Magnesium in PDB 7cnn: Vinorelbine in Complex with Tubulin

Protein crystallography data

The structure of Vinorelbine in Complex with Tubulin, PDB code: 7cnn was solved by Y.X.Wang, C.Y.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.96 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.878, 156.129, 183, 90, 90, 90
R / Rfree (%) 19.9 / 22.9

Other elements in 7cnn:

The structure of Vinorelbine in Complex with Tubulin 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 Vinorelbine in Complex with Tubulin (pdb code 7cnn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Vinorelbine in Complex with Tubulin, PDB code: 7cnn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7cnn

Go back to Magnesium Binding Sites List in 7cnn
Magnesium binding site 1 out of 5 in the Vinorelbine in Complex with Tubulin


Mono view


Stereo pair view

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

b:44.3
occ:1.00
O1B A:GTP501 2.2 58.5 1.0
O1G A:GTP501 2.6 55.5 1.0
O A:HOH661 2.7 34.2 1.0
OE1 A:GLU71 3.1 62.8 1.0
PB A:GTP501 3.5 51.7 1.0
OD2 A:ASP69 3.6 43.2 1.0
PG A:GTP501 3.7 31.2 1.0
CG A:GLU71 3.7 52.2 1.0
CD A:GLU71 3.8 58.0 1.0
OD1 A:ASP69 3.9 42.4 1.0
O2G A:GTP501 4.0 29.2 1.0
O3B A:GTP501 4.0 38.4 1.0
CB A:GLN11 4.1 32.7 1.0
CG A:ASP69 4.2 39.5 1.0
OD2 A:ASP98 4.3 42.6 1.0
O3A A:GTP501 4.4 29.2 1.0
CB A:ASP98 4.4 37.3 1.0
NZ B:LYS254 4.4 30.8 1.0
N A:GLN11 4.4 33.4 1.0
CG A:ASP98 4.7 37.0 1.0
O2B A:GTP501 4.7 35.5 1.0
OE1 A:GLN11 4.8 41.7 1.0
O1A A:GTP501 4.8 50.9 1.0
CA A:GLN11 4.9 33.9 1.0
CB A:GLU71 5.0 49.9 1.0
OE2 A:GLU71 5.0 55.9 1.0

Magnesium binding site 2 out of 5 in 7cnn

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Magnesium binding site 2 out of 5 in the Vinorelbine in Complex with Tubulin


Mono view


Stereo pair view

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

b:58.8
occ:1.00
NE2 B:GLN11 2.1 54.1 1.0
O B:HOH683 2.3 52.8 1.0
O B:HOH601 2.5 51.1 1.0
O1A B:GDP501 2.5 26.1 1.0
O B:HOH653 2.8 25.6 1.0
CD B:GLN11 3.3 52.0 1.0
PA B:GDP501 3.8 24.7 1.0
OE1 B:GLN11 4.0 53.6 1.0
O3A B:GDP501 4.1 24.3 1.0
CB B:GLN11 4.1 27.5 1.0
CG B:GLN11 4.2 39.4 1.0
C5' B:GDP501 4.5 22.2 1.0
O5' B:GDP501 4.6 21.2 1.0
OD1 B:ASN101 4.7 34.8 1.0
O1B B:GDP501 4.7 25.6 1.0
O2A B:GDP501 4.8 30.4 1.0

Magnesium binding site 3 out of 5 in 7cnn

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Magnesium binding site 3 out of 5 in the Vinorelbine in Complex with Tubulin


Mono view


Stereo pair view

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

b:89.3
occ:1.00
O B:HOH684 3.2 53.3 1.0
OD2 B:ASP120 3.8 49.9 1.0
O B:HOH618 4.1 56.0 1.0
OD1 B:ASP120 4.1 49.0 1.0
CG B:ASP120 4.4 58.7 1.0
CB B:ASP116 4.8 40.1 1.0

Magnesium binding site 4 out of 5 in 7cnn

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Magnesium binding site 4 out of 5 in the Vinorelbine in Complex with Tubulin


Mono view


Stereo pair view

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

b:37.5
occ:1.00
O C:HOH669 1.9 27.4 1.0
O1G C:GTP501 2.2 35.7 1.0
O1B C:GTP501 2.2 32.5 1.0
O C:HOH659 2.2 28.2 1.0
O C:HOH635 2.4 24.2 1.0
OE1 C:GLU71 3.2 44.6 1.0
PG C:GTP501 3.4 36.0 1.0
PB C:GTP501 3.5 28.9 1.0
O3B C:GTP501 3.8 38.4 1.0
O2G C:GTP501 3.8 37.2 1.0
NZ D:LYS254 3.9 47.2 1.0
CG C:GLU71 4.0 29.7 1.0
CD C:GLU71 4.0 37.8 1.0
OD2 C:ASP98 4.0 34.7 1.0
O3A C:GTP501 4.1 40.6 1.0
OD2 C:ASP69 4.1 33.5 1.0
OD1 C:ASP69 4.2 29.9 1.0
CB C:GLN11 4.2 34.3 1.0
CB C:ASP98 4.4 41.4 1.0
OE1 C:GLN11 4.6 38.9 1.0
CG C:ASP69 4.6 33.6 1.0
O3G C:GTP501 4.6 34.3 1.0
CG C:ASP98 4.6 33.5 1.0
N C:GLN11 4.6 30.2 1.0
O2B C:GTP501 4.7 32.5 1.0
O1A C:GTP501 4.7 40.7 1.0
PA C:GTP501 4.9 31.9 1.0
CA C:GLN11 5.0 31.7 1.0

Magnesium binding site 5 out of 5 in 7cnn

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Magnesium binding site 5 out of 5 in the Vinorelbine in Complex with Tubulin


Mono view


Stereo pair view

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

b:63.5
occ:1.00
O2G D:GTP602 2.2 84.9 1.0
O2B D:GTP602 3.0 70.3 1.0
CB D:GLN11 3.5 74.2 1.0
PG D:GTP602 3.5 81.2 1.0
O D:HOH715 3.6 53.4 1.0
O3A D:GTP602 3.7 53.2 1.0
PB D:GTP602 3.8 54.8 1.0
NE2 D:GLN11 3.9 75.0 1.0
O3G D:GTP602 3.9 81.8 1.0
N D:GLN11 4.0 68.7 1.0
OD2 D:ASP69 4.1 63.0 1.0
O3B D:GTP602 4.2 60.5 1.0
CA D:GLN11 4.3 73.3 1.0
CD D:GLN11 4.4 74.2 1.0
OD1 D:ASP69 4.5 63.2 1.0
O2A D:GTP602 4.6 70.3 1.0
CG D:GLN11 4.6 70.6 1.0
PA D:GTP602 4.6 51.4 1.0
O1G D:GTP602 4.7 71.4 1.0
CG D:ASP69 4.8 62.8 1.0
OG1 D:THR74 4.9 77.0 1.0
CG D:GLU71 4.9 73.4 1.0
O1A D:GTP602 5.0 56.2 1.0

Reference:

Y.X.Wang, C.Y.Wu. Vincristinve in Complex with Tubulin To Be Published.
Page generated: Sat Aug 21 16:21:06 2021

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