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Magnesium in PDB 7dae: Epb in Complex with Tubulin

Protein crystallography data

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

Resolution Low / High (Å) 49.71 / 2.39
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.792, 157.21, 181.53, 90, 90, 90
R / Rfree (%) 17.4 / 22.2

Other elements in 7dae:

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

Magnesium binding site 1 out of 4 in 7dae

Go back to Magnesium Binding Sites List in 7dae
Magnesium binding site 1 out of 4 in the Epb 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 Epb in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:26.9
occ:1.00
O A:HOH692 2.1 25.1 1.0
O A:HOH646 2.1 28.6 1.0
O1G A:GTP501 2.1 25.9 1.0
O A:HOH679 2.1 29.5 1.0
O A:HOH619 2.1 25.3 1.0
O1B A:GTP501 2.1 24.0 1.0
PG A:GTP501 3.2 30.7 1.0
PB A:GTP501 3.2 25.0 1.0
O3B A:GTP501 3.6 35.0 1.0
O2G A:GTP501 3.7 26.9 1.0
O3A A:GTP501 3.8 32.8 1.0
NZ B:LYS252 3.9 34.3 1.0
CB A:GLN11 4.1 26.5 1.0
OE1 A:GLU71 4.2 45.1 1.0
OD1 A:ASP69 4.2 29.3 1.0
OD2 A:ASP69 4.3 28.2 1.0
CG A:GLU71 4.3 47.2 1.0
OD2 A:ASP98 4.3 34.5 1.0
N A:GLN11 4.4 25.1 1.0
O1A A:GTP501 4.5 24.9 1.0
O3G A:GTP501 4.5 27.3 1.0
O2B A:GTP501 4.5 33.2 1.0
CB A:ASP98 4.6 31.2 1.0
CG A:ASP69 4.7 27.5 1.0
PA A:GTP501 4.7 25.6 1.0
CD A:GLU71 4.7 44.9 1.0
CG A:ASP98 4.8 32.3 1.0
NE2 A:GLN11 4.8 29.1 1.0
CA A:GLN11 4.8 26.8 1.0

Magnesium binding site 2 out of 4 in 7dae

Go back to Magnesium Binding Sites List in 7dae
Magnesium binding site 2 out of 4 in the Epb 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 Epb in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:27.4
occ:1.00
OE1 B:GLN11 2.2 42.3 1.0
O1A B:GDP501 2.3 27.8 1.0
O C:HOH737 2.3 35.4 1.0
O B:HOH618 3.0 44.3 1.0
CD B:GLN11 3.4 52.1 1.0
OD2 B:ASP177 3.4 55.6 1.0
PA B:GDP501 3.4 25.4 1.0
O3A B:GDP501 3.6 28.5 1.0
OD1 B:ASN99 4.1 32.4 1.0
O5' B:GDP501 4.2 21.6 1.0
C5' B:GDP501 4.2 25.1 1.0
CB B:GLN11 4.3 19.6 1.0
CG B:GLN11 4.3 33.3 1.0
NE2 B:GLN11 4.3 39.4 1.0
O C:HOH705 4.5 43.0 1.0
CG B:ASP177 4.5 36.7 1.0
O1B B:GDP501 4.6 25.5 1.0
O2A B:GDP501 4.6 26.8 1.0
OE1 C:GLU254 4.7 38.7 1.0
PB B:GDP501 4.8 26.5 1.0
C8 B:GDP501 4.8 27.9 1.0
ND2 B:ASN99 4.9 22.4 1.0
CG B:ASN99 4.9 29.4 1.0

Magnesium binding site 3 out of 4 in 7dae

Go back to Magnesium Binding Sites List in 7dae
Magnesium binding site 3 out of 4 in the Epb 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 Epb in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg506

b:63.6
occ:1.00
O B:HOH704 2.4 62.6 1.0
O B:HOH634 2.8 50.4 1.0
OD2 B:ASP118 3.9 47.1 1.0
OD1 B:ASP118 4.0 42.6 1.0
O B:HOH658 4.0 43.4 1.0
CG B:ASP118 4.4 43.8 1.0
CB B:ASP114 4.6 36.4 1.0
OD2 B:ASP114 4.9 58.4 1.0

Magnesium binding site 4 out of 4 in 7dae

Go back to Magnesium Binding Sites List in 7dae
Magnesium binding site 4 out of 4 in the Epb 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 Epb in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:25.2
occ:1.00
O C:HOH688 2.1 27.6 1.0
O1B C:GTP501 2.1 17.2 1.0
O C:HOH627 2.1 26.6 1.0
O1G C:GTP501 2.1 20.7 1.0
O C:HOH654 2.3 23.9 1.0
PB C:GTP501 3.3 22.3 1.0
PG C:GTP501 3.3 27.1 1.0
O3B C:GTP501 3.7 28.7 1.0
OD1 C:ASP69 3.8 27.2 1.0
O2G C:GTP501 3.8 24.8 1.0
OE1 C:GLU71 3.8 49.0 1.0
O3A C:GTP501 3.8 24.8 1.0
OD2 C:ASP69 3.9 26.9 1.0
NZ D:LYS252 4.1 25.3 1.0
CG C:GLU71 4.1 27.9 1.0
CB C:GLN11 4.2 17.0 1.0
CG C:ASP69 4.3 28.0 1.0
N C:GLN11 4.3 22.4 1.0
O C:HOH608 4.4 55.2 1.0
OD2 C:ASP98 4.4 36.2 1.0
CD C:GLU71 4.5 39.8 1.0
CB C:ASP98 4.5 27.9 1.0
O2B C:GTP501 4.6 22.9 1.0
O3G C:GTP501 4.6 21.4 1.0
O1A C:GTP501 4.7 27.6 1.0
O C:HOH637 4.7 34.2 1.0
CA C:GLN11 4.8 25.0 1.0
OE1 C:GLN11 4.8 37.8 1.0
CG C:ASP98 4.9 32.4 1.0
PA C:GTP501 4.9 25.6 1.0
OG1 C:THR145 5.0 25.7 1.0

Reference:

Q.Xiao, T.Xue, W.Shuai, C.Wu, Z.Zhang, T.Zhang, S.Zeng, B.Sun, Y.Wang. High-Resolution X-Ray Structure of Three Microtubule-Stabilizing Agents in Complex with Tubulin Provide A Rationale For Drug Design. Biochem.Biophys.Res.Commun. V. 534 330 2021.
ISSN: ESSN 1090-2104
PubMed: 33272565
DOI: 10.1016/J.BBRC.2020.11.082
Page generated: Wed Oct 2 15:44:03 2024

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