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Magnesium in PDB 4zi7: Crystal Structure of Tubulin-Stathmin-Ttl-HTI286 Complex

Protein crystallography data

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-HTI286 Complex, PDB code: 4zi7 was solved by Y.Wang, R.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.367, 157.343, 181.963, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23.9

Other elements in 4zi7:

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-HTI286 Complex also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Tubulin-Stathmin-Ttl-HTI286 Complex (pdb code 4zi7). 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 Tubulin-Stathmin-Ttl-HTI286 Complex, PDB code: 4zi7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4zi7

Go back to Magnesium Binding Sites List in 4zi7
Magnesium binding site 1 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-HTI286 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 Tubulin-Stathmin-Ttl-HTI286 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:35.4
occ:1.00
O1G A:GTP501 1.8 28.7 1.0
O A:HOH603 1.8 36.9 1.0
O1B A:GTP501 2.0 26.6 1.0
O A:HOH625 2.0 27.7 1.0
O A:HOH629 2.1 29.5 1.0
O A:HOH628 2.1 22.3 1.0
PG A:GTP501 2.8 31.8 1.0
PB A:GTP501 3.0 31.4 1.0
O3B A:GTP501 3.2 33.9 1.0
O2G A:GTP501 3.3 31.7 1.0
O3A A:GTP501 3.7 32.8 1.0
NZ B:LYS254 3.8 45.0 1.0
OD1 A:ASP69 4.2 54.6 1.0
O3G A:GTP501 4.2 33.9 1.0
OD2 A:ASP98 4.3 46.3 1.0
O1A A:GTP501 4.3 32.4 1.0
O2B A:GTP501 4.3 34.5 1.0
OD2 A:ASP69 4.4 47.9 1.0
OE1 A:GLU71 4.5 70.8 1.0
CG A:GLU71 4.5 68.6 1.0
CB A:ASP98 4.5 42.8 1.0
CB A:GLN11 4.5 35.6 1.0
N A:GLN11 4.6 37.2 1.0
PA A:GTP501 4.6 31.7 1.0
CG A:ASP98 4.6 46.2 1.0
OG1 A:THR145 4.8 33.3 1.0
CG A:ASP69 4.8 47.4 1.0
CE B:LYS254 4.9 41.0 1.0
CD A:GLU71 5.0 74.3 1.0

Magnesium binding site 2 out of 4 in 4zi7

Go back to Magnesium Binding Sites List in 4zi7
Magnesium binding site 2 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-HTI286 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 Tubulin-Stathmin-Ttl-HTI286 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:57.5
occ:1.00
O B:HOH608 1.9 75.6 1.0
O B:HOH602 2.9 42.2 1.0
O1B B:GDP501 2.9 30.9 1.0
O C:HOH664 3.1 53.9 1.0
OE2 B:GLU71 3.2 85.8 1.0
O B:HOH632 3.3 42.3 1.0
NE2 B:GLN11 3.4 64.3 1.0
CB B:GLN11 3.4 44.0 1.0
O1A B:GDP501 3.8 31.9 1.0
PB B:GDP501 3.9 29.6 1.0
O3A B:GDP501 3.9 28.9 1.0
O B:HOH601 4.1 30.4 1.0
CD B:GLN11 4.1 65.7 1.0
O3B B:GDP501 4.2 34.5 1.0
O B:HOH622 4.2 56.5 1.0
PA B:GDP501 4.2 30.0 1.0
CG B:GLN11 4.3 53.7 1.0
CD B:GLU71 4.3 73.8 1.0
N B:GLN11 4.4 39.5 1.0
CA B:GLN11 4.5 38.7 1.0
O2A B:GDP501 4.9 30.5 1.0
CG B:GLU71 4.9 62.4 1.0

Magnesium binding site 3 out of 4 in 4zi7

Go back to Magnesium Binding Sites List in 4zi7
Magnesium binding site 3 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-HTI286 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 Tubulin-Stathmin-Ttl-HTI286 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:37.8
occ:1.00
O C:HOH605 1.8 32.3 1.0
O C:HOH629 1.9 29.7 1.0
O1G C:GTP502 1.9 29.9 1.0
O1B C:GTP502 2.1 28.8 1.0
O C:HOH621 2.1 30.7 1.0
O C:HOH616 2.1 28.8 1.0
PG C:GTP502 3.1 36.0 1.0
PB C:GTP502 3.1 29.3 1.0
O3B C:GTP502 3.5 28.3 1.0
O2G C:GTP502 3.6 34.1 1.0
O3A C:GTP502 3.8 30.4 1.0
OD1 C:ASP69 3.8 42.6 1.0
OE1 C:GLU71 3.9 68.7 1.0
NZ D:LYS254 3.9 42.6 1.0
OD2 C:ASP69 4.0 42.6 1.0
OD2 C:ASP98 4.1 42.7 1.0
CB C:GLN11 4.3 31.5 1.0
O2B C:GTP502 4.4 31.6 1.0
CG C:ASP69 4.4 40.0 1.0
N C:GLN11 4.4 32.4 1.0
O3G C:GTP502 4.4 28.6 1.0
CB C:ASP98 4.4 44.2 1.0
O1A C:GTP502 4.5 34.5 1.0
CG C:ASP98 4.6 41.4 1.0
PA C:GTP502 4.7 35.2 1.0
OG1 C:THR145 4.7 36.8 1.0
CD C:GLU71 4.9 68.9 1.0
CA C:GLN11 4.9 29.9 1.0

Magnesium binding site 4 out of 4 in 4zi7

Go back to Magnesium Binding Sites List in 4zi7
Magnesium binding site 4 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-HTI286 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 Tubulin-Stathmin-Ttl-HTI286 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:72.3
occ:1.00
O D:HOH605 1.6 46.5 1.0
O D:HOH602 1.7 30.7 1.0
O D:HOH610 1.8 63.4 1.0
O D:HOH603 2.0 35.2 1.0
O1B D:GDP501 2.5 44.1 1.0
O3B D:GDP501 2.8 51.3 1.0
PB D:GDP501 3.0 58.0 1.0
O D:HOH601 3.3 37.7 1.0
O3A D:GDP501 3.9 52.9 1.0
OG1 D:THR145 4.0 71.5 1.0
CG D:GLU71 4.2 87.3 1.0
O2B D:GDP501 4.3 66.2 1.0
OD1 D:ASP69 4.3 57.6 1.0
O1A D:GDP501 4.5 60.5 1.0
PA D:GDP501 4.7 51.6 1.0
CB D:THR145 4.7 58.5 1.0
CB D:GLN11 4.8 64.2 1.0
N D:GLN11 4.8 52.5 1.0
OD2 D:ASP69 4.9 58.5 1.0
OE1 D:GLN11 4.9 79.5 1.0
CB D:GLU71 5.0 73.2 1.0

Reference:

Y.Wang, F.W.Benz, Y.Wu, Q.Wang, Y.Chen, X.Chen, H.Li, Y.Zhang, R.Zhang, J.Yang. Structural Insights Into the Pharmacophore of Vinca Domain Inhibitors of Microtubules Mol.Pharmacol. V. 89 233 2016.
ISSN: ESSN 1521-0111
PubMed: 26660762
DOI: 10.1124/MOL.115.100149
Page generated: Sun Sep 29 00:02:39 2024

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