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

Protein crystallography data

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

Magnesium Binding Sites:

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 4e6n

Go back to Magnesium Binding Sites List in 4e6n
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 4e6n

Go back to Magnesium Binding Sites List in 4e6n
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

Reference:

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
Page generated: Mon Dec 14 13:37:35 2020

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