Magnesium in PDB 6sup: Crystal Structure of TCDB2-TCCC3-CDC42

All present enzymatic activity of Crystal Structure of TCDB2-TCCC3-CDC42:
3.6.5.2;

The structure of Crystal Structure of TCDB2-TCCC3-CDC42, PDB code: 6sup was solved by D.Roderer, E.Schubert, O.Sitsel, S.Raunser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.17 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.350, 156.550, 179.460, 90.00, 90.00, 90.00
R / Rfree (%)	28.7 / 32

The binding sites of Magnesium atom in the Crystal Structure of TCDB2-TCCC3-CDC42 (pdb code 6sup). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of TCDB2-TCCC3-CDC42, PDB code: 6sup:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of TCDB2-TCCC3-CDC42


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of TCDB2-TCCC3-CDC42 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2401 b:41.6 occ:1.00 CD2 A:HIS744 3.0 56.6 1.0 CB A:HIS744 3.2 47.1 1.0 CG A:HIS744 3.4 53.3 1.0 N A:SER716 3.5 31.1 1.0 CA A:HIS744 3.5 41.2 1.0 CD2 A:LEU670 3.6 42.9 1.0 O A:HOH3519 3.6 36.1 1.0 C A:ARG715 3.7 31.6 1.0 O A:HOH2676 3.8 37.8 1.0 CA A:SER716 3.9 28.4 1.0 N A:ARG715 4.0 34.5 1.0 CB A:TYR714 4.0 36.7 1.0 CA A:ARG715 4.1 31.5 1.0 O A:ARG715 4.2 30.3 1.0 C A:TYR714 4.3 34.1 1.0 NE2 A:HIS744 4.3 57.0 1.0 CB A:SER716 4.4 31.7 1.0 C A:HIS744 4.4 38.5 1.0 O A:TYR714 4.6 29.3 1.0 N A:HIS744 4.7 38.5 1.0 ND1 A:HIS744 4.8 55.9 1.0 N A:THR745 4.8 35.6 1.0 CA A:TYR714 4.8 33.7 1.0 O A:GLY669 4.9 42.4 1.0 CA A:LEU670 4.9 41.5 1.0 CG A:LEU670 4.9 44.4 1.0 CB A:LYS695 4.9 38.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of TCDB2-TCCC3-CDC42


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of TCDB2-TCCC3-CDC42 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2402 b:32.3 occ:1.00 N A:VAL1017 3.3 31.1 1.0 CA A:TYR1016 3.7 25.9 1.0 CG2 A:VAL1017 3.7 40.4 1.0 CD1 A:TYR1016 3.8 31.6 1.0 CB A:TYR1016 3.9 30.8 1.0 C A:TYR1016 4.0 27.8 1.0 CG1 A:VAL1017 4.1 39.2 1.0 CB A:VAL1017 4.3 38.6 1.0 O A:HOH3112 4.3 45.4 1.0 CG A:TYR1016 4.4 31.1 1.0 CA A:VAL1017 4.4 31.9 1.0 O A:THR1015 4.5 25.9 1.0 CE1 A:TYR1016 4.9 29.5 1.0 N A:TYR1016 4.9 24.4 1.0 O A:VAL1017 5.0 31.8 1.0 OD1 A:ASN1020 5.0 66.6 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of TCDB2-TCCC3-CDC42


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of TCDB2-TCCC3-CDC42 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2403 b:32.9 occ:1.00 O A:HOH2599 3.1 50.7 1.0 NH1 A:ARG1524 3.4 33.5 1.0 CD A:ARG1524 3.7 23.8 1.0 CD A:LYS1545 3.9 36.5 1.0 CD1 A:TYR1542 3.9 27.3 1.0 O A:HOH3518 3.9 29.5 1.0 CG2 A:ILE1537 3.9 22.1 1.0 CE1 A:TYR1542 4.0 29.2 1.0 OE1 A:GLN1526 4.3 46.7 1.0 CE A:LYS1545 4.3 35.9 1.0 CZ A:ARG1524 4.4 31.3 1.0 NE A:ARG1524 4.5 26.9 1.0 CG A:ARG1524 4.6 21.7 1.0 CB A:ARG1524 4.7 24.8 1.0 CD1 A:ILE1537 4.8 26.9 1.0 O A:HOH2770 4.8 41.7 1.0 OE1 A:GLN1546 4.9 50.5 1.0 CB A:ILE1537 5.0 22.2 1.0

D.Roderer, E.Schubert, O.Sitsel, S.Raunser. Towards the Application of Tc Toxins As A Universal Protein Translocation System. Nat Commun V. 10 5263 2019.
ISSN: ESSN 2041-1723
PubMed: 31748551
DOI: 10.1038/S41467-019-13253-8