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Magnesium in PDB 4iij: Crystal Structure of Tubulin-Stathmin-Ttl-Apo Complex

Protein crystallography data

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Apo Complex, PDB code: 4iij 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) 62.28 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 103.530, 155.910, 181.020, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23.5

Other elements in 4iij:

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

Calcium (Ca) 3 atoms
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 5 in 4iij

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

b:40.0
occ:1.00
O A:HOH612 2.4 48.8 1.0
O A:HOH611 2.4 49.3 1.0
O1G A:GTP501 2.5 29.6 1.0
O A:HOH601 2.5 33.4 1.0
O A:HOH610 2.5 55.0 1.0
O1B A:GTP501 2.6 32.7 1.0
HB2 A:GLN11 2.9 56.3 1.0
OE2 A:GLU71 3.2 72.5 1.0
HZ1 B:LYS254 3.3 74.1 1.0
H A:GLN11 3.7 52.0 1.0
PB A:GTP501 3.7 37.6 1.0
HZ2 B:LYS254 3.8 74.1 1.0
PG A:GTP501 3.8 46.6 1.0
CB A:GLN11 3.8 46.9 1.0
HB3 A:GLN11 3.9 56.3 1.0
OE1 A:GLN11 3.9 55.3 1.0
O3A A:GTP501 3.9 63.2 1.0
NZ B:LYS254 3.9 61.8 1.0
HZ3 B:LYS254 4.2 74.1 1.0
O3B A:GTP501 4.2 60.5 1.0
OD1 A:ASP69 4.2 55.6 1.0
O2G A:GTP501 4.3 39.0 1.0
OD2 A:ASP69 4.3 56.0 1.0
N A:GLN11 4.3 43.3 1.0
HB2 A:ASP98 4.3 64.9 1.0
HG21 A:VAL74 4.4 60.2 1.0
CD A:GLU71 4.4 72.7 1.0
HB3 A:GLU71 4.5 72.1 1.0
O1A A:GTP501 4.6 47.9 1.0
CD A:GLN11 4.6 51.5 1.0
CA A:GLN11 4.6 50.5 1.0
CG A:GLN11 4.7 50.6 1.0
HB3 A:ASP98 4.7 64.9 1.0
CG A:ASP69 4.7 58.0 1.0
OD2 A:ASP98 4.8 49.2 1.0
PA A:GTP501 4.8 39.7 1.0
HG23 A:VAL74 4.8 60.2 1.0
HA A:GLN11 4.9 60.6 1.0
CB A:ASP98 4.9 54.1 1.0
HG3 A:GLN11 4.9 60.8 1.0
O3G A:GTP501 5.0 42.1 1.0
OE1 A:GLU71 5.0 74.6 1.0
O2B A:GTP501 5.0 62.1 1.0

Magnesium binding site 2 out of 5 in 4iij

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Magnesium binding site 2 out of 5 in the Crystal Structure of Tubulin-Stathmin-Ttl-Apo 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-Apo Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:41.3
occ:1.00
O1A B:GDP501 2.4 44.6 1.0
OE1 B:GLN11 2.6 51.6 1.0
HD22 B:ASN101 3.2 54.1 1.0
OD1 B:ASP179 3.5 52.2 1.0
PA B:GDP501 3.6 31.8 1.0
CD B:GLN11 3.6 55.5 1.0
H8 B:GDP501 3.8 40.3 1.0
O3A B:GDP501 3.8 40.3 1.0
HB3 B:GLN11 3.8 56.1 1.0
ND2 B:ASN101 4.0 45.1 1.0
C5' B:GDP501 4.1 26.6 1.0
HE22 B:GLN11 4.2 89.7 1.0
OE1 C:GLU254 4.2 62.5 1.0
O5' B:GDP501 4.3 22.0 1.0
HB2 B:GLN11 4.3 56.1 1.0
NE2 B:GLN11 4.3 74.7 1.0
CB B:GLN11 4.4 46.8 1.0
HD21 B:ASN101 4.4 54.1 1.0
CG B:ASP179 4.6 54.0 1.0
CG B:GLN11 4.6 53.4 1.0
HB3 B:ASP179 4.7 58.1 1.0
C8 B:GDP501 4.8 33.6 1.0
O2A B:GDP501 4.8 43.2 1.0
OD1 B:ASN101 4.9 51.0 1.0
CG B:ASN101 4.9 40.7 1.0
CD C:GLU254 5.0 61.2 1.0
H2' B:GDP501 5.0 56.2 1.0

Magnesium binding site 3 out of 5 in 4iij

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

b:42.6
occ:1.00
O C:HOH602 2.5 37.1 1.0
O1G C:GTP501 2.6 30.8 1.0
O1B C:GTP501 2.7 34.5 1.0
HB2 C:GLN11 3.2 43.1 1.0
OE2 C:GLU71 3.5 65.5 1.0
HZ1 D:LYS254 3.5 60.3 1.0
OD1 C:ASP69 3.8 41.0 1.0
H C:GLN11 3.8 37.9 1.0
PG C:GTP501 3.9 35.0 1.0
PB C:GTP501 3.9 33.2 1.0
HB3 C:GLU71 3.9 64.7 1.0
HZ2 D:LYS254 4.0 60.3 1.0
NZ D:LYS254 4.1 50.2 1.0
OD2 C:ASP69 4.1 48.0 1.0
HB2 C:ASP98 4.1 43.7 1.0
CB C:GLN11 4.2 36.0 1.0
HZ3 D:LYS254 4.2 60.3 1.0
O3A C:GTP501 4.2 58.8 1.0
HG21 C:VAL74 4.2 60.4 1.0
O2G C:GTP501 4.2 31.6 1.0
CG C:ASP69 4.3 44.9 1.0
O3B C:GTP501 4.4 51.0 1.0
OE1 C:GLN11 4.4 54.9 1.0
HB3 C:ASP98 4.4 43.7 1.0
N C:GLN11 4.5 31.5 1.0
HB3 C:GLN11 4.5 43.1 1.0
CD C:GLU71 4.5 68.8 1.0
HG23 C:VAL74 4.6 60.4 1.0
OD2 C:ASP98 4.6 48.3 1.0
CB C:ASP98 4.7 36.4 1.0
CB C:GLU71 4.7 53.9 1.0
HB2 C:GLU71 4.8 64.7 1.0
CA C:GLN11 4.8 33.6 1.0
CG2 C:VAL74 4.9 50.3 1.0
HG1 C:THR145 4.9 42.3 1.0
HA C:GLN11 4.9 40.4 1.0
HA2 C:GLY10 5.0 46.4 1.0

Magnesium binding site 4 out of 5 in 4iij

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Magnesium binding site 4 out of 5 in the Crystal Structure of Tubulin-Stathmin-Ttl-Apo 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-Apo Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:74.5
occ:1.00
O1A D:GDP600 2.8 99.6 1.0
OE1 D:GLN11 3.0 97.7 1.0
OD1 D:ASN101 3.1 0.2 1.0
O3A D:GDP600 3.6 56.8 1.0
PA D:GDP600 3.8 76.9 1.0
O3B D:GDP600 3.9 81.6 1.0
HD22 D:ASN101 4.0 0.6 1.0
HB2 D:GLN11 4.0 94.6 1.0
PB D:GDP600 4.1 68.9 1.0
CG D:ASN101 4.2 0.1 1.0
CD D:GLN11 4.2 0.6 1.0
O2B D:GDP600 4.2 52.0 1.0
HB3 D:GLN11 4.5 94.6 1.0
ND2 D:ASN101 4.5 0.1 1.0
CB D:GLN11 4.6 78.8 1.0
O5' D:GDP600 4.7 65.7 1.0
C5' D:GDP600 4.8 67.2 1.0
O2A D:GDP600 4.9 63.6 1.0
HA3 D:GLY143 4.9 77.6 1.0
O D:HOH705 4.9 57.1 1.0
H D:ASN101 5.0 0.1 1.0
HE22 D:GLN11 5.0 0.6 1.0

Magnesium binding site 5 out of 5 in 4iij

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Magnesium binding site 5 out of 5 in the Crystal Structure of Tubulin-Stathmin-Ttl-Apo 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-Apo Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:99.8
occ:1.00
OE2 F:GLU331 3.5 0.9 1.0
OE1 F:GLU331 3.8 0.1 1.0
CD F:GLU331 4.1 0.5 1.0
HD3 F:LYS74 4.9 0.5 1.0

Reference:

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
Page generated: Fri Aug 16 16:44:46 2024

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