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Magnesium in PDB 7dbc: Pra in Complex with Tubulin

Protein crystallography data

The structure of Pra in Complex with Tubulin, PDB code: 7dbc 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) 19.92 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.417, 158.27, 180.747, 90, 90, 90
R / Rfree (%) 19.8 / 23.4

Other elements in 7dbc:

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

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 5 in 7dbc

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Magnesium binding site 1 out of 5 in the Pra 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 Pra in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:32.8
occ:1.00
O1G A:GTP501 1.9 30.6 1.0
O1B A:GTP501 2.0 28.5 1.0
O A:HOH613 2.2 32.1 1.0
O A:HOH607 2.3 39.7 1.0
O A:HOH619 2.3 34.5 1.0
O A:HOH601 2.4 48.3 1.0
PG A:GTP501 3.1 36.8 1.0
PB A:GTP501 3.1 34.0 1.0
O3B A:GTP501 3.5 36.5 1.0
O3A A:GTP501 3.6 34.9 1.0
O2G A:GTP501 3.6 35.1 1.0
OE1 A:GLU71 3.8 46.6 1.0
NZ B:LYS252 3.8 40.3 1.0
CB A:GLN11 3.9 30.8 1.0
OD2 A:ASP69 4.0 37.7 1.0
OD1 A:ASP69 4.1 37.0 1.0
N A:GLN11 4.1 30.7 1.0
OD2 A:ASP98 4.3 40.7 1.0
O2A A:GTP501 4.3 33.3 1.0
O3G A:GTP501 4.4 30.2 1.0
O2B A:GTP501 4.5 33.3 1.0
PA A:GTP501 4.5 32.9 1.0
CG A:ASP69 4.5 40.2 1.0
CA A:GLN11 4.6 35.8 1.0
CB A:ASP98 4.6 38.2 1.0
OE1 A:GLN11 4.7 45.9 1.0
ND2 B:ASN247 4.8 72.4 1.0
CG A:ASP98 4.8 43.6 1.0
CD A:GLU71 5.0 48.5 1.0

Magnesium binding site 2 out of 5 in 7dbc

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Magnesium binding site 2 out of 5 in the Pra 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 Pra in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:41.7
occ:1.00
OE1 B:GLN11 1.8 49.4 1.0
O1A B:GDP503 2.1 45.2 1.0
O B:HOH604 2.3 55.9 1.0
O B:HOH613 2.5 81.1 1.0
O B:HOH660 2.5 77.8 1.0
O B:HOH629 2.9 43.0 1.0
CD B:GLN11 3.1 51.0 1.0
OD2 B:ASP177 3.3 47.1 1.0
PA B:GDP503 3.5 36.0 1.0
CG B:GLN11 4.0 44.9 1.0
NE2 B:GLN11 4.0 42.4 1.0
CB B:GLN11 4.1 34.4 1.0
O3A B:GDP503 4.1 33.8 1.0
C5' B:GDP503 4.3 36.7 1.0
O5' B:GDP503 4.4 33.9 1.0
O2A B:GDP503 4.5 33.8 1.0
CG B:ASP177 4.5 46.5 1.0
OD1 B:ASN99 4.6 38.9 1.0
C8 B:GDP503 4.7 37.0 1.0
O1B B:GDP503 4.7 32.6 1.0
OE2 C:GLU254 4.8 47.2 1.0

Magnesium binding site 3 out of 5 in 7dbc

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Magnesium binding site 3 out of 5 in the Pra 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 Pra in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:28.5
occ:1.00
O1G C:GTP501 1.9 28.5 1.0
O1B C:GTP501 2.1 27.5 1.0
O C:HOH608 2.1 26.6 1.0
O C:HOH636 2.3 25.7 1.0
O C:HOH610 2.3 26.8 1.0
O C:HOH626 2.4 26.9 1.0
PG C:GTP501 3.1 28.7 1.0
PB C:GTP501 3.3 27.0 1.0
O3B C:GTP501 3.6 29.0 1.0
O2G C:GTP501 3.6 30.0 1.0
NZ D:LYS252 3.8 30.3 1.0
OE1 C:GLU71 3.9 45.0 1.0
O3A C:GTP501 3.9 32.5 1.0
OD1 C:ASP69 4.0 34.7 1.0
OD2 C:ASP69 4.0 32.4 1.0
CB C:GLN11 4.2 29.6 1.0
O2A C:GTP501 4.2 33.8 1.0
OD2 C:ASP98 4.2 38.4 1.0
CB C:ASP98 4.3 33.5 1.0
N C:GLN11 4.4 27.3 1.0
O3G C:GTP501 4.5 30.9 1.0
CG C:ASP69 4.5 30.4 1.0
O2B C:GTP501 4.5 26.3 1.0
CG C:ASP98 4.7 35.0 1.0
NE2 C:GLN11 4.7 42.4 1.0
PA C:GTP501 4.8 30.8 1.0
CA C:GLN11 4.9 30.0 1.0
CE D:LYS252 5.0 35.2 1.0

Magnesium binding site 4 out of 5 in 7dbc

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Magnesium binding site 4 out of 5 in the Pra 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 Pra in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:85.2
occ:1.00
O D:HOH613 2.2 135.0 1.0
O2G D:GTP501 2.4 94.3 1.0
O2B D:GTP501 2.8 88.9 1.0
CB D:GLN11 3.5 75.1 1.0
PG D:GTP501 3.7 144.0 1.0
PB D:GTP501 3.8 77.0 1.0
OE1 D:GLN11 4.0 88.8 1.0
O3A D:GTP501 4.1 91.2 1.0
N D:GLN11 4.1 67.8 1.0
O3B D:GTP501 4.1 104.3 1.0
OD2 D:ASP67 4.2 73.0 1.0
O3G D:GTP501 4.2 103.7 1.0
CA D:GLN11 4.4 73.1 1.0
O2A D:GTP501 4.4 97.3 1.0
CD D:GLN11 4.5 84.4 1.0
CG D:GLN11 4.6 76.5 1.0
PA D:GTP501 4.7 80.6 1.0
OD1 D:ASP67 4.8 73.0 1.0
CG2 D:THR72 4.8 102.0 1.0
CB D:GLU69 4.8 94.7 1.0
O1G D:GTP501 4.9 109.6 1.0
CG D:ASP67 4.9 71.7 1.0
O1A D:GTP501 5.0 87.9 1.0

Magnesium binding site 5 out of 5 in 7dbc

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Magnesium binding site 5 out of 5 in the Pra 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 Pra in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg402

b:97.6
occ:1.00
O2B F:ACP401 2.3 100.1 1.0
O1G F:ACP401 2.5 95.8 1.0
OE2 F:GLU331 2.6 88.8 1.0
OE1 F:GLU331 2.7 90.2 1.0
CD F:GLU331 3.0 86.4 1.0
PB F:ACP401 3.7 96.8 1.0
PG F:ACP401 3.8 102.0 1.0
NZ F:LYS74 3.9 85.0 1.0
O1B F:ACP401 4.0 102.4 1.0
C3B F:ACP401 4.3 95.3 1.0
ND2 F:ASN333 4.3 81.0 1.0
CG F:GLU331 4.5 77.1 1.0
CE F:LYS74 4.5 82.2 1.0
O2G F:ACP401 4.6 100.8 1.0
O3G F:ACP401 4.9 103.8 1.0
CG F:ASN333 5.0 74.3 1.0
O3A F:ACP401 5.0 95.2 1.0

Reference:

C.Y.Wu, Y.X.Wang. Pra in Complex with Tubulin To Be Published.
Page generated: Wed Oct 2 15:45:10 2024

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