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Magnesium in PDB 7dba: Ryx in Complex with Tubulin

Protein crystallography data

The structure of Ryx in Complex with Tubulin, PDB code: 7dba 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) 31.30 / 2.46
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.449, 158.876, 181.608, 90, 90, 90
R / Rfree (%) 18.8 / 22.8

Other elements in 7dba:

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

Calcium (Ca) 2 atoms
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 7dba

Go back to Magnesium Binding Sites List in 7dba
Magnesium binding site 1 out of 4 in the Ryx 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 Ryx in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:32.4
occ:1.00
O1G A:GTP501 2.0 26.4 1.0
O A:HOH623 2.1 28.8 1.0
O A:HOH641 2.1 35.3 1.0
O1B A:GTP501 2.2 25.0 1.0
O A:HOH612 2.2 44.2 1.0
O A:HOH616 2.3 29.4 1.0
PG A:GTP501 3.0 36.2 1.0
PB A:GTP501 3.3 28.4 1.0
O2G A:GTP501 3.4 36.4 1.0
O3B A:GTP501 3.4 48.7 1.0
OD1 A:ASP69 3.9 36.7 1.0
O3A A:GTP501 4.0 42.8 1.0
NZ B:LYS252 4.0 36.4 1.0
OD2 A:ASP69 4.0 37.0 1.0
CG A:GLU71 4.1 62.5 1.0
OE1 A:GLU71 4.2 52.3 1.0
CB A:ASP98 4.2 32.1 1.0
OD2 A:ASP98 4.4 42.3 1.0
CG A:ASP69 4.4 41.6 1.0
O3G A:GTP501 4.4 31.5 1.0
CB A:GLN11 4.4 30.5 1.0
N A:GLN11 4.5 34.9 1.0
CG A:ASP98 4.5 39.4 1.0
O2B A:GTP501 4.5 43.0 1.0
CD A:GLU71 4.6 60.4 1.0
OG1 A:THR145 4.7 32.4 1.0
O1A A:GTP501 4.9 39.9 1.0
PA A:GTP501 5.0 40.4 1.0
NE2 A:GLN11 5.0 48.0 1.0

Magnesium binding site 2 out of 4 in 7dba

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Magnesium binding site 2 out of 4 in the Ryx 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 Ryx in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:23.1
occ:1.00
OE1 B:GLN11 2.1 34.8 1.0
O B:HOH655 2.1 38.0 1.0
O1A B:GDP501 2.2 33.3 1.0
O C:HOH694 2.2 38.4 1.0
O B:HOH677 2.5 35.3 1.0
O B:HOH624 2.7 42.5 1.0
CD B:GLN11 3.2 43.9 1.0
PA B:GDP501 3.5 27.6 1.0
OD2 B:ASP177 3.7 49.6 1.0
O3A B:GDP501 3.9 31.9 1.0
CB B:GLN11 4.0 26.0 1.0
CG B:GLN11 4.0 34.7 1.0
C5' B:GDP501 4.3 27.5 1.0
NE2 B:GLN11 4.3 33.0 1.0
O5' B:GDP501 4.4 20.9 1.0
OD1 B:ASN99 4.4 34.4 1.0
O2A B:GDP501 4.5 31.4 1.0
O1B B:GDP501 4.6 27.8 1.0
C8 B:GDP501 4.7 27.8 1.0
CG B:ASP177 4.7 36.9 1.0
OE1 C:GLU254 4.7 45.1 1.0
PB B:GDP501 4.9 26.7 1.0

Magnesium binding site 3 out of 4 in 7dba

Go back to Magnesium Binding Sites List in 7dba
Magnesium binding site 3 out of 4 in the Ryx 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 Ryx in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:31.3
occ:1.00
O1G C:GTP501 2.0 26.0 1.0
O C:HOH656 2.0 28.8 1.0
O1B C:GTP501 2.1 28.2 1.0
O C:HOH630 2.1 28.8 1.0
O C:HOH704 2.1 29.6 1.0
O C:HOH648 2.2 29.4 1.0
PG C:GTP501 3.1 29.6 1.0
PB C:GTP501 3.1 22.3 1.0
O3B C:GTP501 3.4 36.8 1.0
O2G C:GTP501 3.6 29.1 1.0
O3A C:GTP501 3.8 41.0 1.0
OD1 C:ASP69 3.9 28.1 1.0
NZ D:LYS252 3.9 30.2 1.0
OE1 C:GLU71 4.1 55.8 1.0
OD2 C:ASP69 4.2 29.7 1.0
CG C:GLU71 4.2 32.8 1.0
CB C:GLN11 4.2 22.7 1.0
OD2 C:ASP98 4.4 36.1 1.0
N C:GLN11 4.4 26.1 1.0
CB C:ASP98 4.4 30.0 1.0
O3G C:GTP501 4.4 24.1 1.0
O2B C:GTP501 4.4 32.8 1.0
CG C:ASP69 4.5 31.1 1.0
O1A C:GTP501 4.6 33.0 1.0
CD C:GLU71 4.7 47.7 1.0
PA C:GTP501 4.7 26.7 1.0
CG C:ASP98 4.8 40.7 1.0
OE1 C:GLN11 4.8 45.1 1.0
OG1 C:THR145 4.9 29.0 1.0
CA C:GLN11 4.9 29.9 1.0

Magnesium binding site 4 out of 4 in 7dba

Go back to Magnesium Binding Sites List in 7dba
Magnesium binding site 4 out of 4 in the Ryx 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 Ryx in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:57.7
occ:1.00
O1A D:GDP501 2.1 80.8 1.0
NE2 D:GLN11 2.4 54.0 1.0
O D:HOH621 3.0 48.9 1.0
OD1 D:ASN99 3.6 63.8 1.0
PA D:GDP501 3.6 51.3 1.0
CD D:GLN11 3.7 76.3 1.0
C5' D:GDP501 4.2 53.0 1.0
O3A D:GDP501 4.2 51.4 1.0
O5' D:GDP501 4.4 55.3 1.0
CG D:ASN99 4.5 63.5 1.0
OE1 D:GLN11 4.5 82.5 1.0
O1B D:GDP501 4.5 58.3 1.0
CB D:GLN11 4.6 62.5 1.0
O2A D:GDP501 4.6 49.7 1.0
ND2 D:ASN99 4.6 76.2 1.0
CG D:GLN11 4.7 63.1 1.0
O D:HOH605 4.9 46.5 1.0
PB D:GDP501 4.9 54.0 1.0

Reference:

C.Y.Wu, Y.X.Wang. Ryx in Complex with Tubulin To Be Published.
Page generated: Wed Oct 2 15:44:23 2024

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