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Magnesium in PDB 5s5l: Tubulin-Z1492796719-Complex

Protein crystallography data

The structure of Tubulin-Z1492796719-Complex, PDB code: 5s5l 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) 62.67 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.12, 159.02, 179.19, 90, 90, 90
R / Rfree (%) 20.4 / 23.5

Other elements in 5s5l:

The structure of Tubulin-Z1492796719-Complex also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tubulin-Z1492796719-Complex (pdb code 5s5l). 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-Z1492796719-Complex, PDB code: 5s5l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5s5l

Go back to Magnesium Binding Sites List in 5s5l
Magnesium binding site 1 out of 5 in the Tubulin-Z1492796719-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z1492796719-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:45.2
occ:1.00
O A:HOH609 2.0 44.1 1.0
O1G A:GTP501 2.0 38.7 1.0
O A:HOH621 2.1 45.3 1.0
O A:HOH622 2.1 45.1 1.0
O A:HOH647 2.1 46.3 1.0
O1B A:GTP501 2.2 41.5 1.0
PG A:GTP501 3.2 47.7 1.0
PB A:GTP501 3.3 40.7 1.0
O3B A:GTP501 3.6 48.1 1.0
OE1 A:GLU71 3.7 56.7 1.0
O2G A:GTP501 3.8 43.4 1.0
O3A A:GTP501 3.8 45.8 1.0
NZ B:LYS254 3.9 57.5 1.0
OD1 A:ASP69 4.0 49.8 1.0
CB A:GLN11 4.2 42.6 1.0
OD2 A:ASP69 4.2 52.4 1.0
CB A:ASP98 4.2 50.8 1.0
N A:GLN11 4.4 44.0 1.0
O3G A:GTP501 4.5 45.3 1.0
OD2 A:ASP98 4.5 61.5 1.0
NE2 A:GLN11 4.5 54.2 1.0
CG A:ASP69 4.6 52.3 1.0
O2B A:GTP501 4.6 49.0 1.0
O1A A:GTP501 4.6 47.2 1.0
CG A:ASP98 4.8 53.6 1.0
PA A:GTP501 4.8 43.8 1.0
CA A:GLN11 4.9 46.4 1.0
CD A:GLU71 4.9 61.5 1.0
CE B:LYS254 5.0 55.3 1.0
OG1 A:THR145 5.0 50.5 1.0

Magnesium binding site 2 out of 5 in 5s5l

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Magnesium binding site 2 out of 5 in the Tubulin-Z1492796719-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z1492796719-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:33.8
occ:1.00
O B:HOH647 1.9 37.6 1.0
O B:HOH651 2.0 44.8 1.0
OE1 B:GLN11 2.1 41.0 1.0
O1A B:GDP501 2.2 37.0 1.0
O B:HOH656 2.3 43.7 1.0
O B:HOH629 2.5 41.3 1.0
CD B:GLN11 3.3 46.0 1.0
PA B:GDP501 3.5 39.3 1.0
O3A B:GDP501 3.9 38.8 1.0
CB B:GLN11 4.0 41.3 1.0
OD2 B:ASP179 4.0 46.5 1.0
CG B:GLN11 4.1 41.4 1.0
O C:HOH681 4.3 46.3 1.0
NE2 B:GLN11 4.3 55.8 1.0
OD1 B:ASN101 4.4 37.2 1.0
C5' B:GDP501 4.4 40.2 1.0
O B:HOH681 4.4 61.3 1.0
O5' B:GDP501 4.5 40.2 1.0
O1B B:GDP501 4.5 38.4 1.0
OE1 C:GLU254 4.6 45.2 1.0
O2A B:GDP501 4.6 41.2 1.0
C8 B:GDP501 4.8 44.0 1.0
PB B:GDP501 4.9 36.6 1.0
CG B:ASP179 5.0 44.0 1.0
ND2 B:ASN101 5.0 41.9 1.0

Magnesium binding site 3 out of 5 in 5s5l

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Magnesium binding site 3 out of 5 in the Tubulin-Z1492796719-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z1492796719-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:40.5
occ:1.00
O1G C:GTP501 1.9 39.1 1.0
O C:HOH670 2.0 40.4 1.0
O C:HOH644 2.0 40.8 1.0
O1B C:GTP501 2.1 37.0 1.0
O C:HOH716 2.1 38.8 1.0
O C:HOH669 2.2 42.3 1.0
PG C:GTP501 3.0 40.0 1.0
PB C:GTP501 3.1 36.7 1.0
O3B C:GTP501 3.4 44.5 1.0
O2G C:GTP501 3.4 37.2 1.0
O3A C:GTP501 3.6 39.9 1.0
NZ D:LYS254 3.9 39.9 1.0
OD1 C:ASP69 4.0 43.9 1.0
OE2 C:GLU71 4.2 50.6 1.0
OD2 C:ASP69 4.3 37.9 1.0
CG C:GLU71 4.3 48.5 1.0
O3G C:GTP501 4.3 37.8 1.0
CB C:ASP98 4.4 43.4 1.0
CB C:GLN11 4.4 37.5 1.0
OD2 C:ASP98 4.4 47.1 1.0
N C:GLN11 4.4 36.1 1.0
O2B C:GTP501 4.4 40.8 1.0
CG C:ASP69 4.6 39.6 1.0
CG C:ASP98 4.6 44.0 1.0
O1A C:GTP501 4.7 40.9 1.0
PA C:GTP501 4.7 38.0 1.0
CD C:GLU71 4.8 47.7 1.0
CE D:LYS254 5.0 42.9 1.0
OG1 C:THR145 5.0 40.0 1.0

Magnesium binding site 4 out of 5 in 5s5l

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Magnesium binding site 4 out of 5 in the Tubulin-Z1492796719-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z1492796719-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:62.7
occ:1.00
O D:HOH605 1.9 65.1 1.0
OE1 D:GLN11 2.0 67.0 1.0
O1A D:GDP501 2.2 76.7 1.0
CD D:GLN11 3.2 69.3 1.0
PA D:GDP501 3.7 65.5 1.0
CB D:GLN11 4.0 64.2 1.0
CG D:GLN11 4.1 68.9 1.0
NE2 D:GLN11 4.1 69.0 1.0
O D:HOH623 4.2 76.5 1.0
O1B D:GDP501 4.4 62.1 1.0
C5' D:GDP501 4.4 66.5 1.0
O3A D:GDP501 4.4 63.3 1.0
O2A D:GDP501 4.5 64.2 1.0
O5' D:GDP501 4.5 65.9 1.0
OD1 D:ASN101 4.6 74.8 1.0
C8 D:GDP501 4.9 64.7 1.0
PB D:GDP501 5.0 66.3 1.0

Magnesium binding site 5 out of 5 in 5s5l

Go back to Magnesium Binding Sites List in 5s5l
Magnesium binding site 5 out of 5 in the Tubulin-Z1492796719-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z1492796719-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg402

b:93.8
occ:1.00
O1B F:ACP401 2.3 103.7 1.0
O3G F:ACP401 2.3 97.1 1.0
OE2 F:GLU331 2.5 94.3 1.0
OD1 F:ASN333 3.1 89.4 1.0
CD F:GLU331 3.3 93.6 1.0
OE1 F:GLU331 3.4 99.3 1.0
PB F:ACP401 3.4 105.0 1.0
O2B F:ACP401 3.7 108.4 1.0
NZ F:LYS74 3.7 103.1 1.0
PG F:ACP401 3.8 111.5 1.0
CG F:ASN333 4.3 84.2 1.0
C3B F:ACP401 4.3 105.4 1.0
O1G F:ACP401 4.6 104.2 1.0
O3A F:ACP401 4.7 107.1 1.0
CG F:GLU331 4.8 83.1 1.0
ND2 F:ASN333 4.8 82.2 1.0
O2G F:ACP401 4.9 94.0 1.0
CE F:LYS74 4.9 100.9 1.0
O1A F:ACP401 4.9 102.8 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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