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Magnesium in PDB 5s5b: Tubulin-Z906021418-Complex

Protein crystallography data

The structure of Tubulin-Z906021418-Complex, PDB code: 5s5b 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) 63.37 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.02, 158.92, 179.41, 90, 90, 90
R / Rfree (%) 20.9 / 24.4

Other elements in 5s5b:

The structure of Tubulin-Z906021418-Complex also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tubulin-Z906021418-Complex (pdb code 5s5b). 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-Z906021418-Complex, PDB code: 5s5b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5s5b

Go back to Magnesium Binding Sites List in 5s5b
Magnesium binding site 1 out of 5 in the Tubulin-Z906021418-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z906021418-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:47.5
occ:1.00
O1G A:GTP501 2.0 45.1 1.0
O A:HOH606 2.0 50.9 1.0
O A:HOH632 2.1 48.8 1.0
O A:HOH631 2.2 48.4 1.0
O A:HOH621 2.2 51.5 1.0
O1B A:GTP501 2.2 44.1 1.0
PG A:GTP501 3.2 47.7 1.0
PB A:GTP501 3.4 43.0 1.0
OE1 A:GLU71 3.6 67.9 1.0
O3B A:GTP501 3.6 54.0 1.0
O2G A:GTP501 3.7 47.5 1.0
NZ B:LYS254 3.8 61.1 1.0
O3A A:GTP501 3.9 51.7 1.0
OD1 A:ASP69 4.1 54.2 1.0
CB A:GLN11 4.1 47.3 1.0
CB A:ASP98 4.1 53.6 1.0
OD2 A:ASP69 4.2 58.6 1.0
N A:GLN11 4.4 48.3 1.0
O3G A:GTP501 4.5 49.3 1.0
OD2 A:ASP98 4.5 65.1 1.0
CG A:ASP69 4.5 55.6 1.0
O1A A:GTP501 4.6 49.5 1.0
O2B A:GTP501 4.6 50.1 1.0
CG A:ASP98 4.7 58.7 1.0
NE2 A:GLN11 4.7 57.5 1.0
O B:HOH632 4.8 59.0 1.0
CE B:LYS254 4.8 55.4 1.0
CD A:GLU71 4.8 67.8 1.0
PA A:GTP501 4.8 48.5 1.0
CA A:GLN11 4.8 49.8 1.0

Magnesium binding site 2 out of 5 in 5s5b

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Magnesium binding site 2 out of 5 in the Tubulin-Z906021418-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z906021418-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:36.9
occ:1.00
O B:HOH603 1.9 59.3 1.0
OE1 B:GLN11 2.1 50.3 1.0
O C:HOH686 2.2 45.1 1.0
O B:HOH637 2.2 47.4 1.0
O1A B:GDP501 2.2 43.3 1.0
O B:HOH659 2.3 45.8 1.0
CD B:GLN11 3.3 50.7 1.0
PA B:GDP501 3.5 43.8 1.0
O3A B:GDP501 3.9 43.4 1.0
OD2 B:ASP179 3.9 49.1 1.0
CB B:GLN11 4.0 46.7 1.0
CG B:GLN11 4.2 48.1 1.0
OD1 B:ASN101 4.3 45.0 1.0
NE2 B:GLN11 4.3 56.9 1.0
O1B B:GDP501 4.3 41.5 1.0
O C:HOH712 4.4 60.3 1.0
C5' B:GDP501 4.4 45.0 1.0
O5' B:GDP501 4.4 44.2 1.0
OE1 C:GLU254 4.5 55.1 1.0
O2A B:GDP501 4.6 44.2 1.0
PB B:GDP501 4.8 38.7 1.0
ND2 B:ASN101 4.8 47.7 1.0
CG B:ASP179 4.9 49.4 1.0
CG B:ASN101 4.9 47.6 1.0
C8 B:GDP501 4.9 48.1 1.0

Magnesium binding site 3 out of 5 in 5s5b

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Magnesium binding site 3 out of 5 in the Tubulin-Z906021418-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z906021418-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:44.2
occ:1.00
O C:HOH680 2.0 46.0 1.0
O1G C:GTP501 2.0 44.3 1.0
O1B C:GTP501 2.0 42.4 1.0
O C:HOH630 2.1 46.0 1.0
O C:HOH688 2.1 46.1 1.0
O C:HOH643 2.1 49.1 1.0
PG C:GTP501 3.1 43.2 1.0
PB C:GTP501 3.1 42.3 1.0
O3B C:GTP501 3.4 47.9 1.0
O2G C:GTP501 3.6 45.9 1.0
O3A C:GTP501 3.7 49.2 1.0
NZ D:LYS254 3.9 47.2 1.0
OD2 C:ASP98 3.9 53.4 1.0
OD1 C:ASP69 4.0 48.8 1.0
OE2 C:GLU71 4.1 58.2 1.0
CG C:GLU71 4.2 56.8 1.0
OD2 C:ASP69 4.3 41.8 1.0
CB C:ASP98 4.4 48.7 1.0
CB C:GLN11 4.4 45.7 1.0
O3G C:GTP501 4.4 44.7 1.0
O2B C:GTP501 4.4 43.4 1.0
N C:GLN11 4.5 42.4 1.0
CG C:ASP98 4.6 50.3 1.0
CG C:ASP69 4.6 46.4 1.0
O1A C:GTP501 4.6 45.0 1.0
CD C:GLU71 4.7 58.3 1.0
PA C:GTP501 4.8 43.9 1.0
OE1 C:GLN11 4.9 56.0 1.0
OG1 C:THR145 4.9 49.3 1.0
CE D:LYS254 5.0 48.4 1.0

Magnesium binding site 4 out of 5 in 5s5b

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Magnesium binding site 4 out of 5 in the Tubulin-Z906021418-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z906021418-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:71.9
occ:1.00
O D:HOH603 1.9 74.4 1.0
OE1 D:GLN11 2.0 73.1 1.0
O1A D:GDP501 2.2 88.7 1.0
CD D:GLN11 3.1 76.9 1.0
PA D:GDP501 3.5 74.7 1.0
CB D:GLN11 3.8 71.0 1.0
O2A D:GDP501 3.9 69.4 1.0
CG D:GLN11 3.9 71.1 1.0
O D:HOH631 4.1 74.1 1.0
NE2 D:GLN11 4.1 73.2 1.0
O1B D:GDP501 4.3 69.1 1.0
C5' D:GDP501 4.4 73.1 1.0
O5' D:GDP501 4.5 70.6 1.0
O3A D:GDP501 4.7 73.5 1.0
C8 D:GDP501 4.8 69.8 1.0
OD1 D:ASN101 4.8 80.4 1.0
PB D:GDP501 5.0 70.3 1.0

Magnesium binding site 5 out of 5 in 5s5b

Go back to Magnesium Binding Sites List in 5s5b
Magnesium binding site 5 out of 5 in the Tubulin-Z906021418-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z906021418-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg402

b:98.4
occ:1.00
O3G F:ACP401 2.3 103.1 1.0
OE2 F:GLU331 2.4 101.4 1.0
O1B F:ACP401 2.5 113.1 1.0
OD1 F:ASN333 2.8 94.0 1.0
CD F:GLU331 3.2 100.2 1.0
OE1 F:GLU331 3.4 104.2 1.0
PB F:ACP401 3.6 115.5 1.0
PG F:ACP401 3.7 117.5 1.0
O2B F:ACP401 3.8 118.0 1.0
CG F:ASN333 3.9 88.0 1.0
NZ F:LYS74 4.1 112.5 1.0
C3B F:ACP401 4.3 114.4 1.0
O1G F:ACP401 4.4 109.1 1.0
ND2 F:ASN333 4.4 85.6 1.0
CG F:GLU331 4.7 88.3 1.0
O2G F:ACP401 4.8 102.3 1.0
O3A F:ACP401 5.0 114.6 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 02:48:02 2024

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