Magnesium in PDB 4ihj: Crystal Structure of Tubulin-Stathmin-Ttl-Adp Complex

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Adp Complex, PDB code: 4ihj was solved by A.E.Prota, M.M.Magiera, M.Kuijpers, K.Bargsten, D.Frey, M.Wieser, R.Jaussi, C.C.Hoogenraad, R.A.Kammerer, C.Janke, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.10 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.520, 157.310, 180.990, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 21.7

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

Calcium	(Ca)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of Tubulin-Stathmin-Ttl-Adp Complex (pdb code 4ihj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Tubulin-Stathmin-Ttl-Adp Complex, PDB code: 4ihj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Crystal Structure of Tubulin-Stathmin-Ttl-Adp 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-Adp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:28.9 occ:1.00 O A:HOH811 2.1 25.3 1.0 O1B A:GTP501 2.1 29.5 1.0 O1G A:GTP501 2.1 25.6 1.0 O A:HOH683 2.2 30.7 1.0 O A:HOH681 2.2 30.4 1.0 O A:HOH602 2.3 29.4 1.0 PG A:GTP501 3.2 28.2 1.0 PB A:GTP501 3.2 27.5 1.0 HZ1 B:LYS254 3.2 43.2 1.0 HB2 A:GLN11 3.4 28.8 1.0 O3B A:GTP501 3.5 28.0 1.0 H A:GLN11 3.6 31.9 1.0 O2G A:GTP501 3.6 27.6 1.0 HB2 A:ASP98 3.8 35.7 1.0 O3A A:GTP501 3.8 28.5 1.0 HG3 A:GLU71 3.9 66.4 1.0 HG2 A:GLU71 3.9 66.4 1.0 OD2 A:ASP69 3.9 28.5 1.0 NZ B:LYS254 4.0 36.0 1.0 OE1 A:GLU71 4.0 58.1 1.0 HZ2 B:LYS254 4.1 43.2 1.0 HB3 A:GLN11 4.1 28.8 1.0 OD1 A:ASP69 4.2 28.5 1.0 CB A:GLN11 4.2 24.0 1.0 CG A:GLU71 4.3 55.4 1.0 N A:GLN11 4.3 26.6 1.0 HB3 A:ASP98 4.3 35.7 1.0 HZ3 B:LYS254 4.4 43.2 1.0 OD2 A:ASP98 4.5 29.1 1.0 CB A:ASP98 4.5 29.8 1.0 CG A:ASP69 4.5 35.1 1.0 O2B A:GTP501 4.5 26.9 1.0 O3G A:GTP501 4.5 28.7 1.0 HG1 A:THR145 4.6 39.5 1.0 O1A A:GTP501 4.6 26.0 1.0 O A:HOH758 4.6 46.3 1.0 HA2 A:GLY10 4.7 28.9 1.0 CD A:GLU71 4.7 54.6 1.0 PA A:GTP501 4.8 27.1 1.0 HB A:THR145 4.8 32.7 1.0 CG A:ASP98 4.8 28.9 1.0 CA A:GLN11 4.8 21.7 1.0 OE1 A:GLN11 4.9 38.7 1.0 HE3 B:LYS254 4.9 36.3 1.0 HG21 A:VAL74 4.9 43.1 1.0 OG1 A:THR145 4.9 32.9 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of Tubulin-Stathmin-Ttl-Adp 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-Adp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:27.7 occ:1.00 O B:HOH681 2.3 39.9 1.0 O1A B:GDP501 2.4 22.1 1.0 OE1 B:GLN11 2.4 41.8 1.0 O C:HOH782 2.5 49.8 1.0 O B:HOH621 2.5 38.4 1.0 O B:HOH786 2.6 35.0 1.0 O B:HOH785 2.9 68.0 1.0 HB3 B:GLN11 3.5 31.1 1.0 PA B:GDP501 3.6 23.2 1.0 CD B:GLN11 3.6 53.7 1.0 OD1 B:ASP179 3.7 29.9 1.0 H8 B:GDP501 3.8 32.6 1.0 O3A B:GDP501 3.8 25.6 1.0 HB2 B:GLN11 4.0 31.1 1.0 CB B:GLN11 4.1 25.9 1.0 C5' B:GDP501 4.3 25.0 1.0 O5' B:GDP501 4.3 26.0 1.0 CG B:GLN11 4.4 35.1 1.0 OD1 B:ASN101 4.4 33.9 1.0 HD22 B:ASN101 4.4 43.2 1.0 OE1 C:GLU254 4.6 38.3 1.0 HG2 B:GLN11 4.6 42.1 1.0 NE2 B:GLN11 4.6 41.8 1.0 HE22 B:GLN11 4.6 50.2 1.0 O C:HOH667 4.6 43.2 1.0 O2B B:GDP501 4.7 27.7 1.0 O2A B:GDP501 4.7 23.1 1.0 CG B:ASP179 4.7 42.8 1.0 C8 B:GDP501 4.8 27.2 1.0 PB B:GDP501 4.9 26.4 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of Tubulin-Stathmin-Ttl-Adp 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-Adp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:27.3 occ:1.00 O C:HOH779 2.1 21.9 1.0 O1G C:GTP501 2.1 22.7 1.0 O C:HOH764 2.2 27.4 1.0 O1B C:GTP501 2.2 23.1 1.0 O C:HOH959 2.2 21.5 1.0 O C:HOH807 2.2 27.8 1.0 HZ1 D:LYS254 3.0 35.9 1.0 PG C:GTP501 3.2 24.3 1.0 PB C:GTP501 3.2 23.8 1.0 O3B C:GTP501 3.5 24.2 1.0 HB2 C:GLN11 3.6 19.2 1.0 O2G C:GTP501 3.6 24.4 1.0 O3A C:GTP501 3.7 24.9 1.0 H C:GLN11 3.7 23.6 1.0 HB2 C:ASP98 3.8 36.9 1.0 HG2 C:GLU71 3.8 49.5 1.0 NZ D:LYS254 3.8 29.9 1.0 HZ2 D:LYS254 3.9 35.9 1.0 HG3 C:GLU71 3.9 49.5 1.0 OD2 C:ASP69 4.0 30.0 1.0 OE1 C:GLU71 4.1 42.6 1.0 HB3 C:GLN11 4.1 19.2 1.0 OD1 C:ASP69 4.2 25.9 1.0 HZ3 D:LYS254 4.2 35.9 1.0 HB3 C:ASP98 4.2 36.9 1.0 CB C:GLN11 4.2 16.0 1.0 CG C:GLU71 4.3 41.2 1.0 CB C:ASP98 4.4 30.7 1.0 N C:GLN11 4.4 19.7 1.0 OD2 C:ASP98 4.4 29.7 1.0 O3G C:GTP501 4.5 23.5 1.0 CG C:ASP69 4.5 25.3 1.0 O2B C:GTP501 4.5 22.8 1.0 O1A C:GTP501 4.5 22.6 1.0 O C:HOH650 4.6 46.5 1.0 HG1 C:THR145 4.7 34.1 1.0 CD C:GLU71 4.7 47.5 1.0 HB C:THR145 4.7 31.9 1.0 CG C:ASP98 4.7 28.7 1.0 PA C:GTP501 4.8 24.6 1.0 HA2 C:GLY10 4.9 25.9 1.0 HE3 D:LYS254 4.9 32.1 1.0 CA C:GLN11 4.9 18.6 1.0 CE D:LYS254 4.9 26.7 1.0 O C:HOH934 4.9 70.6 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of Tubulin-Stathmin-Ttl-Adp 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-Adp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:99.3 occ:1.00 O1A D:GDP600 2.7 53.1 1.0 OE1 D:GLN11 3.5 65.0 1.0 H8 D:GDP600 3.7 64.5 1.0 O D:HOH795 3.8 71.8 1.0 C5' D:GDP600 3.8 54.7 1.0 PA D:GDP600 3.9 53.9 1.0 MG D:MG602 4.0 0.2 1.0 H2' D:GDP600 4.1 66.5 1.0 O3A D:GDP600 4.3 54.7 1.0 O5' D:GDP600 4.3 54.7 1.0 OD1 D:ASN101 4.4 57.1 1.0 HH D:TYR224 4.6 72.3 1.0 H3' D:GDP600 4.6 67.3 1.0 CD D:GLN11 4.6 0.6 1.0 HD22 D:ASN101 4.7 82.5 1.0 HB3 D:GLN11 4.7 63.5 1.0 C8 D:GDP600 4.8 53.8 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of Tubulin-Stathmin-Ttl-Adp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Tubulin-Stathmin-Ttl-Adp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:0.2 occ:1.00 O D:HOH795 2.5 71.8 1.0 O D:HOH807 2.7 49.6 1.0 O D:HOH806 2.7 77.5 1.0 O3A D:GDP600 3.0 54.7 1.0 O3B D:GDP600 3.2 54.1 1.0 PB D:GDP600 3.4 54.0 1.0 O2B D:GDP600 3.4 54.4 1.0 OD1 D:ASN101 3.7 57.1 1.0 H D:ASN101 4.0 90.8 1.0 MG D:MG601 4.0 99.3 1.0 O1A D:GDP600 4.1 53.1 1.0 H D:GLY144 4.2 73.0 1.0 PA D:GDP600 4.2 53.9 1.0 H D:GLY100 4.4 60.0 1.0 O D:HOH805 4.5 58.1 1.0 CG D:ASN101 4.5 83.6 1.0 N D:ASN101 4.6 75.6 1.0 HA3 D:GLY143 4.6 57.9 1.0 HB2 D:GLN11 4.7 63.5 1.0 HB3 D:ALA99 4.7 80.0 1.0 HA D:ASN101 4.8 55.6 1.0 HA2 D:GLY143 4.8 57.9 1.0 HD22 D:ASN101 4.8 82.5 1.0 H D:ALA99 4.9 61.1 1.0 O1B D:GDP600 4.9 53.9 1.0 O5' D:GDP600 5.0 54.7 1.0 N D:GLY144 5.0 60.8 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of Tubulin-Stathmin-Ttl-Adp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Tubulin-Stathmin-Ttl-Adp Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg701 b:55.0 occ:1.00 OD2 F:ASP318 2.4 59.6 1.0 OE2 F:GLU331 2.5 53.0 1.0 O3A F:ADP703 2.5 79.0 1.0 O A:HOH817 2.9 92.0 1.0 O F:HOH867 3.0 65.1 1.0 O2A F:ADP703 3.2 77.4 1.0 O1B F:ADP703 3.4 83.0 1.0 HH12 F:ARG222 3.5 82.7 1.0 H5'1 F:ADP703 3.5 88.7 1.0 CD F:GLU331 3.5 0.1 1.0 HG2 F:GLU331 3.5 55.9 1.0 PB F:ADP703 3.5 81.3 1.0 CG F:ASP318 3.6 46.7 1.0 PA F:ADP703 3.6 76.7 1.0 HD22 F:ASN333 3.6 72.5 1.0 HD22 F:ASN242 3.9 0.7 1.0 O2B F:ADP703 3.9 81.4 1.0 CG F:GLU331 4.0 46.6 1.0 NH1 F:ARG222 4.1 68.9 1.0 HH21 F:ARG202 4.2 53.9 1.0 HB3 F:ASP318 4.2 55.7 1.0 HB2 F:ASP318 4.3 55.7 1.0 CB F:ASP318 4.3 46.4 1.0 HG3 F:GLU331 4.3 55.9 1.0 HH11 F:ARG222 4.3 82.7 1.0 ND2 F:ASN242 4.4 88.1 1.0 ND2 F:ASN333 4.4 60.4 1.0 MG F:MG702 4.4 66.2 1.0 C5' F:ADP703 4.5 73.9 1.0 OD1 F:ASP318 4.5 63.9 1.0 HD21 F:ASN242 4.5 0.7 1.0 OE1 F:GLU331 4.6 62.7 1.0 O5' F:ADP703 4.6 75.2 1.0 O3' F:ADP703 4.6 71.1 1.0 O1A F:ADP703 4.7 77.1 1.0 HH22 F:ARG202 4.7 53.9 1.0 H3' F:ADP703 4.7 86.1 1.0 NH2 F:ARG202 4.8 44.9 1.0 HH22 F:ARG222 4.8 67.3 1.0 HO3' F:ADP703 4.8 85.3 1.0 OD1 F:ASN333 4.8 66.5 1.0 O3B F:ADP703 4.8 82.3 1.0 HD21 F:ASN333 5.0 72.5 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of Tubulin-Stathmin-Ttl-Adp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Tubulin-Stathmin-Ttl-Adp Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg702 b:66.2 occ:1.00 O2B F:ADP703 2.4 81.4 1.0 O F:HOH867 2.6 65.1 1.0 OE1 F:GLU331 2.7 62.7 1.0 OE2 F:GLU331 2.7 53.0 1.0 OD1 F:ASN333 2.9 66.5 1.0 CD F:GLU331 3.0 0.1 1.0 HZ2 F:LYS74 3.2 83.4 1.0 HZ1 F:LYS74 3.7 83.4 1.0 PB F:ADP703 3.7 81.3 1.0 NZ F:LYS74 3.9 69.5 1.0 HB2 A:GLU450 3.9 0.2 1.0 O1B F:ADP703 4.0 83.0 1.0 CG F:ASN333 4.0 0.7 1.0 OE2 A:GLU450 4.1 0.2 1.0 HD22 F:ASN333 4.3 72.5 1.0 O3A F:ADP703 4.3 79.0 1.0 HZ3 F:LYS74 4.4 83.4 1.0 MG F:MG701 4.4 55.0 1.0 CG F:GLU331 4.5 46.6 1.0 ND2 F:ASN333 4.6 60.4 1.0 HB3 A:GLU450 4.6 0.2 1.0 CB A:GLU450 4.7 88.5 1.0 CD A:GLU450 4.7 0.2 1.0 HE3 F:LYS74 4.7 0.8 1.0 HG3 F:GLU331 4.8 55.9 1.0 O3B F:ADP703 4.9 82.3 1.0 CE F:LYS74 4.9 0.0 1.0 HG2 F:GLU331 5.0 55.9 1.0

A.E.Prota, M.M.Magiera, M.Kuijpers, K.Bargsten, D.Frey, M.Wieser, R.Jaussi, C.C.Hoogenraad, R.A.Kammerer, C.Janke, M.O.Steinmetz. Structural Basis of Tubulin Tyrosination By Tubulin Tyrosine Ligase. J.Cell Biol. V. 200 259 2013.
ISSN: ISSN 0021-9525
PubMed: 23358242
DOI: 10.1083/JCB.201211017