Magnesium in PDB 5yl2: Crystal Structure of T2R-Ttl-Y28 Complex

Protein crystallography data

The structure of Crystal Structure of T2R-Ttl-Y28 Complex, PDB code: 5yl2 was solved by J.H.Yang, T.Yang, J.L.Wen, L.J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.542, 158.199, 181.797, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 25.4

Other elements in 5yl2:

The structure of Crystal Structure of T2R-Ttl-Y28 Complex also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-Y28 Complex (pdb code 5yl2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of T2R-Ttl-Y28 Complex, PDB code: 5yl2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5yl2

Go back to Magnesium Binding Sites List in 5yl2
Magnesium binding site 1 out of 4 in the Crystal Structure of T2R-Ttl-Y28 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 T2R-Ttl-Y28 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:17.0
occ:1.00
O1G A:GTP501 2.0 12.8 1.0
O A:HOH658 2.1 23.5 1.0
O A:HOH637 2.2 25.1 1.0
O1B A:GTP501 2.2 12.7 1.0
O A:HOH687 2.2 16.0 1.0
O A:HOH735 2.3 18.5 1.0
OE1 A:GLU71 3.1 36.6 1.0
PG A:GTP501 3.3 13.0 1.0
PB A:GTP501 3.4 12.4 1.0
O3B A:GTP501 3.7 13.1 1.0
O A:HOH612 3.8 18.9 1.0
O3A A:GTP501 3.9 12.7 1.0
O2G A:GTP501 3.9 13.5 1.0
CD A:GLU71 4.0 33.1 1.0
CB A:GLN11 4.1 15.4 1.0
OD1 A:ASP69 4.1 19.9 1.0
OD2 A:ASP69 4.1 20.2 1.0
OE2 A:GLU71 4.2 33.4 1.0
CB A:ASP98 4.3 25.5 1.0
N A:GLN11 4.3 15.9 1.0
OD2 A:ASP98 4.4 25.1 1.0
OE1 A:GLN11 4.5 16.2 1.0
O3G A:GTP501 4.5 12.8 1.0
CG A:ASP69 4.5 20.6 1.0
CG A:ASP98 4.7 25.8 1.0
O2B A:GTP501 4.7 13.4 1.0
O1A A:GTP501 4.7 12.0 1.0
CA A:GLN11 4.7 15.8 1.0
PA A:GTP501 4.9 12.4 1.0

Magnesium binding site 2 out of 4 in 5yl2

Go back to Magnesium Binding Sites List in 5yl2
Magnesium binding site 2 out of 4 in the Crystal Structure of T2R-Ttl-Y28 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 T2R-Ttl-Y28 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:12.4
occ:1.00
O1A B:GDP501 2.0 15.9 1.0
OE1 B:GLN11 2.2 19.6 1.0
O C:HOH802 2.3 22.1 1.0
O B:HOH660 2.6 19.4 1.0
O B:HOH611 2.8 21.2 1.0
O C:HOH784 3.3 32.6 1.0
OD2 B:ASP177 3.3 31.2 1.0
CD B:GLN11 3.4 19.3 1.0
PA B:GDP501 3.4 15.6 1.0
O3A B:GDP501 3.8 14.9 1.0
CB B:GLN11 4.1 17.4 1.0
C5' B:GDP501 4.2 16.0 1.0
O5' B:GDP501 4.2 15.3 1.0
CG B:GLN11 4.3 18.4 1.0
OD1 B:ASN99 4.3 16.8 1.0
NE2 B:GLN11 4.3 19.5 1.0
CG B:ASP177 4.5 29.5 1.0
O1B B:GDP501 4.5 14.1 1.0
O2A B:GDP501 4.6 16.1 1.0
C8 B:GDP501 4.8 17.2 1.0
OE1 C:GLU254 4.8 25.7 1.0
PB B:GDP501 4.9 14.4 1.0
O C:HOH791 5.0 32.9 1.0

Magnesium binding site 3 out of 4 in 5yl2

Go back to Magnesium Binding Sites List in 5yl2
Magnesium binding site 3 out of 4 in the Crystal Structure of T2R-Ttl-Y28 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 T2R-Ttl-Y28 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:10.6
occ:1.00
O C:HOH609 2.0 14.0 1.0
O1G C:GTP501 2.0 10.7 1.0
O C:HOH676 2.1 23.5 1.0
O C:HOH724 2.1 15.3 1.0
O1B C:GTP501 2.2 11.0 1.0
O C:HOH644 2.2 11.5 1.0
PG C:GTP501 3.3 11.1 1.0
PB C:GTP501 3.3 10.8 1.0
O3B C:GTP501 3.7 10.9 1.0
O3A C:GTP501 3.7 11.5 1.0
O2G C:GTP501 3.9 11.2 1.0
OE1 C:GLU71 4.0 21.4 1.0
O C:HOH815 4.1 16.5 1.0
OD2 C:ASP69 4.1 14.5 1.0
CB C:GLN11 4.1 13.6 1.0
OD1 C:ASP69 4.2 14.6 1.0
NE2 C:GLN11 4.4 15.1 1.0
N C:GLN11 4.4 13.2 1.0
O1A C:GTP501 4.4 12.3 1.0
O3G C:GTP501 4.5 10.6 1.0
OD2 C:ASP98 4.6 19.5 1.0
CB C:ASP98 4.6 19.1 1.0
CG C:ASP69 4.6 14.5 1.0
O2B C:GTP501 4.6 11.0 1.0
PA C:GTP501 4.7 12.0 1.0
CA C:GLN11 4.9 13.5 1.0
CG C:ASP98 5.0 19.3 1.0

Magnesium binding site 4 out of 4 in 5yl2

Go back to Magnesium Binding Sites List in 5yl2
Magnesium binding site 4 out of 4 in the Crystal Structure of T2R-Ttl-Y28 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 T2R-Ttl-Y28 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:22.9
occ:1.00
O2G D:GTP501 2.0 34.7 1.0
O D:HOH618 2.0 19.7 1.0
O1B D:GTP501 2.4 36.6 1.0
PG D:GTP501 2.9 38.9 1.0
O1G D:GTP501 3.0 35.6 1.0
O D:HOH631 3.2 27.9 1.0
PB D:GTP501 3.3 37.8 1.0
O3B D:GTP501 3.5 37.1 1.0
O3A D:GTP501 3.6 38.8 1.0
O1A D:GTP501 4.0 41.1 1.0
CB D:GLN11 4.1 37.6 1.0
O3G D:GTP501 4.3 34.0 1.0
PA D:GTP501 4.3 39.4 1.0
OE1 D:GLN11 4.6 41.9 1.0
N D:GLN11 4.6 36.6 1.0
O2B D:GTP501 4.7 40.5 1.0
OD2 D:ASP67 4.8 39.3 1.0
OD1 D:ASP67 4.8 38.1 1.0
CD D:GLN11 4.9 41.3 1.0
CB D:GLU69 4.9 55.1 1.0
O2A D:GTP501 4.9 39.6 1.0
CA D:GLN11 5.0 36.4 1.0

Reference:

Y.Jianhong, Y.Wei, Y.Yamei, W.Yuxi, Y.Tao, X.Linlin, Y.Xue, L.Caofeng, L.Zuowei, C.Xiaoxin, H.Mengshi, Z.Li, Q.Qiang, P.Heying, L.Dan, W.Fang, B.Peng, W.Jiaolin, Y.Haoyu, C.Lijuan. The Compound Millepachine and Its Derivatives Inhibit Tubulin Polymerization By Irreversibly Binding to the Colchicine-Binding Site in Beta-Tubulin. J. Biol. Chem. 2018.
ISSN: ESSN 1083-351X
PubMed: 29691282
DOI: 10.1074/JBC.RA117.001658
Page generated: Mon Dec 14 22:13:54 2020

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