Magnesium in PDB 1s9f: Dpo with at Matched

All present enzymatic activity of Dpo with at Matched:
2.7.7.7;

The structure of Dpo with at Matched, PDB code: 1s9f was solved by J.Trincao, R.E.Johnson, W.T.Wolfle, C.R.Escalante, S.Prakash, L.Prakash, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	104.800, 100.300, 110.800, 90.00, 95.20, 90.00
R / Rfree (%)	20.5 / 23.9

The structure of Dpo with at Matched also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Dpo with at Matched (pdb code 1s9f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Dpo with at Matched, PDB code: 1s9f:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Dpo with at Matched


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dpo with at Matched within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4007 b:38.1 occ:1.00 O A:ALA181 2.4 34.2 1.0 O A:ILE186 2.5 30.4 1.0 O A:HOH4077 2.5 41.7 1.0 O E:HOH195 2.5 32.9 1.0 O E:HOH1120 2.7 57.0 1.0 C A:ALA181 3.6 33.7 1.0 C A:ILE186 3.6 28.7 1.0 CA A:GLY187 4.1 31.0 1.0 N A:GLY187 4.3 29.6 1.0 OP1 E:DT12 4.3 27.6 1.0 OP2 E:DT12 4.4 27.2 1.0 CA A:ALA181 4.4 33.2 1.0 N A:ASP182 4.6 32.1 1.0 CB A:ALA181 4.7 33.5 1.0 O A:VAL183 4.7 26.1 1.0 C A:GLY187 4.7 32.2 1.0 CA A:ASP182 4.7 33.5 1.0 CA A:ILE186 4.8 28.4 1.0 O A:HOH4118 4.8 43.1 1.0 P E:DT12 4.9 32.1 1.0 CB A:ILE186 5.0 26.8 1.0 O A:HOH4168 5.0 45.2 1.0 N A:ILE186 5.0 27.4 1.0

Magnesium binding site 2 out of 4 in the Dpo with at Matched


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dpo with at Matched within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4008 b:39.7 occ:1.00 O B:ALA181 2.4 34.5 1.0 O B:ILE186 2.5 31.1 1.0 O B:HOH4030 2.5 25.9 1.0 O B:HOH4141 2.5 38.5 1.0 O F:HOH147 2.6 26.1 1.0 C B:ALA181 3.6 36.3 1.0 C B:ILE186 3.7 29.2 1.0 CA B:GLY187 4.3 29.7 1.0 OP1 F:DT12 4.4 36.5 1.0 CA B:ALA181 4.4 35.7 1.0 N B:GLY187 4.4 28.6 1.0 N B:ASP182 4.5 36.6 1.0 O B:VAL183 4.5 31.3 1.0 CA B:ASP182 4.6 36.5 1.0 CB B:ALA181 4.7 34.9 1.0 C B:GLY187 4.7 29.9 1.0 OP2 F:DT12 4.7 32.0 1.0 CA B:ILE186 4.8 29.8 1.0 CB B:ILE186 4.9 29.2 1.0 O B:GLY187 5.0 29.2 1.0 C B:ASP182 5.0 35.2 1.0

Magnesium binding site 3 out of 4 in the Dpo with at Matched


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dpo with at Matched within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg4005 b:29.0 occ:1.00 O C:ALA181 2.4 34.8 1.0 O C:ILE186 2.4 30.5 1.0 O C:HOH4039 2.5 33.4 1.0 O C:HOH4121 2.5 42.4 1.0 O G:HOH261 2.6 28.7 1.0 C C:ALA181 3.5 35.0 1.0 C C:ILE186 3.6 27.4 1.0 CA C:GLY187 4.2 27.9 1.0 O C:VAL183 4.3 28.7 1.0 N C:ASP182 4.3 33.8 1.0 N C:GLY187 4.4 27.5 1.0 CA C:ALA181 4.4 33.1 1.0 CA C:ASP182 4.4 35.4 1.0 OP1 G:DT12 4.4 30.4 1.0 CB C:ALA181 4.6 30.6 1.0 CA C:ILE186 4.7 27.6 1.0 C C:GLY187 4.8 30.1 1.0 CB C:ILE186 4.8 28.3 1.0 C C:ASP182 4.8 32.9 1.0 OP2 G:DT12 4.8 28.5 1.0 O C:HOH4135 4.9 48.7 1.0 N C:VAL183 4.9 30.1 1.0 N C:ILE186 4.9 26.7 1.0

Magnesium binding site 4 out of 4 in the Dpo with at Matched


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dpo with at Matched within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg4006 b:35.0 occ:1.00 O D:ALA181 2.3 31.4 1.0 O H:HOH137 2.4 30.4 1.0 O D:ILE186 2.4 30.2 1.0 O H:HOH55 2.5 30.1 1.0 C D:ALA181 3.5 31.4 1.0 C D:ILE186 3.6 29.6 1.0 CA D:GLY187 4.2 30.3 1.0 OP1 H:DT12 4.4 29.8 1.0 N D:GLY187 4.4 29.1 1.0 CA D:ALA181 4.4 30.9 1.0 N D:ASP182 4.5 31.6 1.0 CA D:ASP182 4.5 32.2 1.0 O D:VAL183 4.5 23.8 1.0 OP2 H:DT12 4.6 28.6 1.0 CA D:ILE186 4.7 29.4 1.0 CB D:ALA181 4.8 31.1 1.0 C D:GLY187 4.8 31.4 1.0 CB D:ILE186 4.8 29.4 1.0 C D:ASP182 4.9 30.6 1.0 N D:ILE186 4.9 27.2 1.0

J.Trincao, R.E.Johnson, W.T.Wolfle, C.R.Escalante, S.Prakash, L.Prakash, A.K.Aggarwal. DPO4 Is Hindered in Extending A G.T Mismatch By A Reverse Wobble Nat.Struct.Mol.Biol. V. 11 457 2004.
ISSN: ISSN 1545-9993
PubMed: 15077104
DOI: 10.1038/NSMB755