Magnesium in PDB 7dad: Epd in Complex with Tubulin

Protein crystallography data

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

Resolution Low / High (Å) 49.91 / 2.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.163, 158.506, 181.605, 90, 90, 90
R / Rfree (%) 17.9 / 22.6

Other elements in 7dad:

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

Magnesium binding site 1 out of 5 in 7dad

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Magnesium binding site 1 out of 5 in the Epd 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 Epd in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:31.6
occ:1.00
O1G A:GTP501 2.1 38.0 1.0
O1B A:GTP501 2.4 29.9 1.0
PG A:GTP501 3.3 34.5 1.0
O2G A:GTP501 3.5 29.1 1.0
PB A:GTP501 3.6 26.8 1.0
OE1 A:GLU71 3.7 61.5 1.0
O3B A:GTP501 3.9 42.8 1.0
CG A:GLU71 3.9 50.6 1.0
OD2 A:ASP69 3.9 43.7 1.0
NZ B:LYS252 4.0 41.4 1.0
OD1 A:ASP69 4.0 40.2 1.0
O3A A:GTP501 4.1 51.0 1.0
CB A:GLN11 4.2 36.1 1.0
CD A:GLU71 4.3 63.1 1.0
CG A:ASP69 4.4 38.4 1.0
N A:GLN11 4.5 32.2 1.0
CB A:ASP98 4.5 29.8 1.0
O3G A:GTP501 4.6 26.3 1.0
NE2 A:GLN11 4.7 36.2 1.0
OD2 A:ASP98 4.7 41.9 1.0
O1A A:GTP501 4.8 29.1 1.0
CG A:ASP98 4.8 35.2 1.0
O2B A:GTP501 4.8 42.7 1.0
CA A:GLN11 4.9 32.4 1.0

Magnesium binding site 2 out of 5 in 7dad

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Magnesium binding site 2 out of 5 in the Epd 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 Epd in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:37.9
occ:1.00
OE1 B:GLN11 2.4 42.2 1.0
O1A B:GDP501 2.6 40.1 1.0
CD B:GLN11 3.5 49.0 1.0
OD2 B:ASP177 3.6 55.4 1.0
PA B:GDP501 3.8 19.6 1.0
O3A B:GDP501 3.8 40.1 1.0
OD1 B:ASN99 3.8 26.1 1.0
OE1 C:GLU254 4.3 34.6 1.0
NE2 B:GLN11 4.3 30.4 1.0
C5' B:GDP501 4.4 22.3 1.0
CG B:ASP177 4.5 44.6 1.0
CG B:GLN11 4.5 33.0 1.0
O5' B:GDP501 4.5 17.9 1.0
CB B:GLN11 4.7 31.0 1.0
CG B:ASN99 4.8 25.8 1.0
O2A B:GDP501 4.9 30.4 1.0
CB B:ASP177 4.9 38.1 1.0
ND2 B:ASN99 4.9 25.2 1.0
PB B:GDP501 5.0 29.6 1.0
CD C:GLU254 5.0 45.4 1.0
OE2 C:GLU254 5.0 48.2 1.0

Magnesium binding site 3 out of 5 in 7dad

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Magnesium binding site 3 out of 5 in the Epd 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 Epd in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg506

b:68.9
occ:1.00
OD2 B:ASP118 3.9 58.3 1.0
OD1 B:ASP118 4.0 38.1 1.0
CG B:ASP118 4.4 53.6 1.0
CB B:ASP114 4.4 29.3 1.0
OD2 B:ASP114 4.7 72.3 1.0
CG B:ASP114 4.8 37.8 1.0

Magnesium binding site 4 out of 5 in 7dad

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Magnesium binding site 4 out of 5 in the Epd 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 Epd in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:28.2
occ:1.00
O1B C:GTP501 2.2 40.2 1.0
O1G C:GTP501 2.2 34.7 1.0
PG C:GTP501 3.4 29.9 1.0
OE1 C:GLU71 3.4 47.8 1.0
PB C:GTP501 3.5 23.6 1.0
O2G C:GTP501 3.7 29.6 1.0
CG C:GLU71 3.9 40.8 1.0
OD2 C:ASP69 3.9 28.8 1.0
O3B C:GTP501 3.9 39.0 1.0
NZ D:LYS252 4.0 26.2 1.0
CD C:GLU71 4.1 47.5 1.0
OD1 C:ASP69 4.2 31.0 1.0
OD2 C:ASP98 4.2 46.4 1.0
CB C:ASP98 4.3 35.8 1.0
O3A C:GTP501 4.3 47.4 1.0
CB C:GLN11 4.4 25.9 1.0
CG C:ASP69 4.5 26.1 1.0
CG C:ASP98 4.6 36.7 1.0
N C:GLN11 4.6 19.1 1.0
O2B C:GTP501 4.6 31.7 1.0
O3G C:GTP501 4.7 18.1 1.0
O1A C:GTP501 4.8 24.3 1.0
OE1 C:GLN11 4.8 38.2 1.0

Magnesium binding site 5 out of 5 in 7dad

Go back to Magnesium Binding Sites List in 7dad
Magnesium binding site 5 out of 5 in the Epd 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 Epd in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg402

b:75.4
occ:1.00
O2B F:ACP401 2.5 99.3 1.0
O2G F:ACP401 2.5 111.0 1.0
OE2 F:GLU331 2.7 98.5 1.0
OD1 F:ASN333 2.8 102.6 1.0
OE1 F:GLU331 2.8 85.3 1.0
CD F:GLU331 3.1 93.2 1.0
PB F:ACP401 3.5 128.4 1.0
PG F:ACP401 3.6 128.6 1.0
C3B F:ACP401 3.7 102.1 1.0
CG F:ASN333 4.0 89.6 1.0
NZ F:LYS74 4.0 87.2 1.0
O3A F:ACP401 4.3 109.0 1.0
O1G F:ACP401 4.3 99.5 1.0
CG F:GLU331 4.6 71.1 1.0
CE F:LYS74 4.8 79.0 1.0
O1B F:ACP401 4.8 124.4 1.0
ND2 F:ASN333 4.8 96.1 1.0
O3G F:ACP401 4.8 116.7 1.0
CB F:ASN333 5.0 52.6 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: Sat Apr 3 17:03:45 2021

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