0 48.8 1.0
O B:HOH637 2.1 56.3 1.0
O1A B:GDP501 2.2 41.9 1.0
O B:HOH649 2.2 41.6 1.0
O B:HOH611 2.3 49.8 1.0
CD B:GLN11 3.2 46.4 1.0
PA B:GDP501 3.5 36.8 1.0
OD2 B:ASP179 3.7 55.6 1.0
O3A B:GDP501 4.0 35.6 1.0
CB B:GLN11 4.0 34.6 1.0
CG B:GLN11 4.1 42.1 1.0
NE2 B:GLN11 4.2 45.0 1.0
OD1 B:ASN101 4.3 43.3 1.0
C5' B:GDP501 4.4 35.9 1.0
O5' B:GDP501 4.4 31.1 1.0
O1B B:GDP501 4.5 38.2 1.0
O2A B:GDP501 4.6 34.1 1.0
OE1 C:GLU254 4.6 45.7 1.0
CG B:ASP179 4.7 46.1 1.0
C8 B:GDP501 4.9 40.4 1.0
PB B:GDP501 4.9 43.6 1.0

Magnesium binding site 3 out of 6 in 6lsn

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Magnesium binding site 3 out of 6 in the Crystal Structure of Tubulin-Inhibitor Complex


Mono view


Stereo pair view

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

b:72.4
occ:1.00
O B:HOH608 2.2 70.2 1.0
OD2 B:ASP120 4.1 56.4 1.0
OD1 B:ASP120 4.2 61.5 1.0
CB B:ASP116 4.5 42.7 1.0
CG B:ASP120 4.6 60.9 1.0
CG B:ASP116 4.9 56.8 1.0
OD2 B:ASP116 4.9 70.1 1.0

Magnesium binding site 4 out of 6 in 6lsn

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Magnesium binding site 4 out of 6 in the Crystal Structure of Tubulin-Inhibitor Complex


Mono view


Stereo pair view

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

b:39.5
occ:1.00
O1G C:GTP501 2.1 34.0 1.0
O C:HOH622 2.1 30.1 1.0
O C:HOH621 2.1 31.0 1.0
O C:HOH671 2.2 30.2 1.0
O1B C:GTP501 2.4 38.2 1.0
PG C:GTP501 3.3 48.7 1.0
PB C:GTP501 3.5 39.7 1.0
O2G C:GTP501 3.6 37.7 1.0
NZ D:LYS254 3.6 41.9 1.0
OE1 C:GLU71 3.6 64.5 1.0
O3B C:GTP501 3.8 39.5 1.0
OD2 C:ASP98 3.9 49.2 1.0
O3A C:GTP501 4.0 37.8 1.0
CG C:GLU71 4.1 54.6 1.0
OD2 C:ASP69 4.3 37.0 1.0
OD1 C:ASP69 4.3 40.5 1.0
CB C:ASP98 4.3 42.2 1.0
CD C:GLU71 4.3 54.7 1.0
CB C:GLN11 4.4 26.8 1.0
CG C:ASP98 4.5 43.2 1.0
O3G C:GTP501 4.6 33.4 1.0
OE1 C:GLN11 4.7 48.8 1.0
O1A C:GTP501 4.7 36.1 1.0
CG C:ASP69 4.7 38.5 1.0
N C:GLN11 4.7 27.1 1.0
O2B C:GTP501 4.8 41.0 1.0
CE D:LYS254 4.8 34.5 1.0
PA C:GTP501 5.0 43.3 1.0
O D:HOH720 5.0 40.5 1.0

Magnesium binding site 5 out of 6 in 6lsn

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Magnesium binding site 5 out of 6 in the Crystal Structure of Tubulin-Inhibitor Complex


Mono view


Stereo pair view

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

b:68.9
occ:1.00
O1A D:GDP600 2.3 77.2 1.0
OE1 D:GLN11 2.4 90.1 1.0
CD D:GLN11 3.4 93.3 1.0
PA D:GDP600 3.5 59.1 1.0
O3A D:GDP600 3.8 56.8 1.0
OD1 D:ASN101 3.8 88.4 1.0
NE2 D:GLN11 3.9 90.1 1.0
C5' D:GDP600 4.0 58.9 1.0
O5' D:GDP600 4.1 64.0 1.0
CB D:GLN11 4.5 86.1 1.0
ND2 D:ASN101 4.6 94.9 1.0
CG D:GLN11 4.6 92.3 1.0
CG D:ASN101 4.6 89.2 1.0
O2A D:GDP600 4.7 56.6 1.0
O1B D:GDP600 4.7 71.3 1.0
PB D:GDP600 4.8 64.6 1.0

Magnesium binding site 6 out of 6 in 6lsn

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Magnesium binding site 6 out of 6 in the Crystal Structure of Tubulin-Inhibitor Complex


Mono view


Stereo pair view

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

b:78.3
occ:1.00
O2B F:ACP402 2.5 132.0 1.0
O1G F:ACP402 3.0 147.8 1.0
OE1 F:GLU331 3.1 87.5 1.0
NZ F:LYS74 3.2 86.7 1.0
OE2 F:GLU331 3.3 106.4 1.0
OD1 F:ASN333 3.4 115.7 1.0
CD F:GLU331 3.6 91.6 1.0
PB F:ACP402 3.9 135.9 1.0
CG F:ASN333 4.3 100.2 1.0
PG F:ACP402 4.3 148.4 1.0
C3B F:ACP402 4.5 153.0 1.0
CE F:LYS74 4.5 82.9 1.0
O1B F:ACP402 4.6 133.7 1.0
ND2 F:ASN333 4.6 110.6 1.0
O3A F:ACP402 4.9 121.5 1.0
O2G F:ACP402 5.0 150.7 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 08:52:42 2021

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