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

Protein crystallography data

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

Other elements in 4ihj:

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

Magnesium Binding Sites:

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 4ihj

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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 4ihj

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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 4ihj

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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 4ihj

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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 4ihj

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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 4ihj

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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 4ihj

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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

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 16:43:21 2024

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