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Magnesium in PDB 7db9: IC1 in Complex with Tubulin

Protein crystallography data

The structure of IC1 in Complex with Tubulin, PDB code: 7db9 was solved by C.Y.Wu, Y.X.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.87 / 2.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.124, 157.684, 182.116, 90, 90, 90
R / Rfree (%) 18.6 / 23.3

Other elements in 7db9:

The structure of IC1 in Complex with Tubulin also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the IC1 in Complex with Tubulin (pdb code 7db9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the IC1 in Complex with Tubulin, PDB code: 7db9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7db9

Go back to Magnesium Binding Sites List in 7db9
Magnesium binding site 1 out of 5 in the IC1 in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of IC1 in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:29.3
occ:1.00
O1G A:GTP501 2.3 43.9 1.0
O1B A:GTP501 2.5 25.2 1.0
PG A:GTP501 3.5 43.4 1.0
OE1 A:GLU71 3.7 49.8 1.0
PB A:GTP501 3.7 31.1 1.0
O2G A:GTP501 3.9 30.3 1.0
OD2 A:ASP69 4.0 57.5 1.0
OD1 A:ASP69 4.0 36.0 1.0
CG A:GLU71 4.0 53.8 1.0
O3B A:GTP501 4.1 45.1 1.0
OD2 A:ASP98 4.1 60.0 1.0
CB A:GLN11 4.2 41.4 1.0
CD A:GLU71 4.4 52.1 1.0
NE2 A:GLN11 4.4 40.7 1.0
O3A A:GTP501 4.4 42.5 1.0
CG A:ASP69 4.4 45.9 1.0
N A:GLN11 4.5 34.4 1.0
CB A:ASP98 4.6 38.4 1.0
CG A:ASP98 4.7 47.0 1.0
O1A A:GTP501 4.8 36.8 1.0
O3G A:GTP501 4.8 25.2 1.0
CA A:GLN11 4.8 37.0 1.0
O2B A:GTP501 4.9 38.9 1.0

Magnesium binding site 2 out of 5 in 7db9

Go back to Magnesium Binding Sites List in 7db9
Magnesium binding site 2 out of 5 in the IC1 in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of IC1 in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:43.2
occ:1.00
OE1 B:GLN11 2.2 58.8 1.0
O1A B:GDP501 2.4 40.9 1.0
OD2 B:ASP177 3.1 47.8 1.0
CD B:GLN11 3.4 58.2 1.0
PA B:GDP501 3.7 20.6 1.0
O3A B:GDP501 4.0 34.5 1.0
OD1 B:ASN99 4.0 38.1 1.0
CG B:ASP177 4.1 47.8 1.0
NE2 B:GLN11 4.1 37.8 1.0
C5' B:GDP501 4.3 21.7 1.0
CG B:GLN11 4.4 42.8 1.0
CB B:GLN11 4.5 29.7 1.0
O5' B:GDP501 4.5 15.1 1.0
OE1 C:GLU254 4.7 49.1 1.0
CB B:ASP177 4.8 42.1 1.0
O2A B:GDP501 4.9 22.5 1.0
OE2 C:GLU254 4.9 46.7 1.0
CG B:ASN99 4.9 30.8 1.0
OD1 B:ASP177 5.0 49.4 1.0
C8 B:GDP501 5.0 27.2 1.0

Magnesium binding site 3 out of 5 in 7db9

Go back to Magnesium Binding Sites List in 7db9
Magnesium binding site 3 out of 5 in the IC1 in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of IC1 in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg506

b:82.4
occ:1.00
OD2 B:ASP118 3.8 51.8 1.0
OD1 B:ASP118 4.3 41.9 1.0
CB B:ASP114 4.4 26.8 1.0
CG B:ASP118 4.5 42.0 1.0
OD2 B:ASP114 4.8 71.2 1.0
CG B:ASP114 4.8 47.6 1.0

Magnesium binding site 4 out of 5 in 7db9

Go back to Magnesium Binding Sites List in 7db9
Magnesium binding site 4 out of 5 in the IC1 in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of IC1 in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:35.6
occ:1.00
O1B C:GTP501 2.0 36.1 1.0
O1G C:GTP501 2.3 33.3 1.0
PB C:GTP501 3.3 27.9 1.0
PG C:GTP501 3.5 29.7 1.0
OE1 C:GLU71 3.6 63.3 1.0
O3B C:GTP501 3.9 30.8 1.0
ND2 D:ASN247 4.0 104.3 1.0
OD2 C:ASP69 4.0 31.8 1.0
O3A C:GTP501 4.0 50.4 1.0
O2G C:GTP501 4.0 34.8 1.0
OD1 C:ASP69 4.0 35.5 1.0
CG C:GLU71 4.2 41.3 1.0
CB C:GLN11 4.3 28.5 1.0
OD2 C:ASP98 4.3 42.0 1.0
NZ D:LYS252 4.4 62.4 1.0
CD C:GLU71 4.4 45.8 1.0
N C:GLN11 4.4 17.8 1.0
CG C:ASP69 4.4 37.2 1.0
CB C:ASP98 4.5 31.8 1.0
O2B C:GTP501 4.5 23.3 1.0
O1A C:GTP501 4.7 36.5 1.0
OE1 C:GLN11 4.7 37.6 1.0
CG C:ASP98 4.8 37.3 1.0
O3G C:GTP501 4.8 26.2 1.0
PA C:GTP501 4.9 29.2 1.0
CA C:GLN11 4.9 29.8 1.0
CG D:ASN247 5.0 109.8 1.0

Magnesium binding site 5 out of 5 in 7db9

Go back to Magnesium Binding Sites List in 7db9
Magnesium binding site 5 out of 5 in the IC1 in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of IC1 in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:66.2
occ:1.00
O1A D:GDP501 2.6 71.5 1.0
OE1 D:GLN11 3.3 61.6 1.0
OD1 D:ASN99 3.8 58.9 1.0
PA D:GDP501 3.8 62.8 1.0
O3A D:GDP501 4.0 78.1 1.0
C5' D:GDP501 4.3 60.5 1.0
O1B D:GDP501 4.4 79.8 1.0
O5' D:GDP501 4.5 56.2 1.0
CD D:GLN11 4.5 80.6 1.0
PB D:GDP501 4.7 80.6 1.0
CB D:GLN11 4.7 77.7 1.0
CG D:ASN99 4.7 72.3 1.0
ND2 D:ASN99 4.8 82.9 1.0
O2A D:GDP501 4.9 57.0 1.0

Reference:

C.Y.Wu, Y.X.Wang. IC1 in Complex with Tubulin To Be Published.
Page generated: Wed Oct 2 15:44:22 2024

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