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Magnesium in PDB 3n2k: Tubulin-Nsc 613862: RB3 Stathmin-Like Domain Complex

Protein crystallography data

The structure of Tubulin-Nsc 613862: RB3 Stathmin-Like Domain Complex, PDB code: 3n2k was solved by P.Barbier, A.Dorleans, F.Devred, L.Sanz, D.Allegro, C.Alfonso, M.Knossow, V.Peyrot, J.M.Andreu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 4.00
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 326.321, 326.321, 54.057, 90.00, 90.00, 120.00
R / Rfree (%) 22.3 / 25

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tubulin-Nsc 613862: RB3 Stathmin-Like Domain Complex (pdb code 3n2k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Tubulin-Nsc 613862: RB3 Stathmin-Like Domain Complex, PDB code: 3n2k:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3n2k

Go back to Magnesium Binding Sites List in 3n2k
Magnesium binding site 1 out of 3 in the Tubulin-Nsc 613862: RB3 Stathmin-Like Domain Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Nsc 613862: RB3 Stathmin-Like Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:40.0
occ:1.00
O2B A:GTP600 1.5 64.6 1.0
O3G A:GTP600 1.9 65.9 1.0
PB A:GTP600 2.9 66.7 1.0
N A:THR145 3.0 0.8 1.0
CA A:GLY144 3.1 0.9 1.0
CG2 A:THR145 3.2 0.9 1.0
PG A:GTP600 3.2 66.7 1.0
N A:GLY144 3.2 0.3 1.0
CB A:ALA99 3.4 0.1 1.0
O3A A:GTP600 3.5 65.3 1.0
OD1 A:ASP98 3.5 0.2 1.0
O3B A:GTP600 3.5 66.7 1.0
C A:GLY144 3.5 0.7 1.0
NZ B:LYS254 3.8 0.3 1.0
O2G A:GTP600 3.9 66.2 1.0
N A:ASN101 3.9 0.3 1.0
O1B A:GTP600 4.1 66.2 1.0
CA A:THR145 4.1 0.4 1.0
CB A:THR145 4.2 0.2 1.0
CA A:ALA99 4.2 0.3 1.0
N A:ALA100 4.3 0.8 1.0
C A:ALA99 4.3 0.4 1.0
O1G A:GTP600 4.3 65.8 1.0
N A:ALA99 4.4 0.6 1.0
C A:GLY143 4.5 0.6 1.0
CA A:ASN101 4.6 0.7 1.0
OG1 A:THR145 4.7 0.6 1.0
CG A:ASP98 4.7 0.1 1.0
O A:GLY144 4.8 0.8 1.0
C A:ALA100 4.8 0.1 1.0
N A:GLY146 4.8 0.5 1.0
CA A:ALA100 4.9 0.3 1.0
O A:ALA99 5.0 0.8 1.0

Magnesium binding site 2 out of 3 in 3n2k

Go back to Magnesium Binding Sites List in 3n2k
Magnesium binding site 2 out of 3 in the Tubulin-Nsc 613862: RB3 Stathmin-Like Domain Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Nsc 613862: RB3 Stathmin-Like Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:59.7
occ:1.00
OE1 B:GLN11 2.9 0.1 1.0
O2A B:GDP600 3.4 67.4 1.0
OD1 B:ASN101 3.6 0.8 1.0
OE2 C:GLU254 4.0 0.2 1.0
O2B B:GDP600 4.1 65.0 1.0
CD B:GLN11 4.1 0.7 1.0
CG B:ASN101 4.3 0.1 1.0
PA B:GDP600 4.5 67.8 1.0
CD C:GLU254 4.5 0.3 1.0
OD2 B:ASP179 4.5 0.9 1.0
O3A B:GDP600 4.7 66.7 1.0
OE1 C:GLU254 4.7 0.8 1.0
ND2 B:ASN101 4.7 1.0 1.0
PB B:GDP600 4.9 65.1 1.0
O1A B:GDP600 4.9 67.4 1.0
NE2 B:GLN11 5.0 0.0 1.0

Magnesium binding site 3 out of 3 in 3n2k

Go back to Magnesium Binding Sites List in 3n2k
Magnesium binding site 3 out of 3 in the Tubulin-Nsc 613862: RB3 Stathmin-Like Domain Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Nsc 613862: RB3 Stathmin-Like Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:43.0
occ:1.00
O2B C:GTP600 1.6 56.5 1.0
O3G C:GTP600 1.9 60.2 1.0
PB C:GTP600 3.0 57.3 1.0
OD1 C:ASP98 3.1 0.4 1.0
PG C:GTP600 3.1 60.4 1.0
CB C:ALA99 3.2 0.6 1.0
NZ D:LYS254 3.3 0.1 1.0
CA C:GLY144 3.3 0.6 1.0
N C:THR145 3.3 0.5 1.0
CG2 C:THR145 3.4 0.6 1.0
N C:ASN101 3.4 0.2 1.0
N C:GLY144 3.5 0.7 1.0
O3B C:GTP600 3.6 59.0 1.0
N C:ALA100 3.6 0.3 1.0
O2G C:GTP600 3.7 61.5 1.0
O3A C:GTP600 3.8 60.8 1.0
C C:GLY144 3.8 0.2 1.0
CA C:ALA99 3.8 0.0 1.0
C C:ALA99 3.9 0.8 1.0
N C:ALA99 3.9 0.5 1.0
O1B C:GTP600 4.1 55.5 1.0
CA C:ASN101 4.2 0.9 1.0
C C:ALA100 4.3 0.9 1.0
CA C:ALA100 4.3 0.6 1.0
CG C:ASP98 4.3 0.6 1.0
O1G C:GTP600 4.3 60.6 1.0
CA C:THR145 4.5 0.1 1.0
CB C:THR145 4.6 0.5 1.0
O C:ALA99 4.6 0.6 1.0
CE D:LYS254 4.7 0.5 1.0
OD2 C:ASP98 4.8 0.3 1.0
C C:GLY143 4.8 0.7 1.0
N C:ASN102 5.0 0.7 1.0

Reference:

P.Barbier, A.Dorleans, F.Devred, L.Sanz, D.Allegro, C.Alfonso, M.Knossow, V.Peyrot, J.M.Andreu. Stathmin and Interfacial Microtubule Inhibitors Recognize A Naturally Curved Conformation of Tubulin Dimers. J.Biol.Chem. V. 285 31672 2010.
ISSN: ISSN 0021-9258
PubMed: 20675373
DOI: 10.1074/JBC.M110.141929
Page generated: Mon Dec 14 08:27:32 2020

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