Magnesium in PDB 4itr: Crystal Structure of IBPAFIC2-H3717A in Complex with Adenylylated CDC42

All present enzymatic activity of Crystal Structure of IBPAFIC2-H3717A in Complex with Adenylylated CDC42:
2.7.7.1;

The structure of Crystal Structure of IBPAFIC2-H3717A in Complex with Adenylylated CDC42, PDB code: 4itr was solved by J.Xiao, J.E.Dixon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.95 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.495, 90.997, 190.969, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 22.6

The binding sites of Magnesium atom in the Crystal Structure of IBPAFIC2-H3717A in Complex with Adenylylated CDC42 (pdb code 4itr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of IBPAFIC2-H3717A in Complex with Adenylylated CDC42, PDB code: 4itr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of IBPAFIC2-H3717A in Complex with Adenylylated 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 IBPAFIC2-H3717A in Complex with Adenylylated CDC42 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg203 b:26.9 occ:1.00 O C:HOH345 1.8 14.9 1.0 OG1 C:THR17 2.1 19.4 1.0 O2B C:GDP202 2.1 16.7 1.0 O C:HOH302 2.1 20.9 1.0 O C:THR35 2.1 21.0 1.0 CB C:THR17 3.2 19.7 1.0 C C:THR35 3.2 22.6 1.0 PB C:GDP202 3.3 19.5 1.0 O1B C:GDP202 3.5 18.9 1.0 OD2 C:ASP57 3.8 30.4 1.0 CA C:THR35 4.0 23.0 1.0 N C:THR17 4.0 16.9 1.0 O C:PRO34 4.0 17.1 1.0 O C:HOH304 4.1 21.6 1.0 O1A C:GDP202 4.1 19.6 1.0 CA C:THR17 4.2 21.6 1.0 O3B C:GDP202 4.2 18.3 1.0 N C:VAL36 4.3 20.4 1.0 CG2 C:THR17 4.3 13.4 1.0 O3A C:GDP202 4.5 22.6 1.0 OD1 C:ASP57 4.5 18.2 1.0 CA C:VAL36 4.5 26.8 1.0 O C:THR58 4.5 21.2 1.0 CG C:ASP57 4.6 28.6 1.0 O C:HOH351 4.6 20.6 1.0 PA C:GDP202 4.6 25.3 1.0 O2A C:GDP202 4.7 21.0 1.0 C C:PRO34 4.9 18.5 1.0 CB C:LYS16 4.9 20.3 1.0 NZ C:LYS16 4.9 20.9 1.0 N C:THR35 4.9 17.7 1.0 CE C:LYS16 4.9 19.9 1.0 CB C:THR35 5.0 22.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of IBPAFIC2-H3717A in Complex with Adenylylated 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 IBPAFIC2-H3717A in Complex with Adenylylated CDC42 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg203 b:28.4 occ:1.00 O D:HOH302 2.0 25.1 1.0 O D:HOH387 2.1 20.6 1.0 O2B D:GDP202 2.1 19.5 1.0 O D:HOH340 2.1 23.8 1.0 OG1 D:THR17 2.1 22.6 1.0 O D:THR35 2.3 24.9 1.0 PB D:GDP202 3.2 20.8 1.0 O1B D:GDP202 3.2 22.7 1.0 CB D:THR17 3.2 23.3 1.0 C D:THR35 3.4 21.3 1.0 OD2 D:ASP57 3.9 27.5 1.0 N D:THR17 3.9 25.1 1.0 O1A D:GDP202 4.0 25.1 1.0 CA D:THR35 4.0 24.6 1.0 O D:PRO34 4.0 21.9 1.0 O3B D:GDP202 4.1 18.3 1.0 CA D:THR17 4.1 28.6 1.0 O D:HOH305 4.3 17.6 1.0 CG2 D:THR17 4.3 21.4 1.0 O3A D:GDP202 4.3 29.5 1.0 O D:HOH339 4.4 29.8 1.0 N D:VAL36 4.4 22.2 1.0 OD1 D:ASP57 4.5 21.5 1.0 PA D:GDP202 4.5 25.9 1.0 O2A D:GDP202 4.6 15.4 1.0 CG D:ASP57 4.6 31.2 1.0 O D:HOH395 4.6 27.2 1.0 O D:THR58 4.7 25.7 1.0 CA D:VAL36 4.8 21.9 1.0 CB D:LYS16 4.9 24.2 1.0 NZ D:LYS16 4.9 18.1 1.0 C D:PRO34 4.9 23.9 1.0 CE D:LYS16 5.0 18.6 1.0 N D:THR35 5.0 17.8 1.0

J.Xiao, C.A.Worby, S.Mattoo, B.Sankaran, J.E.Dixon. Structural Basis of Fic-Mediated Adenylylation. Nat.Struct.Mol.Biol. V. 17 1004 2010.
ISSN: ISSN 1545-9993
PubMed: 20622875
DOI: 10.1038/NSMB.1867