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Magnesium in PDB 5ng1: Tubulin-Mtc-Zampanolide Complex

Protein crystallography data

The structure of Tubulin-Mtc-Zampanolide Complex, PDB code: 5ng1 was solved by J.J.Field, B.Pera, J.Estevez Gallego, E.Calvo, J.Rodriguez-Salarichs, G.Saez-Calvo, D.Zuwerra, M.Jordi, A.E.Prota, G.Menchon, J.H.Miller, K.-H.Altmann, J.F.Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.69 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.237, 157.418, 178.858, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 22

Other elements in 5ng1:

The structure of Tubulin-Mtc-Zampanolide Complex also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tubulin-Mtc-Zampanolide Complex (pdb code 5ng1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Tubulin-Mtc-Zampanolide Complex, PDB code: 5ng1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5ng1

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Magnesium binding site 1 out of 5 in the Tubulin-Mtc-Zampanolide Complex


Mono view


Stereo pair view

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

b:36.5
occ:1.00
O1G A:GTP501 2.0 37.3 1.0
O A:HOH622 2.0 39.7 1.0
O A:HOH631 2.0 38.6 1.0
O A:HOH615 2.0 35.7 1.0
O A:HOH634 2.1 39.5 1.0
O1B A:GTP501 2.2 31.7 1.0
PG A:GTP501 3.1 45.4 1.0
PB A:GTP501 3.2 36.9 1.0
O2G A:GTP501 3.4 42.1 1.0
O3B A:GTP501 3.5 49.5 1.0
O3A A:GTP501 3.8 40.0 1.0
NZ B:LYS254 3.9 52.6 1.0
OD1 A:ASP69 4.0 44.0 1.0
OE1 A:GLU71 4.0 65.0 1.0
OD2 A:ASP98 4.1 50.8 1.0
OD2 A:ASP69 4.1 41.9 1.0
CB A:GLN11 4.1 39.2 1.0
N A:GLN11 4.3 36.3 1.0
O3G A:GTP501 4.4 35.7 1.0
CB A:ASP98 4.4 37.1 1.0
CG A:ASP69 4.4 48.3 1.0
CG A:ASP98 4.5 49.7 1.0
O2B A:GTP501 4.5 45.4 1.0
ND2 B:ASN249 4.6 0.1 1.0
O1A A:GTP501 4.7 38.3 1.0
CA A:GLN11 4.8 42.8 1.0
PA A:GTP501 4.8 39.5 1.0
OG1 A:THR145 4.8 39.2 1.0
CE B:LYS254 5.0 39.0 1.0

Magnesium binding site 2 out of 5 in 5ng1

Go back to Magnesium Binding Sites List in 5ng1
Magnesium binding site 2 out of 5 in the Tubulin-Mtc-Zampanolide Complex


Mono view


Stereo pair view

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

b:35.9
occ:1.00
O1A B:GDP501 2.3 36.3 1.0
OE1 B:GLN11 2.3 43.8 1.0
O C:HOH657 2.3 44.0 1.0
O B:HOH664 2.3 42.2 1.0
O B:HOH651 2.4 65.5 1.0
O B:HOH603 2.6 47.5 1.0
PA B:GDP501 3.5 35.9 1.0
CD B:GLN11 3.5 44.9 1.0
O3A B:GDP501 3.7 40.1 1.0
OD2 B:ASP179 3.9 52.5 1.0
CB B:GLN11 4.2 32.0 1.0
OD1 B:ASN101 4.2 46.3 1.0
CG B:GLN11 4.3 39.6 1.0
O5' B:GDP501 4.3 37.8 1.0
C5' B:GDP501 4.4 39.0 1.0
O C:HOH652 4.4 46.6 1.0
OE1 C:GLU254 4.4 56.7 1.0
NE2 B:GLN11 4.5 45.5 1.0
O2A B:GDP501 4.6 36.8 1.0
O1B B:GDP501 4.6 31.5 1.0
C8 B:GDP501 4.8 36.1 1.0
PB B:GDP501 4.8 35.5 1.0
ND2 B:ASN101 4.8 34.4 1.0
CG B:ASP179 4.9 50.0 1.0
CG B:ASN101 4.9 44.0 1.0

Magnesium binding site 3 out of 5 in 5ng1

Go back to Magnesium Binding Sites List in 5ng1
Magnesium binding site 3 out of 5 in the Tubulin-Mtc-Zampanolide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Mtc-Zampanolide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:35.0
occ:1.00
O1G C:GTP501 2.0 33.0 1.0
O C:HOH717 2.0 32.2 1.0
O C:HOH625 2.0 32.0 1.0
O C:HOH610 2.1 34.8 1.0
O1B C:GTP501 2.1 30.6 1.0
O C:HOH607 2.2 37.0 1.0
PG C:GTP501 3.1 36.5 1.0
PB C:GTP501 3.2 30.0 1.0
O3B C:GTP501 3.6 39.9 1.0
O2G C:GTP501 3.6 34.5 1.0
O3A C:GTP501 3.7 34.0 1.0
NZ D:LYS254 3.8 47.3 1.0
OE1 C:GLU71 3.9 64.3 1.0
CB C:GLN11 4.1 28.5 1.0
OD1 C:ASP69 4.1 47.2 1.0
OD2 C:ASP98 4.2 55.0 1.0
OD2 C:ASP69 4.3 33.7 1.0
CG C:GLU71 4.3 47.9 1.0
N C:GLN11 4.4 31.7 1.0
O1A C:GTP501 4.4 35.6 1.0
O3G C:GTP501 4.4 33.5 1.0
O2B C:GTP501 4.5 34.3 1.0
CB C:ASP98 4.5 38.5 1.0
OE1 C:GLN11 4.6 50.3 1.0
CD C:GLU71 4.6 57.0 1.0
ND2 D:ASN249 4.6 78.5 1.0
CG C:ASP69 4.6 36.0 1.0
PA C:GTP501 4.7 35.4 1.0
CG C:ASP98 4.7 46.5 1.0
CA C:GLN11 4.8 34.2 1.0
CE D:LYS254 5.0 45.3 1.0

Magnesium binding site 4 out of 5 in 5ng1

Go back to Magnesium Binding Sites List in 5ng1
Magnesium binding site 4 out of 5 in the Tubulin-Mtc-Zampanolide Complex


Mono view


Stereo pair view

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

b:55.0
occ:1.00
O D:HOH606 2.1 57.6 1.0
OE1 D:GLN11 2.2 72.4 1.0
O D:HOH676 2.5 65.4 1.0
O1A D:GDP501 2.5 64.0 1.0
CD D:GLN11 3.4 66.9 1.0
PA D:GDP501 3.6 56.4 1.0
O3A D:GDP501 3.7 56.5 1.0
CB D:GLN11 4.0 60.5 1.0
O D:HOH683 4.1 59.7 1.0
CG D:GLN11 4.2 63.7 1.0
OD1 D:ASN101 4.3 68.6 1.0
NE2 D:GLN11 4.4 67.2 1.0
C5' D:GDP501 4.4 51.8 1.0
O5' D:GDP501 4.4 56.3 1.0
O1B D:GDP501 4.6 44.5 1.0
O2A D:GDP501 4.7 55.1 1.0
PB D:GDP501 4.8 55.4 1.0
C8 D:GDP501 4.9 47.9 1.0

Magnesium binding site 5 out of 5 in 5ng1

Go back to Magnesium Binding Sites List in 5ng1
Magnesium binding site 5 out of 5 in the Tubulin-Mtc-Zampanolide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Mtc-Zampanolide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg702

b:61.2
occ:1.00
O1G F:ACP701 2.2 94.9 1.0
O1B F:ACP701 2.3 0.8 1.0
OE2 F:GLU331 2.4 81.4 1.0
ND2 F:ASN333 2.4 95.3 1.0
OE1 F:GLU331 3.0 82.8 1.0
CD F:GLU331 3.1 73.8 1.0
NZ F:LYS74 3.2 89.1 1.0
CG F:ASN333 3.6 87.0 1.0
PG F:ACP701 3.6 0.7 1.0
PB F:ACP701 3.7 0.5 1.0
OD1 F:ASN333 4.1 92.8 1.0
O2B F:ACP701 4.1 0.8 1.0
CE F:LYS74 4.2 83.7 1.0
C3B F:ACP701 4.2 0.3 1.0
O2G F:ACP701 4.3 86.8 1.0
CG F:GLU331 4.6 61.0 1.0
O3G F:ACP701 4.7 0.7 1.0
CB F:ASN333 4.8 70.4 1.0
O3A F:ACP701 5.0 0.5 1.0

Reference:

J.J.Field, B.Pera, J.E.Gallego, E.Calvo, J.Rodriguez-Salarichs, G.Saez-Calvo, D.Zuwerra, M.Jordi, J.M.Andreu, A.E.Prota, G.Menchon, J.H.Miller, K.H.Altmann, J.F.Diaz. Zampanolide Binding to Tubulin Indicates Cross-Talk of Taxane Site with Colchicine and Nucleotide Sites. J. Nat. Prod. V. 81 494 2018.
ISSN: ESSN 1520-6025
PubMed: 29023132
DOI: 10.1021/ACS.JNATPROD.7B00704
Page generated: Sun Sep 29 23:15:56 2024

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