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Magnesium in PDB 5xp3: Crystal Structure of Apo T2R-Ttl

Protein crystallography data

The structure of Crystal Structure of Apo T2R-Ttl, PDB code: 5xp3 was solved by Y.Wang, J.Yang, T.Wang, L.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.168, 157.964, 181.408, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 24

Other elements in 5xp3:

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

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Apo T2R-Ttl (pdb code 5xp3). 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 Apo T2R-Ttl, PDB code: 5xp3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5xp3

Go back to Magnesium Binding Sites List in 5xp3
Magnesium binding site 1 out of 4 in the Crystal Structure of Apo T2R-Ttl


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 Apo T2R-Ttl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:42.2
occ:1.00
O1G A:GTP501 2.0 39.9 1.0
O A:HOH630 2.0 37.7 1.0
O A:HOH642 2.1 33.0 1.0
O A:HOH608 2.1 40.6 1.0
O A:HOH604 2.2 42.3 1.0
O1B A:GTP501 2.2 39.8 1.0
PG A:GTP501 3.1 42.0 1.0
PB A:GTP501 3.3 37.8 1.0
O2G A:GTP501 3.4 43.7 1.0
O3B A:GTP501 3.5 45.1 1.0
NZ B:LYS252 3.8 52.1 1.0
O3A A:GTP501 3.9 40.7 1.0
OE2 A:GLU71 4.1 78.5 1.0
OD1 A:ASP69 4.2 44.7 1.0
OD2 A:ASP98 4.2 46.5 1.0
OD2 A:ASP69 4.3 47.3 1.0
CB A:GLN11 4.4 40.0 1.0
O3G A:GTP501 4.4 40.5 1.0
CB A:ASP98 4.4 45.8 1.0
N A:GLN11 4.5 40.2 1.0
O1A A:GTP501 4.5 39.9 1.0
O2B A:GTP501 4.6 44.2 1.0
CG A:ASP98 4.6 47.2 1.0
CG A:ASP69 4.7 47.7 1.0
PA A:GTP501 4.8 38.0 1.0
CD A:GLU71 4.9 72.0 1.0
CE B:LYS252 4.9 49.5 1.0
O B:HOH610 5.0 50.3 1.0

Magnesium binding site 2 out of 4 in 5xp3

Go back to Magnesium Binding Sites List in 5xp3
Magnesium binding site 2 out of 4 in the Crystal Structure of Apo T2R-Ttl


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 Apo T2R-Ttl within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:37.5
occ:1.00
O B:HOH627 2.0 53.2 1.0
OE1 B:GLN11 2.1 47.9 1.0
O1A B:GDP501 2.2 39.7 1.0
O C:HOH678 2.3 47.9 1.0
O B:HOH652 2.5 49.1 1.0
O B:HOH606 2.6 52.1 1.0
CD B:GLN11 3.4 52.7 1.0
O B:HOH665 3.6 62.4 1.0
PA B:GDP501 3.6 34.8 1.0
OD2 B:ASP177 3.8 54.1 1.0
O3A B:GDP501 3.8 36.4 1.0
CB B:GLN11 4.2 39.6 1.0
CG B:GLN11 4.2 48.6 1.0
NE2 B:GLN11 4.3 49.0 1.0
C5' B:GDP501 4.4 35.6 1.0
O5' B:GDP501 4.4 36.1 1.0
OD1 B:ASN99 4.4 42.5 1.0
O B:HOH663 4.6 61.8 1.0
CG B:ASP177 4.7 53.5 1.0
OE1 C:GLU254 4.7 58.1 1.0
O2A B:GDP501 4.8 36.5 1.0
C8 B:GDP501 4.8 39.0 1.0
O1B B:GDP501 4.8 30.2 1.0
PB B:GDP501 5.0 34.5 1.0

Magnesium binding site 3 out of 4 in 5xp3

Go back to Magnesium Binding Sites List in 5xp3
Magnesium binding site 3 out of 4 in the Crystal Structure of Apo T2R-Ttl


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 Apo T2R-Ttl within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:36.7
occ:1.00
O1G C:GTP501 2.0 36.0 1.0
O C:HOH603 2.0 35.5 1.0
O C:HOH611 2.1 40.4 1.0
O C:HOH665 2.1 36.3 1.0
O1B C:GTP501 2.1 34.8 1.0
O C:HOH651 2.1 33.0 1.0
PG C:GTP501 3.2 38.3 1.0
PB C:GTP501 3.3 33.6 1.0
O3B C:GTP501 3.6 38.1 1.0
O2G C:GTP501 3.7 38.4 1.0
O3A C:GTP501 3.8 34.9 1.0
NZ D:LYS252 3.9 41.8 1.0
OD1 C:ASP69 4.1 37.2 1.0
OE1 C:GLU71 4.1 59.3 1.0
OD2 C:ASP69 4.1 34.0 1.0
CB C:GLN11 4.2 34.5 1.0
OD2 C:ASP98 4.2 45.8 1.0
N C:GLN11 4.4 32.4 1.0
O1A C:GTP501 4.5 38.8 1.0
O3G C:GTP501 4.5 32.8 1.0
CB C:ASP98 4.5 42.5 1.0
CG C:ASP69 4.5 37.5 1.0
O2B C:GTP501 4.6 36.0 1.0
PA C:GTP501 4.7 36.4 1.0
NE2 C:GLN11 4.7 43.6 1.0
CG C:ASP98 4.7 42.5 1.0
CA C:GLN11 4.9 35.3 1.0
CB C:GLU71 4.9 52.9 1.0

Magnesium binding site 4 out of 4 in 5xp3

Go back to Magnesium Binding Sites List in 5xp3
Magnesium binding site 4 out of 4 in the Crystal Structure of Apo T2R-Ttl


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 Apo T2R-Ttl within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:69.7
occ:1.00
O1G D:GTP501 2.2 77.9 1.0
O1B D:GTP501 2.7 65.1 1.0
PG D:GTP501 3.5 88.0 1.0
CB D:GLN11 3.6 68.2 1.0
PB D:GTP501 3.7 61.6 1.0
O3G D:GTP501 4.0 79.3 1.0
O3A D:GTP501 4.0 61.7 1.0
O3B D:GTP501 4.0 74.9 1.0
O1A D:GTP501 4.1 63.3 1.0
CD D:GLN11 4.2 85.3 1.0
NE2 D:GLN11 4.3 84.7 1.0
O D:HOH607 4.3 55.9 1.0
OE1 D:GLN11 4.4 84.3 1.0
N D:GLN11 4.4 61.4 1.0
CG D:GLN11 4.5 76.1 1.0
PA D:GTP501 4.6 59.5 1.0
CA D:GLN11 4.6 61.8 1.0
O2G D:GTP501 4.7 74.9 1.0
OD2 D:ASP67 4.8 64.1 1.0
CB D:GLU69 4.8 82.1 1.0
CG D:GLU69 5.0 98.8 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 Sep 30 09:38:00 2024

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