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Magnesium in PDB 5yls: Crystal Structure of T2R-Ttl-Y50 Complex

Protein crystallography data

The structure of Crystal Structure of T2R-Ttl-Y50 Complex, PDB code: 5yls was solved by J.H.Yang, L.J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.79 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.767, 159.054, 183.151, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.3

Other elements in 5yls:

The structure of Crystal Structure of T2R-Ttl-Y50 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-Y50 Complex (pdb code 5yls). 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-Y50 Complex, PDB code: 5yls:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5yls

Go back to Magnesium Binding Sites List in 5yls
Magnesium binding site 1 out of 4 in the Crystal Structure of T2R-Ttl-Y50 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-Y50 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:49.0
occ:1.00
O1G A:GTP501 1.9 44.2 1.0
O1B A:GTP501 2.0 41.3 1.0
O A:HOH603 2.0 48.1 1.0
O A:HOH602 2.1 54.0 1.0
O A:HOH604 2.4 71.9 1.0
O A:HOH605 2.5 29.4 1.0
PG A:GTP501 3.1 45.5 1.0
PB A:GTP501 3.1 43.2 1.0
O3B A:GTP501 3.4 45.1 1.0
O2G A:GTP501 3.6 44.8 1.0
O3A A:GTP501 3.8 44.1 1.0
O A:HOH601 3.9 35.1 1.0
OD1 A:ASP69 4.2 62.8 1.0
CB A:GLN11 4.3 54.7 1.0
OD2 A:ASP69 4.3 67.6 1.0
CB A:ASP98 4.3 60.1 1.0
O3G A:GTP501 4.4 42.6 1.0
O2B A:GTP501 4.4 44.7 1.0
OE2 A:GLU71 4.5 80.3 1.0
N A:GLN11 4.5 55.2 1.0
CG A:ASP98 4.6 61.8 1.0
OG1 A:THR145 4.6 53.1 1.0
OD2 A:ASP98 4.6 63.1 1.0
O1A A:GTP501 4.7 44.6 1.0
CG A:ASP69 4.7 66.3 1.0
PA A:GTP501 4.7 44.7 1.0
CD A:GLU71 4.8 77.9 1.0
NZ B:LYS252 4.8 53.5 1.0
OE1 A:GLN11 4.9 57.2 1.0

Magnesium binding site 2 out of 4 in 5yls

Go back to Magnesium Binding Sites List in 5yls
Magnesium binding site 2 out of 4 in the Crystal Structure of T2R-Ttl-Y50 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-Y50 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:48.6
occ:1.00
O C:HOH605 2.0 67.1 1.0
O B:HOH605 2.2 63.4 1.0
OE1 B:GLN11 2.2 65.7 1.0
O B:HOH606 2.3 41.7 1.0
O1A B:GDP501 2.4 43.4 1.0
O B:HOH604 2.8 46.1 1.0
O B:HOH607 3.1 83.4 1.0
CD B:GLN11 3.4 65.5 1.0
PA B:GDP501 3.6 42.3 1.0
O3A B:GDP501 3.7 44.6 1.0
CB B:GLN11 4.1 58.4 1.0
OD2 B:ASP177 4.2 73.9 1.0
NE2 B:GLN11 4.2 67.2 1.0
CG B:GLN11 4.3 62.5 1.0
C5' B:GDP501 4.4 40.7 1.0
O5' B:GDP501 4.5 39.4 1.0
OD1 B:ASN99 4.7 48.8 1.0
OE1 C:GLU254 4.7 72.5 1.0
O1B B:GDP501 4.7 41.5 1.0
O2A B:GDP501 4.8 44.0 1.0
CG B:ASP177 4.8 73.1 1.0
PB B:GDP501 4.9 44.2 1.0

Magnesium binding site 3 out of 4 in 5yls

Go back to Magnesium Binding Sites List in 5yls
Magnesium binding site 3 out of 4 in the Crystal Structure of T2R-Ttl-Y50 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-Y50 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:40.2
occ:1.00
O C:HOH602 2.0 29.8 1.0
O1B C:GTP501 2.0 41.7 1.0
O1G C:GTP501 2.1 39.1 1.0
O C:HOH603 2.2 62.3 1.0
O C:HOH601 2.2 50.5 1.0
O C:HOH604 2.6 24.4 1.0
PG C:GTP501 3.1 39.7 1.0
PB C:GTP501 3.2 43.0 1.0
O2G C:GTP501 3.4 40.5 1.0
O3B C:GTP501 3.4 42.3 1.0
OE1 C:GLU71 3.5 60.2 1.0
O3A C:GTP501 3.8 44.6 1.0
OD1 C:ASP69 4.0 44.7 1.0
O D:HOH601 4.1 38.4 1.0
OD2 C:ASP69 4.3 46.1 1.0
CB C:ASP98 4.3 53.5 1.0
CB C:GLN11 4.4 44.6 1.0
OD2 C:ASP98 4.5 54.7 1.0
O3G C:GTP501 4.5 37.6 1.0
O2B C:GTP501 4.5 43.5 1.0
N C:GLN11 4.5 43.4 1.0
CG C:ASP98 4.6 55.0 1.0
CG C:ASP69 4.6 46.2 1.0
OG1 C:THR145 4.6 44.7 1.0
NZ D:LYS252 4.7 54.9 1.0
CD C:GLU71 4.8 59.4 1.0
O1A C:GTP501 4.8 45.9 1.0
PA C:GTP501 4.8 45.1 1.0

Magnesium binding site 4 out of 4 in 5yls

Go back to Magnesium Binding Sites List in 5yls
Magnesium binding site 4 out of 4 in the Crystal Structure of T2R-Ttl-Y50 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-Y50 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:90.1
occ:1.00
O2G D:GTP501 3.1 92.0 1.0
O1B D:GTP501 3.3 93.1 1.0
O1G D:GTP501 3.4 93.0 1.0
CB D:GLN11 3.5 0.6 1.0
CB D:GLU69 3.6 0.9 1.0
OD2 D:ASP67 3.7 95.1 1.0
PG D:GTP501 3.8 96.3 1.0
CG D:GLU69 3.8 0.1 1.0
CD D:GLN11 4.0 0.3 1.0
OD1 D:ASP67 4.1 96.8 1.0
OE1 D:GLN11 4.1 0.6 1.0
N D:GLN11 4.1 96.2 1.0
OG1 D:THR72 4.1 0.6 1.0
CG D:GLN11 4.1 0.5 1.0
CA D:GLN11 4.2 0.5 1.0
CG D:ASP67 4.3 96.2 1.0
NE2 D:GLN11 4.4 0.2 1.0
PB D:GTP501 4.5 94.4 1.0
CG2 D:THR72 4.6 0.1 1.0
O3B D:GTP501 4.6 96.3 1.0
O3A D:GTP501 4.9 96.5 1.0
CD D:GLU69 4.9 0.8 1.0
OE1 D:GLU69 5.0 0.2 1.0

Reference:

J.H.Yang, W.Yan, Y.M.Yu, Y.X.Wang, T.Yang, L.L.Xue, X.Yuan, C.F.Long, Z.W.Liu, X.X.Chen, M.S.Hu, L.Zheng, Q.Qiu, H.Y.Pei, D.Li, F.Wang, P.Bai, J.L.Wen, H.Y.Ye, L.J.Chen. The Compound Millepachine and Its Derivatives Inhibit Tubulin Polymerization By Irreversibly Binding to the Colchicine-Binding Site in Beta-Tubulin. J. Biol. Chem. V. 293 9461 2018.
ISSN: ESSN 1083-351X
PubMed: 29691282
DOI: 10.1074/JBC.RA117.001658
Page generated: Mon Sep 30 11:22:42 2024

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