Magnesium in PDB 5chi: Crystal Structure of PF2046 in Complex with Ssdna

The structure of Crystal Structure of PF2046 in Complex with Ssdna, PDB code: 5chi was solved by J.S.Kim, K.Y.Hwang, W.C.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.59 / 2.47
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.010, 85.903, 69.204, 90.00, 118.44, 90.00
R / Rfree (%)	18.2 / 22.8

The binding sites of Magnesium atom in the Crystal Structure of PF2046 in Complex with Ssdna (pdb code 5chi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of PF2046 in Complex with Ssdna, PDB code: 5chi:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of PF2046 in Complex with Ssdna


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 PF2046 in Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:44.6 occ:1.00 O A:HOH608 2.2 33.5 1.0 OD1 A:ASP7 2.3 35.2 1.0 O D:HOH102 2.3 31.1 1.0 OD2 A:ASP7 2.4 36.1 1.0 OE2 A:GLU145 2.4 36.1 1.0 CG A:ASP7 2.5 33.4 1.0 OP1 D:DT7 2.6 36.2 1.0 CD A:GLU145 3.0 33.1 1.0 CG A:GLU145 3.0 26.9 1.0 MG A:MG502 3.4 29.1 1.0 CB A:GLU145 3.6 22.0 1.0 OD2 A:ASP80 3.6 33.3 1.0 CB A:ASP7 3.8 27.6 1.0 P D:DT7 4.0 37.1 1.0 OE1 A:GLU145 4.1 36.0 1.0 O A:THR8 4.2 32.0 1.0 CA A:GLU145 4.3 18.9 1.0 CG A:ASP80 4.6 30.6 1.0 O D:HOH101 4.6 33.2 1.0 OP2 D:DT7 4.6 38.2 1.0 OP2 D:DT8 4.7 37.0 1.0 O3' D:DT6 4.8 41.9 1.0 CA A:ASP7 4.9 24.9 1.0 O5' D:DT7 4.9 40.2 1.0 N A:THR8 4.9 25.1 1.0 O A:HOH605 5.0 30.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of PF2046 in Complex with Ssdna


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 PF2046 in Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:29.1 occ:1.00 OD2 A:ASP80 2.1 33.3 1.0 OD1 A:ASP7 2.3 35.2 1.0 O A:HOH612 2.4 24.5 1.0 OP1 D:DT7 2.4 36.2 1.0 O3' D:DT6 2.6 41.9 1.0 O A:HOH605 2.9 30.0 1.0 CG A:ASP80 3.1 30.6 1.0 P D:DT7 3.1 37.1 1.0 MG A:MG501 3.4 44.6 1.0 CB A:ASP80 3.5 23.3 1.0 CG A:ASP7 3.6 33.4 1.0 O A:HOH608 3.9 33.5 1.0 C3' D:DT6 4.0 37.8 1.0 OE1 A:GLU61 4.0 32.8 1.0 OE2 A:GLU61 4.0 30.6 1.0 O5' D:DT7 4.1 40.2 1.0 C5' D:DT7 4.2 34.4 1.0 CD A:GLU61 4.2 27.5 1.0 O A:ASP80 4.2 27.1 1.0 C4' D:DT6 4.2 36.5 1.0 OD1 A:ASP80 4.2 37.0 1.0 OP2 D:DT7 4.3 38.2 1.0 N A:THR8 4.3 25.1 1.0 O A:THR8 4.3 32.0 1.0 OD2 A:ASP7 4.4 36.1 1.0 CB A:ASP7 4.4 27.6 1.0 CA A:ASP7 4.5 24.9 1.0 O D:HOH102 4.6 31.1 1.0 C2' D:DT6 4.7 36.5 1.0 C5' D:DT6 4.7 35.8 1.0 CA A:ASP80 4.9 25.2 1.0 C A:ASP7 5.0 26.9 1.0 C A:ASP80 5.0 26.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of PF2046 in Complex with Ssdna


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 PF2046 in Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:44.4 occ:1.00 OD2 B:ASP80 2.3 41.9 1.0 O B:HOH415 2.3 34.8 1.0 OD1 B:ASP7 2.3 42.1 1.0 O B:HOH417 2.5 34.3 1.0 OP1 E:DT7 2.5 48.4 1.0 O3' E:DT6 2.7 48.9 1.0 P E:DT7 3.2 44.5 1.0 CG B:ASP80 3.4 42.9 1.0 OE2 B:GLU61 3.4 40.2 1.0 CG B:ASP7 3.5 43.8 1.0 O B:THR8 3.6 36.6 1.0 C5' E:DT7 3.8 48.8 1.0 OE1 B:GLU61 3.9 33.5 1.0 CB B:ASP80 3.9 34.4 1.0 C3' E:DT6 3.9 50.0 1.0 O B:HOH402 4.0 48.4 1.0 CD B:GLU61 4.0 38.0 1.0 O5' E:DT7 4.0 53.1 1.0 N B:THR8 4.1 31.2 1.0 OD2 B:ASP7 4.2 44.2 1.0 C4' E:DT6 4.2 49.4 1.0 MG B:MG302 4.3 47.3 1.0 C2' E:DT6 4.4 54.6 1.0 OD1 B:ASP80 4.5 40.8 1.0 OP2 E:DT7 4.5 54.4 1.0 C B:THR8 4.6 34.7 1.0 O B:ASP80 4.6 38.1 1.0 CA B:ASP7 4.6 32.2 1.0 CB B:ASP7 4.6 32.0 1.0 CA B:THR8 4.8 33.8 1.0 C5' E:DT6 4.9 48.0 1.0 C B:ASP7 4.9 33.0 1.0 CB B:THR8 5.0 34.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of PF2046 in Complex with Ssdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of PF2046 in Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:47.3 occ:1.00 OE2 B:GLU145 2.2 41.0 1.0 OP1 E:DT7 2.6 48.4 1.0 OD2 B:ASP7 2.9 44.2 1.0 CD B:GLU145 3.0 41.1 1.0 O B:HOH402 3.1 48.4 1.0 O E:HOH101 3.1 44.7 1.0 CG B:GLU145 3.2 38.0 1.0 OP2 E:DT8 3.2 46.4 1.0 O B:THR8 3.7 36.6 1.0 CG B:ASP7 3.7 43.8 1.0 OD1 B:ASP7 3.8 42.1 1.0 P E:DT7 3.8 44.5 1.0 OP1 E:DT8 3.9 46.2 1.0 P E:DT8 4.0 45.9 1.0 C5' E:DT7 4.0 48.8 1.0 O5' E:DT7 4.2 53.1 1.0 OE1 B:GLU145 4.2 38.1 1.0 CB B:GLU145 4.2 31.1 1.0 MG B:MG301 4.3 44.4 1.0 CA B:GLY9 4.4 30.9 1.0 OP2 E:DT7 4.5 54.4 1.0 CB B:PRO171 4.5 29.3 1.0 O3' E:DT7 4.5 54.7 1.0 C B:THR8 4.6 34.7 1.0 CA B:GLU145 4.8 31.3 1.0 OD2 B:ASP80 4.9 41.9 1.0 C3' E:DT7 4.9 51.5 1.0 N B:GLY9 4.9 35.0 1.0 CG B:PRO171 5.0 28.0 1.0

J.S.Kim, G.D.Sambalkhundev, S.H.Kim, A.Han, S.M.Ko, K.Y.Hwang, W.C.Lee. Structural Basis of Two-Nucleotide Removal of Ssdna By A Cryptic Rnase H Fold 3'-5' Exonuclease PF2046 From Pyrococcus Furiosus To Be Published.