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Magnesium in PDB 5s4p: Tubulin-Z275165822-Complex

Protein crystallography data

The structure of Tubulin-Z275165822-Complex, PDB code: 5s4p 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) 78.52 / 2.29
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.246, 157.049, 178.157, 90, 90, 90
R / Rfree (%) 20.8 / 24.4

Other elements in 5s4p:

The structure of Tubulin-Z275165822-Complex also contains other interesting chemical elements:

Calcium (Ca) 4 atoms
Chlorine (Cl) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tubulin-Z275165822-Complex (pdb code 5s4p). 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-Z275165822-Complex, PDB code: 5s4p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5s4p

Go back to Magnesium Binding Sites List in 5s4p
Magnesium binding site 1 out of 5 in the Tubulin-Z275165822-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z275165822-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:32.7
occ:1.00
O A:HOH618 2.0 35.7 1.0
O1G A:GTP501 2.0 34.3 1.0
O A:HOH621 2.0 36.5 1.0
O1B A:GTP501 2.1 35.9 1.0
O A:HOH643 2.2 38.4 1.0
O A:HOH609 2.2 37.1 1.0
PB A:GTP501 3.2 33.4 1.0
PG A:GTP501 3.2 38.3 1.0
O3A A:GTP501 3.6 39.4 1.0
O3B A:GTP501 3.6 40.6 1.0
OE1 A:GLU71 3.7 55.7 1.0
O2G A:GTP501 3.9 38.9 1.0
CB A:GLN11 3.9 34.4 1.0
NZ B:LYS254 3.9 51.4 1.0
OD1 A:ASP69 4.1 45.0 1.0
N A:GLN11 4.2 38.1 1.0
OD2 A:ASP69 4.2 39.0 1.0
NE2 A:GLN11 4.2 44.1 1.0
CB A:ASP98 4.4 38.9 1.0
OD2 A:ASP98 4.4 45.2 1.0
O1A A:GTP501 4.4 39.6 1.0
O3G A:GTP501 4.5 35.0 1.0
O2B A:GTP501 4.5 36.4 1.0
CG A:ASP69 4.6 41.5 1.0
PA A:GTP501 4.6 35.1 1.0
CA A:GLN11 4.6 39.1 1.0
O B:HOH619 4.8 46.2 1.0
CG A:ASP98 4.9 44.1 1.0
CD A:GLU71 4.9 54.8 1.0

Magnesium binding site 2 out of 5 in 5s4p

Go back to Magnesium Binding Sites List in 5s4p
Magnesium binding site 2 out of 5 in the Tubulin-Z275165822-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z275165822-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:36.5
occ:1.00
O1A B:GDP501 2.2 40.1 1.0
OE1 B:GLN11 2.2 48.7 1.0
O B:HOH616 2.3 49.9 1.0
O C:HOH698 2.4 46.6 1.0
O B:HOH602 2.4 47.4 1.0
O B:HOH629 2.4 35.6 1.0
CD B:GLN11 3.4 44.8 1.0
PA B:GDP501 3.5 30.6 1.0
OD2 B:ASP179 3.8 52.0 1.0
O3A B:GDP501 3.9 37.2 1.0
CB B:GLN11 4.1 36.3 1.0
OD1 B:ASN101 4.2 42.2 1.0
C5' B:GDP501 4.2 43.1 1.0
CG B:GLN11 4.3 40.9 1.0
O5' B:GDP501 4.3 40.3 1.0
NE2 B:GLN11 4.4 48.7 1.0
O1B B:GDP501 4.4 33.1 1.0
O C:HOH616 4.5 55.0 1.0
OE1 C:GLU254 4.5 53.9 1.0
O2A B:GDP501 4.6 37.0 1.0
PB B:GDP501 4.8 37.9 1.0
CG B:ASP179 4.9 52.8 1.0
ND2 B:ASN101 4.9 46.3 1.0
C8 B:GDP501 4.9 44.0 1.0
CG B:ASN101 4.9 41.9 1.0

Magnesium binding site 3 out of 5 in 5s4p

Go back to Magnesium Binding Sites List in 5s4p
Magnesium binding site 3 out of 5 in the Tubulin-Z275165822-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z275165822-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:34.5
occ:1.00
O1G C:GTP501 1.9 29.5 1.0
O1B C:GTP501 1.9 34.4 1.0
O C:HOH630 2.0 34.1 1.0
O C:HOH689 2.0 32.9 1.0
O C:HOH648 2.1 34.3 1.0
O C:HOH649 2.2 35.8 1.0
PG C:GTP501 3.0 36.0 1.0
PB C:GTP501 3.0 33.2 1.0
O3B C:GTP501 3.3 36.4 1.0
O2G C:GTP501 3.5 35.9 1.0
O3A C:GTP501 3.6 35.5 1.0
NZ D:LYS254 3.9 41.1 1.0
OD1 C:ASP69 4.1 37.8 1.0
CB C:GLN11 4.2 32.6 1.0
O3G C:GTP501 4.3 32.3 1.0
OD2 C:ASP98 4.3 45.2 1.0
OD2 C:ASP69 4.3 36.5 1.0
CG C:GLU71 4.3 43.9 1.0
O2B C:GTP501 4.3 34.2 1.0
OE2 C:GLU71 4.3 43.9 1.0
N C:GLN11 4.4 32.7 1.0
CB C:ASP98 4.5 38.4 1.0
O1A C:GTP501 4.5 35.0 1.0
PA C:GTP501 4.6 34.3 1.0
CG C:ASP69 4.6 39.7 1.0
O C:HOH650 4.7 53.6 1.0
CG C:ASP98 4.8 43.1 1.0
OE1 C:GLN11 4.8 46.9 1.0
CD C:GLU71 4.8 42.1 1.0
CA C:GLN11 4.9 36.6 1.0
OG1 C:THR145 4.9 35.6 1.0
CE D:LYS254 4.9 40.4 1.0

Magnesium binding site 4 out of 5 in 5s4p

Go back to Magnesium Binding Sites List in 5s4p
Magnesium binding site 4 out of 5 in the Tubulin-Z275165822-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z275165822-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:63.3
occ:1.00
OE1 D:GLN11 2.1 67.2 1.0
O D:HOH604 2.2 63.1 1.0
O1A D:GDP501 2.2 74.0 1.0
CD D:GLN11 3.3 66.4 1.0
PA D:GDP501 3.7 62.6 1.0
O D:HOH627 3.9 67.5 1.0
CB D:GLN11 4.1 62.4 1.0
NE2 D:GLN11 4.2 69.1 1.0
CG D:GLN11 4.2 62.5 1.0
O2A D:GDP501 4.3 59.9 1.0
C5' D:GDP501 4.4 62.0 1.0
O5' D:GDP501 4.6 60.5 1.0
OD1 D:ASN101 4.6 69.3 1.0
O1B D:GDP501 4.6 55.6 1.0
O3A D:GDP501 4.7 63.3 1.0
C8 D:GDP501 4.8 59.4 1.0

Magnesium binding site 5 out of 5 in 5s4p

Go back to Magnesium Binding Sites List in 5s4p
Magnesium binding site 5 out of 5 in the Tubulin-Z275165822-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z275165822-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg402

b:78.5
occ:1.00
O1B F:ACP401 2.3 91.3 1.0
O3G F:ACP401 2.5 82.0 1.0
OE2 F:GLU331 2.6 81.9 1.0
OD1 F:ASN333 2.9 81.2 1.0
OE1 F:GLU331 3.0 81.8 1.0
CD F:GLU331 3.2 78.8 1.0
PB F:ACP401 3.5 93.9 1.0
NZ F:LYS74 3.7 89.7 1.0
O2B F:ACP401 3.9 99.0 1.0
PG F:ACP401 3.9 99.0 1.0
CG F:ASN333 4.1 72.8 1.0
C3B F:ACP401 4.4 91.7 1.0
ND2 F:ASN333 4.7 70.9 1.0
CG F:GLU331 4.7 68.8 1.0
O1G F:ACP401 4.7 91.8 1.0
O3A F:ACP401 4.8 92.4 1.0
CE F:LYS74 4.8 87.7 1.0
O1A F:ACP401 4.8 86.1 1.0
O2G F:ACP401 5.0 80.5 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: Sat Jul 10 17:08:22 2021

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