Magnesium in PDB 4e6n: Crystal Structure of Bacterial Pnkp-C/HEN1-N Heterodimer

The structure of Crystal Structure of Bacterial Pnkp-C/HEN1-N Heterodimer, PDB code: 4e6n was solved by R.H.Huang, P.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.65 / 2.39
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.630, 59.695, 101.540, 81.38, 87.82, 88.82
R / Rfree (%)	16.8 / 22.3

The binding sites of Magnesium atom in the Crystal Structure of Bacterial Pnkp-C/HEN1-N Heterodimer (pdb code 4e6n). 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 Bacterial Pnkp-C/HEN1-N Heterodimer, PDB code: 4e6n:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Bacterial Pnkp-C/HEN1-N Heterodimer


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 Bacterial Pnkp-C/HEN1-N Heterodimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:40.2 occ:1.00 O2P A:AMP902 2.5 33.6 1.0 O A:HOH1060 2.5 23.7 1.0 O A:HOH1100 2.6 42.0 1.0 O A:HOH1059 2.7 22.9 1.0 O A:HOH1058 2.7 28.3 1.0 O A:HOH1061 2.8 33.4 1.0 P A:AMP902 3.7 26.7 1.0 O A:HOH1086 3.9 33.8 1.0 OE2 A:GLU607 4.0 25.1 1.0 O A:GLY534 4.0 20.5 1.0 NZ A:LYS531 4.1 25.8 1.0 OE2 A:GLU769 4.2 23.9 1.0 O1P A:AMP902 4.5 25.3 1.0 O4' A:AMP902 4.5 24.5 1.0 N A:GLY534 4.6 28.5 1.0 C4' A:AMP902 4.6 29.1 1.0 OE1 A:GLU769 4.7 30.1 1.0 O A:HIS532 4.8 23.9 1.0 C1' A:AMP902 4.8 16.6 1.0 SD A:MET533 4.8 24.3 1.0 CA A:MET533 4.9 25.4 1.0 C A:GLY534 4.9 26.1 1.0 CE A:MET533 4.9 28.2 1.0 CD A:GLU769 4.9 29.6 1.0 O5' A:AMP902 4.9 31.1 1.0 O A:HOH1089 4.9 33.5 1.0 OH A:TYR798 4.9 32.0 1.0 CG A:MET533 5.0 20.0 1.0 O A:HOH1079 5.0 36.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Bacterial Pnkp-C/HEN1-N Heterodimer


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 Bacterial Pnkp-C/HEN1-N Heterodimer within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg901 b:31.6 occ:1.00 O2P C:AMP902 2.5 20.1 1.0 O C:HOH1065 2.5 23.8 1.0 O C:HOH1066 2.6 36.6 1.0 O C:HOH1064 2.7 24.1 1.0 O C:HOH1109 2.7 24.0 1.0 O C:HOH1063 2.7 39.0 1.0 P C:AMP902 3.8 25.0 1.0 O C:HOH1050 3.9 33.3 1.0 NZ C:LYS531 4.0 21.1 1.0 O C:GLY534 4.1 20.7 1.0 OE2 C:GLU607 4.1 27.1 1.0 OE2 C:GLU769 4.2 22.1 1.0 O4' C:AMP902 4.5 30.8 1.0 O1P C:AMP902 4.6 22.4 1.0 OE1 C:GLU769 4.7 29.3 1.0 N C:GLY534 4.7 26.8 1.0 C4' C:AMP902 4.7 20.5 1.0 SD C:MET533 4.8 24.1 1.0 C1' C:AMP902 4.8 16.5 1.0 O C:HIS532 4.8 20.4 1.0 OH C:TYR798 4.9 31.3 1.0 CD C:GLU769 4.9 28.4 1.0 CE C:MET533 4.9 26.9 1.0 CA C:MET533 4.9 25.2 1.0 CG C:MET533 4.9 21.1 1.0 C C:GLY534 5.0 22.6 1.0 O5' C:AMP902 5.0 25.6 1.0

P.Wang, C.M.Chan, D.Christensen, C.Zhang, K.Selvadurai, R.H.Huang. Molecular Basis of Bacterial Protein HEN1 Activating the Ligase Activity of Bacterial Protein Pnkp For Rna Repair. Proc.Natl.Acad.Sci.Usa V. 109 13248 2012.
ISSN: ISSN 0027-8424
PubMed: 22847431
DOI: 10.1073/PNAS.1209805109