Magnesium in PDB 7s0z: Structures of Tcdb in Complex with R-Ras

The structure of Structures of Tcdb in Complex with R-Ras, PDB code: 7s0z was solved by L.Zheng, J.Rongsheng, C.Peng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.02 / 2.34
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.308, 112.112, 101.571, 90, 95.89, 90
R / Rfree (%)	20.1 / 24.1

The structure of Structures of Tcdb in Complex with R-Ras also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Magnesium atom in the Structures of Tcdb in Complex with R-Ras (pdb code 7s0z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structures of Tcdb in Complex with R-Ras, PDB code: 7s0z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Structures of Tcdb in Complex with R-Ras


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structures of Tcdb in Complex with R-Ras within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg619 b:39.3 occ:1.00 O A:HOH904 2.7 33.1 1.0 O1A A:UDP601 2.7 27.7 1.0 O3' A:UDP601 2.8 30.1 1.0 CG A:ASP288 3.1 29.1 1.0 OD2 A:ASP288 3.2 29.0 1.0 C3' A:UDP601 3.3 30.1 1.0 OD1 A:ASP288 3.4 28.8 1.0 CG2 A:VAL287 3.4 30.9 1.0 N A:ASP288 3.4 27.9 1.0 CB A:ASP288 3.5 28.7 1.0 O5' A:UDP601 3.6 29.0 1.0 PA A:UDP601 3.6 28.7 1.0 MG A:MG620 3.6 39.7 1.0 N A:VAL287 3.8 29.3 1.0 CB A:ASP286 3.8 29.6 1.0 C5' A:UDP601 4.0 29.5 1.0 CA A:ASP288 4.1 27.8 1.0 MN A:MN618 4.2 29.4 1.0 O A:HOH755 4.2 28.7 1.0 CG A:ASP286 4.2 30.1 1.0 C A:VAL287 4.2 28.6 1.0 C4' A:UDP601 4.2 30.0 1.0 O2A A:UDP601 4.2 29.2 1.0 CA A:VAL287 4.3 29.4 1.0 C A:ASP286 4.3 29.0 1.0 OD2 A:ASP286 4.5 30.3 1.0 CB A:VAL287 4.5 29.9 1.0 CA A:ASP286 4.5 29.2 1.0 CD1 A:LEU520 4.6 36.0 1.0 C2' A:UDP601 4.7 30.2 1.0 OD1 A:ASP286 4.7 30.3 1.0

Magnesium binding site 2 out of 5 in the Structures of Tcdb in Complex with R-Ras


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structures of Tcdb in Complex with R-Ras within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg620 b:39.7 occ:1.00 O A:HOH904 2.6 33.1 1.0 O A:ASN518 2.8 32.5 1.0 O2A A:UDP601 2.8 29.2 1.0 O A:GLN515 3.0 33.5 1.0 O A:HOH727 3.1 36.2 1.0 OD2 A:ASP288 3.1 29.0 1.0 O1A A:UDP601 3.2 27.7 1.0 PA A:UDP601 3.5 28.7 1.0 MG A:MG619 3.6 39.3 1.0 C A:ASN518 3.8 33.7 1.0 MN A:MN618 3.9 29.4 1.0 CG A:LEU520 3.9 34.7 1.0 CG A:ASP288 3.9 29.1 1.0 C A:GLN515 3.9 32.5 1.0 CD1 A:LEU520 4.1 36.0 1.0 CB A:ASP288 4.1 28.7 1.0 CA A:SER519 4.2 32.7 1.0 N A:LEU520 4.3 32.6 1.0 N A:SER519 4.3 32.9 1.0 C A:SER519 4.5 33.1 1.0 O5' A:UDP601 4.5 29.0 1.0 CA A:GLU516 4.6 29.9 1.0 N A:GLU516 4.7 30.4 1.0 CB A:GLN515 4.7 34.7 1.0 CB A:LEU520 4.8 32.4 1.0 O2B A:UDP601 4.8 28.7 1.0 CA A:ASN518 4.8 35.4 1.0 O A:GLU516 4.8 29.3 1.0 CA A:GLN515 4.8 33.9 1.0 O3A A:UDP601 4.8 28.6 1.0 CD2 A:LEU520 4.9 35.0 1.0 C A:GLU516 4.9 29.6 1.0 N A:ASN518 4.9 34.6 1.0

Magnesium binding site 3 out of 5 in the Structures of Tcdb in Complex with R-Ras


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structures of Tcdb in Complex with R-Ras within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg621 b:51.0 occ:1.00 O A:HOH814 3.0 32.9 1.0 O A:HOH904 3.1 33.1 1.0 CG A:GLN515 4.0 35.7 1.0 CG2 A:VAL287 4.1 30.9 1.0 OE1 A:GLN515 4.2 40.6 1.0 CG2 A:THR110 4.3 38.1 1.0 CB A:GLN515 4.4 34.7 1.0 N A:ALA111 4.4 35.6 1.0 CB A:ALA111 4.4 34.5 1.0 CD A:GLN515 4.5 38.1 1.0 CA A:ALA111 4.5 35.4 1.0 OD1 A:ASN108 4.5 42.5 1.0 CB A:THR110 4.7 38.2 1.0 CZ3 A:TRP102 4.8 37.6 1.0 CD1 A:LEU520 4.9 36.0 1.0 C A:THR110 4.9 36.8 1.0

Magnesium binding site 4 out of 5 in the Structures of Tcdb in Complex with R-Ras


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structures of Tcdb in Complex with R-Ras within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg624 b:66.0 occ:1.00 O2A C:GDP305 3.1 34.5 1.0 O2B C:GDP305 3.1 35.3 1.0 OE2 A:GLU462 3.2 51.1 1.0 O3B C:GDP305 3.3 34.4 1.0 OG C:SER43 3.3 35.9 1.0 PB C:GDP305 3.7 35.2 1.0 O C:HOH448 3.9 49.3 1.0 CD A:GLU462 3.9 45.9 1.0 CB C:SER43 4.1 33.5 1.0 OE1 A:GLU462 4.1 48.4 1.0 PA C:GDP305 4.2 35.2 1.0 O C:HOH406 4.2 48.3 1.0 OD2 C:ASP59 4.2 37.5 0.4 O3A C:GDP305 4.4 34.5 1.0 O1A C:GDP305 4.9 34.4 1.0

Magnesium binding site 5 out of 5 in the Structures of Tcdb in Complex with R-Ras


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structures of Tcdb in Complex with R-Ras within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2303 b:60.9 occ:1.00 OG D:SER43 2.7 38.4 1.0 O D:HOH2407 2.7 45.1 1.0 O2B D:GDP2302 2.9 37.5 1.0 CB D:SER43 3.7 36.5 1.0 OE1 B:GLU462 3.8 55.5 1.0 O1A D:GDP2302 4.0 35.6 1.0 O1B D:GDP2302 4.0 38.1 1.0 PB D:GDP2302 4.0 37.9 1.0 CA D:SER43 4.8 35.4 1.0 CD B:GLU462 4.8 52.7 1.0 N D:SER43 4.8 35.2 1.0 O D:HOH2415 4.9 40.4 1.0 PA D:GDP2302 4.9 38.8 1.0 O D:HOH2457 4.9 50.6 1.0 OD1 B:ASN464 5.0 43.7 1.0 O3A D:GDP2302 5.0 38.2 1.0

L.Zheng, J.Rongsheng, C.Peng. Structures of Tcdb in Complex with R-Ras To Be Published.