Magnesium in PDB 1ql0: Sm Endonuclease From Seratia Marcenscens at Atomic Resolution

All present enzymatic activity of Sm Endonuclease From Seratia Marcenscens at Atomic Resolution:
3.1.30.2;

The structure of Sm Endonuclease From Seratia Marcenscens at Atomic Resolution, PDB code: 1ql0 was solved by M.Perbandt, A.M.Mikhailov, C.H.Betzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	106.390, 73.670, 68.120, 90.00, 90.00, 90.00
R / Rfree (%)	12.8 / 14.7

The binding sites of Magnesium atom in the Sm Endonuclease From Seratia Marcenscens at Atomic Resolution (pdb code 1ql0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Sm Endonuclease From Seratia Marcenscens at Atomic Resolution, PDB code: 1ql0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Sm Endonuclease From Seratia Marcenscens at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sm Endonuclease From Seratia Marcenscens at Atomic Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg300 b:9.4 occ:1.00 O B:HOH2256 2.1 9.7 1.0 OD1 B:ASN119 2.1 10.7 1.0 O B:HOH2230 2.1 8.4 1.0 O B:HOH2254 2.1 9.7 1.0 O B:HOH2205 2.2 9.2 1.0 O B:HOH2239 2.2 13.3 1.0 CG B:ASN119 3.3 9.7 1.0 ND2 B:ASN119 3.9 11.3 1.0 OE2 B:GLU127 4.0 9.2 1.0 O B:HOH2240 4.0 16.8 1.0 OE1 B:GLU127 4.0 9.8 1.0 N B:HIS89 4.0 6.9 1.0 O B:ASN119 4.1 10.3 1.0 O B:HOH2203 4.2 10.9 1.0 NE2 B:GLN114 4.2 7.7 1.0 ND1 B:HIS89 4.4 8.3 1.0 CD1 B:TRP123 4.4 8.2 1.0 CD B:GLU127 4.4 8.7 1.0 CB B:ASN119 4.4 9.8 1.0 O B:HIS89 4.5 7.3 1.0 CA B:GLY88 4.6 8.1 1.0 CB B:HIS89 4.6 7.3 1.0 CA B:ASN119 4.6 9.3 1.0 C B:ASN119 4.7 10.0 1.0 C B:GLY88 4.8 6.9 1.0 CA B:HIS89 4.8 7.2 1.0 NE1 B:TRP123 4.9 8.4 1.0 CG B:HIS89 5.0 7.3 1.0

Magnesium binding site 2 out of 2 in the Sm Endonuclease From Seratia Marcenscens at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sm Endonuclease From Seratia Marcenscens at Atomic Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg300 b:12.2 occ:1.00 O A:HOH2267 2.2 12.9 1.0 O A:HOH2247 2.2 11.0 1.0 O A:HOH2220 2.2 11.9 1.0 OD1 A:ASN119 2.2 14.3 1.0 O A:HOH2269 2.2 13.6 1.0 O A:HOH2254 2.3 18.3 1.0 CG A:ASN119 3.3 11.0 1.0 O A:HOH2144 3.8 37.4 1.0 ND2 A:ASN119 3.9 14.9 1.0 OE2 A:GLU127 3.9 12.5 1.0 N A:HIS89 4.0 7.5 1.0 OE1 A:GLU127 4.0 12.4 1.0 O A:HOH2253 4.0 24.1 1.0 O A:ASN119 4.2 10.7 1.0 O A:HOH2224 4.2 15.8 1.0 NE2 A:GLN114 4.2 8.2 1.0 CD1 A:TRP123 4.3 9.1 1.0 ND1 A:HIS89 4.4 9.1 1.0 CD A:GLU127 4.4 10.8 1.0 CA A:GLY88 4.5 8.2 1.0 CB A:ASN119 4.5 9.9 1.0 CB A:HIS89 4.6 7.8 1.0 O A:HIS89 4.6 7.7 1.0 C A:GLY88 4.7 7.1 1.0 CA A:ASN119 4.7 9.1 1.0 C A:ASN119 4.8 9.5 1.0 CA A:HIS89 4.8 7.3 1.0 NE1 A:TRP123 4.8 9.5 1.0 CG A:HIS89 5.0 8.1 1.0

S.V.Shlyapnikov, V.V.Lunin, M.Perbandt, K.M.Polyakov, V.Y.Lunin, V.M.Levdikov, C.Betzel, A.M.Mikhailov. Atomic Structure of the Serratia Marcescens Endonuclease at 1.1 A Resolution and the Enzyme Reaction Mechanism. Acta Crystallogr.,Sect.D V. 56 567 2000.
ISSN: ISSN 0907-4449
PubMed: 10771425
DOI: 10.1107/S090744490000322X