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Magnesium in PDB 5h74: Crystal Structure of T2R-Ttl-14B Complex

Protein crystallography data

The structure of Crystal Structure of T2R-Ttl-14B Complex, PDB code: 5h74 was solved by Y.Wang, Y.Yu, Q.Chen, J.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.412, 154.025, 185.650, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24.8

Other elements in 5h74:

The structure of Crystal Structure of T2R-Ttl-14B Complex also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-14B Complex (pdb code 5h74). 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-14B Complex, PDB code: 5h74:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5h74

Go back to Magnesium Binding Sites List in 5h74
Magnesium binding site 1 out of 4 in the Crystal Structure of T2R-Ttl-14B 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-14B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:34.4
occ:1.00
O1G A:GTP501 2.0 28.4 1.0
O A:HOH636 2.0 28.3 1.0
O1B A:GTP501 2.0 27.7 1.0
O A:HOH629 2.1 36.6 1.0
O A:HOH645 2.1 23.4 1.0
O A:HOH609 2.3 28.4 1.0
PG A:GTP501 3.2 29.6 1.0
PB A:GTP501 3.2 27.4 1.0
O3B A:GTP501 3.5 29.5 1.0
O3G A:GTP501 3.7 29.9 1.0
O3A A:GTP501 3.8 29.4 1.0
NZ B:LYS252 3.8 34.3 1.0
OD1 A:ASP69 4.2 38.6 1.0
CB A:GLN11 4.3 34.0 1.0
OD2 A:ASP69 4.3 37.9 1.0
OD2 A:ASP98 4.4 35.1 1.0
OE1 A:GLU71 4.4 60.1 1.0
O1A A:GTP501 4.4 28.6 1.0
CB A:ASP98 4.5 36.5 1.0
O2G A:GTP501 4.5 29.9 1.0
N A:GLN11 4.5 35.8 1.0
O2B A:GTP501 4.5 28.9 1.0
CG A:ASP98 4.7 35.7 1.0
CG A:ASP69 4.7 39.2 1.0
PA A:GTP501 4.7 29.5 1.0
NE2 A:GLN11 4.7 34.6 1.0
CA A:GLN11 5.0 34.0 1.0

Magnesium binding site 2 out of 4 in 5h74

Go back to Magnesium Binding Sites List in 5h74
Magnesium binding site 2 out of 4 in the Crystal Structure of T2R-Ttl-14B 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-14B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:38.8
occ:1.00
O B:HOH665 2.1 23.5 1.0
O B:HOH620 2.4 37.8 1.0
O B:HOH664 2.4 35.8 1.0
O B:HOH651 2.8 33.2 1.0
O1B B:GDP501 3.2 30.4 1.0
OE1 B:GLU69 3.3 40.7 1.0
O1A B:GDP501 3.7 28.6 1.0
NE2 B:GLN11 3.7 34.5 1.0
O3A B:GDP501 3.9 29.1 1.0
O B:HOH623 3.9 28.6 1.0
PB B:GDP501 4.1 30.7 1.0
CB B:GLN11 4.2 30.5 1.0
CD B:GLU69 4.2 41.9 1.0
O B:HOH612 4.2 40.4 1.0
O B:HOH626 4.4 28.5 1.0
O B:HOH605 4.4 26.6 1.0
PA B:GDP501 4.4 27.0 1.0
O2B B:GDP501 4.5 30.9 1.0
CD B:GLN11 4.5 33.3 1.0
OE2 B:GLU69 4.5 42.1 1.0
OD1 B:ASN99 4.7 29.1 1.0
CG B:GLN11 4.9 31.4 1.0

Magnesium binding site 3 out of 4 in 5h74

Go back to Magnesium Binding Sites List in 5h74
Magnesium binding site 3 out of 4 in the Crystal Structure of T2R-Ttl-14B 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-14B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:36.6
occ:1.00
O1G C:GTP501 1.9 26.9 1.0
O C:HOH659 2.0 36.0 1.0
O C:HOH663 2.1 33.6 1.0
O C:HOH607 2.1 30.4 1.0
O1B C:GTP501 2.2 28.8 1.0
O C:HOH639 2.3 31.3 1.0
PG C:GTP501 3.1 29.0 1.0
PB C:GTP501 3.2 29.0 1.0
O3B C:GTP501 3.5 28.5 1.0
O3G C:GTP501 3.5 28.3 1.0
O3A C:GTP501 3.7 29.0 1.0
NZ D:LYS252 3.8 32.2 1.0
OD1 C:ASP69 4.2 32.8 1.0
OE1 C:GLU71 4.3 39.1 1.0
OD2 C:ASP98 4.4 35.6 1.0
CB C:GLN11 4.4 28.2 1.0
O2G C:GTP501 4.4 27.0 1.0
O1A C:GTP501 4.4 29.2 1.0
CB C:ASP98 4.4 36.9 1.0
OD2 C:ASP69 4.5 33.9 1.0
N C:GLN11 4.6 28.0 1.0
O2B C:GTP501 4.6 29.0 1.0
PA C:GTP501 4.7 28.2 1.0
CG C:ASP98 4.7 36.8 1.0
CG C:ASP69 4.8 33.5 1.0
NE2 C:GLN11 4.9 29.7 1.0
CE D:LYS252 4.9 32.2 1.0

Magnesium binding site 4 out of 4 in 5h74

Go back to Magnesium Binding Sites List in 5h74
Magnesium binding site 4 out of 4 in the Crystal Structure of T2R-Ttl-14B 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-14B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:71.4
occ:1.00
O2G D:GTP501 2.3 80.0 1.0
OE2 D:GLU69 2.6 83.5 1.0
O1B D:GTP501 2.7 53.0 1.0
PG D:GTP501 3.2 86.8 1.0
O1G D:GTP501 3.3 81.2 1.0
CD D:GLU69 3.6 86.3 1.0
CB D:GLN11 3.6 56.3 1.0
OE1 D:GLN11 3.7 61.4 1.0
PB D:GTP501 3.8 55.4 1.0
O D:HOH604 3.9 45.6 1.0
O3B D:GTP501 3.9 66.8 1.0
CG D:GLU69 4.1 84.2 1.0
O3A D:GTP501 4.2 56.9 1.0
N D:GLN11 4.2 53.0 1.0
O1A D:GTP501 4.3 55.2 1.0
CA D:GLN11 4.4 54.6 1.0
CD D:GLN11 4.5 59.5 1.0
OD2 D:ASP67 4.5 51.8 1.0
CG D:GLN11 4.6 58.0 1.0
CB D:GLU69 4.6 81.3 1.0
O3G D:GTP501 4.6 74.1 1.0
OE1 D:GLU69 4.6 89.3 1.0
PA D:GTP501 4.7 53.6 1.0
OD1 D:ASP67 4.8 49.2 1.0
CG2 D:THR72 4.9 97.8 1.0

Reference:

Y.Wang, Y.Yu, Q.Chen, J.Yang. Structure-Activity Relationship Studies of Tubulysin Analogues: Anticancer N-Alkyltubulysins with Subpicomolar Activity and the Crystal Structure Binding to Tubulin To Be Published.
Page generated: Mon Dec 14 20:26:11 2020

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