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Magnesium in PDB 6eg5: The Structure of Sb-1-202-Tubulin Complex

Protein crystallography data

The structure of The Structure of Sb-1-202-Tubulin Complex, PDB code: 6eg5 was solved by A.K.Banerjee, Y.Wang, H.Chen, D.Miller, W.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.541, 158.033, 181.870, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 23.6

Other elements in 6eg5:

The structure of The Structure of Sb-1-202-Tubulin Complex also contains other interesting chemical elements:

Calcium (Ca) 4 atoms
Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structure of Sb-1-202-Tubulin Complex (pdb code 6eg5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the The Structure of Sb-1-202-Tubulin Complex, PDB code: 6eg5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6eg5

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Magnesium binding site 1 out of 6 in the The Structure of Sb-1-202-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Sb-1-202-Tubulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:28.5
occ:1.00
 O1G A:GTP501 1.9 20.8 1.0
O A:HOH677 2.0 31.6 1.0
O A:HOH668 2.1 20.1 1.0
O1B A:GTP501 2.1 19.7 1.0
O A:HOH625 2.1 23.9 1.0
O A:HOH713 2.2 23.8 1.0
PG A:GTP501 3.1 22.7 1.0
PB A:GTP501 3.2 20.7 1.0
O3B A:GTP501 3.4 22.9 1.0
O2G A:GTP501 3.6 22.6 1.0
O3A A:GTP501 3.8 22.4 1.0
NZ B:LYS252 4.0 39.0 1.0
OD1 A:ASP69 4.2 27.8 1.0
OD2 A:ASP98 4.2 32.7 1.0
CB A:GLN11 4.3 25.6 1.0
O B:HOH611 4.3 34.2 1.0
OD2 A:ASP69 4.3 29.8 1.0
CG A:GLU71 4.4 48.1 1.0
N A:GLN11 4.4 26.8 1.0
O3G A:GTP501 4.4 20.9 1.0
CB A:ASP98 4.4 33.3 1.0
OE2 A:GLU71 4.5 49.7 1.0
O1A A:GTP501 4.5 21.7 1.0
O2B A:GTP501 4.5 23.5 1.0
CD A:GLU71 4.6 51.6 1.0
CG A:ASP98 4.6 33.7 1.0
CG A:ASP69 4.7 29.6 1.0
PA A:GTP501 4.8 22.1 1.0
OE1 A:GLN11 4.8 26.6 1.0
CA A:GLN11 4.9 26.4 1.0

Magnesium binding site 2 out of 6 in 6eg5

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Magnesium binding site 2 out of 6 in the The Structure of Sb-1-202-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Sb-1-202-Tubulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:27.0
occ:1.00
 O B:HOH671 1.9 36.6 1.0
OE1 B:GLN11 2.1 36.8 1.0
O1A B:GDP501 2.3 20.2 1.0
O C:HOH784 2.3 31.7 1.0
O B:HOH623 2.6 37.6 1.0
O B:HOH684 2.6 32.4 1.0
CD B:GLN11 3.4 36.5 1.0
OD2 B:ASP177 3.5 38.2 1.0
PA B:GDP501 3.6 19.4 1.0
O3A B:GDP501 4.0 18.4 1.0
CB B:GLN11 4.2 30.5 1.0
O C:HOH646 4.2 41.4 1.0
CG B:GLN11 4.3 33.9 1.0
C5' B:GDP501 4.3 20.1 1.0
NE2 B:GLN11 4.3 37.1 1.0
OD1 B:ASN99 4.4 26.2 1.0
O5' B:GDP501 4.4 18.3 1.0
CG B:ASP177 4.5 35.4 1.0
O1B B:GDP501 4.7 18.2 1.0
O2A B:GDP501 4.8 18.7 1.0
OE1 C:GLU254 4.8 35.1 1.0
C8 B:GDP501 4.9 22.9 1.0

Magnesium binding site 3 out of 6 in 6eg5

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Magnesium binding site 3 out of 6 in the The Structure of Sb-1-202-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of Sb-1-202-Tubulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:25.8
occ:1.00
 O1G C:GTP501 1.9 19.1 1.0
O C:HOH662 1.9 20.5 1.0
O1B C:GTP501 2.0 18.8 1.0
O C:HOH660 2.0 12.9 1.0
O C:HOH682 2.1 19.4 1.0
O C:HOH731 2.1 18.2 1.0
PG C:GTP501 3.1 20.2 1.0
PB C:GTP501 3.1 18.2 1.0
O3B C:GTP501 3.4 19.4 1.0
O2G C:GTP501 3.7 20.1 1.0
O3A C:GTP501 3.7 19.9 1.0
O D:HOH705 3.7 25.8 1.0
OE1 C:GLU71 4.0 36.4 1.0
OD1 C:ASP69 4.2 20.7 1.0
OD2 C:ASP98 4.2 27.1 1.0
CB C:GLN11 4.2 20.8 1.0
OD2 C:ASP69 4.3 21.6 1.0
O3G C:GTP501 4.4 18.3 1.0
O1A C:GTP501 4.4 20.5 1.0
N C:GLN11 4.4 20.2 1.0
CB C:ASP98 4.4 27.6 1.0
O2B C:GTP501 4.4 18.6 1.0
NZ D:LYS252 4.6 42.4 1.0
PA C:GTP501 4.7 21.1 1.0
CG C:ASP69 4.7 22.3 1.0
CG C:ASP98 4.7 27.1 1.0
OE1 C:GLN11 4.8 24.1 1.0
CA C:GLN11 4.9 20.5 1.0
OG1 C:THR145 5.0 20.7 1.0

Magnesium binding site 4 out of 6 in 6eg5

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Magnesium binding site 4 out of 6 in the The Structure of Sb-1-202-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of Sb-1-202-Tubulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:64.0
occ:1.00
 O3B D:GTP601 2.4 69.2 1.0
O1G D:GTP601 2.5 79.4 1.0
OE1 D:GLU69 2.9 1.0 1.0
PG D:GTP601 3.1 76.5 1.0
CB D:GLN11 3.5 57.4 1.0
PB D:GTP601 3.6 56.2 1.0
O1B D:GTP601 3.8 51.4 1.0
CD D:GLU69 3.8 96.3 1.0
O3A D:GTP601 3.9 56.2 1.0
OE1 D:GLN11 3.9 67.1 1.0
O3G D:GTP601 4.1 72.3 1.0
O2G D:GTP601 4.2 71.2 1.0
CD D:GLN11 4.2 64.5 1.0
N D:GLN11 4.3 48.9 1.0
CG D:GLU69 4.3 92.6 1.0
CA D:GLN11 4.4 53.5 1.0
CG D:GLN11 4.5 60.8 1.0
O1A D:GTP601 4.5 47.8 1.0
OD2 D:ASP67 4.6 52.5 1.0
OG1 D:THR72 4.7 0.9 1.0
OD1 D:ASP67 4.8 49.5 1.0
OE2 D:GLU69 4.8 95.1 1.0
O2B D:GTP601 4.8 56.3 1.0
PA D:GTP601 4.9 50.2 1.0
NE2 D:GLN11 5.0 67.0 1.0

Magnesium binding site 5 out of 6 in 6eg5

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Magnesium binding site 5 out of 6 in the The Structure of Sb-1-202-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structure of Sb-1-202-Tubulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg701

b:72.3
occ:1.00
 O3G F:ACP703 2.1 0.8 1.0
OD2 F:ASP318 2.5 49.7 1.0
O3A F:ACP703 3.0 0.4 1.0
OE1 F:GLU331 3.2 82.8 1.0
CG F:ASP318 3.4 43.8 1.0
O2A F:ACP703 3.4 92.9 1.0
C5' F:ACP703 3.4 97.5 1.0
PG F:ACP703 3.5 0.1 1.0
CB F:ASP318 3.7 41.6 1.0
PA F:ACP703 3.7 0.4 1.0
OD2 F:ASP200 4.1 72.0 1.0
O5' F:ACP703 4.1 0.8 1.0
NH2 F:ARG222 4.2 0.9 1.0
PB F:ACP703 4.2 0.7 1.0
O2G F:ACP703 4.3 99.4 1.0
CB F:GLU331 4.3 64.8 1.0
C3B F:ACP703 4.3 0.7 1.0
CD F:GLU331 4.4 80.5 1.0
OD1 F:ASP318 4.4 44.5 1.0
O1G F:ACP703 4.5 0.5 1.0
CG2 F:ILE330 4.6 64.1 1.0
OD1 F:ASN242 4.6 0.3 1.0
C3' F:ACP703 4.6 89.0 1.0
C4' F:ACP703 4.6 90.8 1.0
OD1 F:ASN333 4.9 59.9 1.0
O3' F:ACP703 5.0 92.8 1.0
O1B F:ACP703 5.0 0.2 1.0
CG F:GLU331 5.0 72.2 1.0

Magnesium binding site 6 out of 6 in 6eg5

Go back to Magnesium Binding Sites List in 6eg5
Magnesium binding site 6 out of 6 in the The Structure of Sb-1-202-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Structure of Sb-1-202-Tubulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg702

b:76.0
occ:1.00
 OE2 F:GLU331 2.5 93.5 1.0
O1B F:ACP703 3.0 0.2 1.0
O2G F:ACP703 3.1 99.4 1.0
ND2 F:ASN333 3.4 62.8 1.0
CD F:GLU331 3.5 80.5 1.0
OE1 F:GLU331 3.8 82.8 1.0
O F:SER152 3.9 0.8 1.0
PB F:ACP703 4.4 0.7 1.0
CB F:ALA155 4.5 0.6 1.0
PG F:ACP703 4.5 0.1 1.0
CG F:GLU331 4.7 72.2 1.0
CG F:ASN333 4.7 57.5 1.0
CE F:LYS74 4.8 84.1 1.0
C3B F:ACP703 4.8 0.7 1.0
O F:HOH853 4.9 40.9 1.0

Reference:

H.Chen, Y.Wang, W.Li. The Structure of Sb-1-202/Sb-2-204-Tubulin Complex To Be Published.
Page generated: Mon Sep 30 23:57:00 2024

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