Magnesium in PDB 4e3y: X-Ray Structure of the Serratia Marcescens Endonuclease at 0.95 A Resolution

All present enzymatic activity of X-Ray Structure of the Serratia Marcescens Endonuclease at 0.95 A Resolution:
3.1.30.2;

The structure of X-Ray Structure of the Serratia Marcescens Endonuclease at 0.95 A Resolution, PDB code: 4e3y was solved by A.A.Lashkov, V.V.Balaev, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 0.95
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	106.265, 73.418, 67.924, 90.00, 90.00, 90.00
R / Rfree (%)	13 / 14.5

The binding sites of Magnesium atom in the X-Ray Structure of the Serratia Marcescens Endonuclease at 0.95 A Resolution (pdb code 4e3y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Structure of the Serratia Marcescens Endonuclease at 0.95 A Resolution, PDB code: 4e3y:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the X-Ray Structure of the Serratia Marcescens Endonuclease at 0.95 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of the Serratia Marcescens Endonuclease at 0.95 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2601 b:7.9 occ:0.68 O A:HOH2704 2.1 8.6 0.6 O A:HOH2701 2.1 8.4 0.7 OD1 A:ASN1119 2.1 12.3 1.0 O A:HOH2703 2.1 9.0 0.5 O A:HOH2705 2.1 9.3 0.8 O A:HOH2702 2.1 7.4 0.8 CG A:ASN1119 3.3 10.6 1.0 H A:HIS1089 3.3 7.2 1.0 HD1 A:TRP1123 3.5 9.5 1.0 HD1 A:HIS1089 3.6 10.1 1.0 HD22 A:ASN1119 3.7 15.5 1.0 HB2 A:HIS1089 3.7 7.9 1.0 HA2 A:GLY1088 3.8 8.2 1.0 ND2 A:ASN1119 3.9 12.9 1.0 OE2 A:GLU1127 3.9 9.5 0.8 OE1 A:GLU1127 4.0 8.7 0.7 O A:HOH2707 4.0 22.9 0.8 N A:HIS1089 4.0 6.0 1.0 O A:ASN1119 4.2 9.9 1.0 O A:HOH2876 4.2 13.4 0.9 OE1 A:GLN1114 4.2 9.0 1.0 HA A:ASN1119 4.2 10.3 1.0 CD1 A:TRP1123 4.3 7.9 1.0 ND1 A:HIS1089 4.4 8.4 1.0 CD A:GLU1127 4.4 10.2 1.0 O A:HOH3015 4.5 36.8 1.0 CB A:ASN1119 4.5 9.4 1.0 CA A:GLY1088 4.5 6.8 1.0 CB A:HIS1089 4.6 6.5 1.0 O A:HIS1089 4.6 6.5 1.0 HE1 A:TRP1123 4.6 9.4 1.0 HH12 A:ARG1057 4.6 27.4 0.7 HA3 A:GLY1088 4.6 8.2 1.0 CA A:ASN1119 4.7 8.6 1.0 C A:GLY1088 4.7 6.0 1.0 HD21 A:ASN1119 4.8 15.5 1.0 C A:ASN1119 4.8 8.7 1.0 HB2 A:ASN1119 4.8 11.3 1.0 CA A:HIS1089 4.8 5.7 1.0 NE1 A:TRP1123 4.8 7.9 1.0 CG A:HIS1089 5.0 7.1 1.0

Magnesium binding site 2 out of 2 in the X-Ray Structure of the Serratia Marcescens Endonuclease at 0.95 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of the Serratia Marcescens Endonuclease at 0.95 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2301 b:8.0 occ:1.00 OD1 B:ASN2119 2.0 9.0 1.0 O B:HOH2405 2.1 7.8 0.9 O B:HOH2403 2.1 7.1 0.8 O B:HOH2402 2.1 8.0 0.7 O B:HOH2404 2.1 7.1 1.0 O B:HOH2401 2.1 8.4 1.0 CG B:ASN2119 3.3 8.0 1.0 H B:HIS2089 3.3 6.4 1.0 HD1 B:TRP2123 3.5 8.8 1.0 HD1 B:HIS2089 3.6 8.4 1.0 HD22 B:ASN2119 3.7 12.4 1.0 HB2 B:HIS2089 3.8 7.1 1.0 HA2 B:GLY2088 3.8 7.4 1.0 ND2 B:ASN2119 3.9 10.3 1.0 OE2 B:GLU2127 4.0 6.8 0.8 O4 B:SO42303 4.0 13.5 0.5 OE1 B:GLU2127 4.0 7.4 0.8 O3 B:SO42303 4.0 17.9 0.5 N B:HIS2089 4.0 5.4 1.0 O B:ASN2119 4.1 9.1 1.0 HA B:ASN2119 4.2 9.2 1.0 OE1 B:GLN2114 4.2 8.0 1.0 O B:HOH2458 4.2 8.7 0.8 CD1 B:TRP2123 4.4 7.4 1.0 ND1 B:HIS2089 4.4 7.0 1.0 O B:HOH2745 4.4 40.1 1.0 CD B:GLU2127 4.4 8.1 1.0 CB B:ASN2119 4.4 7.9 1.0 O B:HIS2089 4.5 6.0 1.0 CA B:GLY2088 4.5 6.2 1.0 CB B:HIS2089 4.6 5.9 1.0 HA3 B:GLY2088 4.6 7.4 1.0 S B:SO42303 4.6 12.4 0.5 HE1 B:TRP2123 4.6 9.2 1.0 CA B:ASN2119 4.6 7.7 1.0 HB2 B:ASN2119 4.7 9.4 1.0 C B:ASN2119 4.7 8.6 1.0 HD21 B:ASN2119 4.7 12.4 1.0 C B:GLY2088 4.8 5.6 1.0 CA B:HIS2089 4.8 5.3 1.0 NE1 B:TRP2123 4.9 7.7 1.0 CG B:HIS2089 5.0 6.1 1.0

A.A.Lashkov, V.V.Balaev, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov. X-Ray Structure of the Serratia Marcescens Endonuclease at 0.95 A Resolution To Be Published.