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Magnesium in PDB 5s5m: Tubulin-Z45527714-Complex

Protein crystallography data

The structure of Tubulin-Z45527714-Complex, PDB code: 5s5m was solved by T.Muehlethaler, D.Gioia, A.E.Prota, M.E.Sharpe, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.92 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.66, 159.8, 179.1, 90, 90, 90
R / Rfree (%) 21.5 / 26.9

Other elements in 5s5m:

The structure of Tubulin-Z45527714-Complex also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tubulin-Z45527714-Complex (pdb code 5s5m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Tubulin-Z45527714-Complex, PDB code: 5s5m:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5s5m

Go back to Magnesium Binding Sites List in 5s5m
Magnesium binding site 1 out of 5 in the Tubulin-Z45527714-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z45527714-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:71.6
occ:1.00
O1G A:GTP501 1.9 70.2 1.0
O A:HOH604 1.9 75.1 1.0
O A:HOH606 2.0 72.3 1.0
O A:HOH603 2.2 66.0 1.0
O1B A:GTP501 2.5 70.3 1.0
PG A:GTP501 3.2 72.9 1.0
OE1 A:GLU71 3.4 84.3 1.0
PB A:GTP501 3.5 68.4 1.0
NZ B:LYS254 3.5 78.0 1.0
O3B A:GTP501 3.7 79.3 1.0
O2G A:GTP501 3.8 71.4 1.0
O3A A:GTP501 3.9 73.8 1.0
CB A:GLN11 4.2 78.4 1.0
CB A:ASP98 4.3 74.8 1.0
O3G A:GTP501 4.4 72.6 1.0
OD1 A:ASP69 4.4 71.3 1.0
NE2 A:GLN11 4.5 92.0 1.0
O1A A:GTP501 4.6 75.7 1.0
CD A:GLU71 4.6 95.9 1.0
N A:GLN11 4.7 71.7 1.0
OD2 A:ASP69 4.7 80.0 1.0
CE B:LYS254 4.8 75.2 1.0
CG A:ASP98 4.8 79.4 1.0
PA A:GTP501 4.8 70.4 1.0
O2B A:GTP501 4.9 77.1 1.0
OD2 A:ASP98 4.9 83.1 1.0
CG A:ASP69 5.0 74.9 1.0

Magnesium binding site 2 out of 5 in 5s5m

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Magnesium binding site 2 out of 5 in the Tubulin-Z45527714-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z45527714-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:63.7
occ:1.00
OE1 B:GLN11 2.0 75.2 1.0
O C:HOH609 2.0 64.7 1.0
O B:HOH605 2.0 58.6 1.0
O1A B:GDP501 2.6 64.3 1.0
O B:HOH618 2.7 63.7 1.0
CD B:GLN11 2.9 72.7 1.0
OD2 B:ASP179 3.5 74.6 1.0
NE2 B:GLN11 3.6 80.8 1.0
CG B:GLN11 4.0 71.1 1.0
PA B:GDP501 4.1 59.5 1.0
CB B:GLN11 4.1 66.7 1.0
OE1 C:GLU254 4.4 73.9 1.0
CG B:ASP179 4.6 66.2 1.0
O3A B:GDP501 4.7 55.7 1.0
O2A B:GDP501 4.8 62.1 1.0
O3B B:GDP501 4.8 63.2 1.0
C8 B:GDP501 4.8 66.8 1.0

Magnesium binding site 3 out of 5 in 5s5m

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Magnesium binding site 3 out of 5 in the Tubulin-Z45527714-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z45527714-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:70.9
occ:1.00
O1G C:GTP501 1.8 63.1 1.0
O C:HOH611 1.9 68.6 1.0
O C:HOH603 2.0 65.3 1.0
O C:HOH620 2.1 73.9 1.0
O1B C:GTP501 2.3 66.4 1.0
O C:HOH602 2.5 67.5 1.0
PG C:GTP501 2.8 68.0 1.0
PB C:GTP501 3.2 63.2 1.0
O2G C:GTP501 3.2 67.4 1.0
O3B C:GTP501 3.3 70.7 1.0
OD2 C:ASP98 3.5 75.0 1.0
NZ D:LYS254 3.6 77.8 1.0
O3A C:GTP501 3.7 66.8 1.0
CB C:ASP98 3.9 67.2 1.0
O3G C:GTP501 4.1 70.0 1.0
CG C:ASP98 4.2 72.0 1.0
OD1 C:ASP69 4.2 65.9 1.0
CG C:GLU71 4.3 76.2 1.0
OE2 C:GLU71 4.5 80.1 1.0
O2B C:GTP501 4.6 67.0 1.0
CE D:LYS254 4.6 71.8 1.0
OD2 C:ASP69 4.7 79.4 1.0
CB C:GLN11 4.8 73.6 1.0
OG1 C:THR145 4.9 67.1 1.0
CG C:ASP69 4.9 69.6 1.0
PA C:GTP501 4.9 64.2 1.0
N C:GLN11 4.9 62.1 1.0
CD C:GLU71 5.0 79.9 1.0

Magnesium binding site 4 out of 5 in 5s5m

Go back to Magnesium Binding Sites List in 5s5m
Magnesium binding site 4 out of 5 in the Tubulin-Z45527714-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z45527714-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:95.7
occ:1.00
OE1 D:GLN11 2.1 106.0 1.0
O D:HOH602 2.2 83.8 1.0
O1A D:GDP501 2.8 109.8 1.0
CD D:GLN11 3.3 105.0 1.0
CB D:GLN11 3.6 109.9 1.0
O1B D:GDP501 3.9 97.9 1.0
PA D:GDP501 4.0 99.9 1.0
O2A D:GDP501 4.0 90.6 1.0
CG D:GLN11 4.1 110.8 1.0
NE2 D:GLN11 4.3 108.5 1.0
O3B D:GDP501 4.3 101.5 1.0
OD1 D:ASN101 4.5 100.6 1.0
PB D:GDP501 4.6 102.7 1.0
O3A D:GDP501 4.8 110.2 1.0
OE2 D:GLU71 4.9 143.3 1.0

Magnesium binding site 5 out of 5 in 5s5m

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Magnesium binding site 5 out of 5 in the Tubulin-Z45527714-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z45527714-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg402

b:135.2
occ:1.00
OE2 F:GLU331 2.5 149.5 1.0
O1B F:ACP401 2.5 150.9 1.0
O3G F:ACP401 2.6 148.0 1.0
OD1 F:ASN333 3.2 137.2 1.0
CD F:GLU331 3.3 147.2 1.0
OE1 F:GLU331 3.4 148.9 1.0
PB F:ACP401 3.6 152.4 1.0
O2B F:ACP401 3.6 154.1 1.0
NZ F:LYS74 3.8 140.2 1.0
PG F:ACP401 4.1 158.2 1.0
CG F:ASN333 4.4 132.1 1.0
C3B F:ACP401 4.6 149.4 1.0
CG F:GLU331 4.7 139.6 1.0
O1G F:ACP401 4.9 156.8 1.0
O3A F:ACP401 4.9 149.4 1.0
ND2 F:ASN333 5.0 131.0 1.0

Reference:

T.Muhlethaler, D.Gioia, A.E.Prota, M.E.Sharpe, A.Cavalli, M.O.Steinmetz. Comprehensive Analysis of Binding Sites in Tubulin. Angew.Chem.Int.Ed.Engl. V. 60 13331 2021.
ISSN: ESSN 1521-3773
PubMed: 33951246
DOI: 10.1002/ANIE.202100273
Page generated: Mon Sep 30 02:52:47 2024

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