Magnesium in PDB 1zbu: Crystal Structure of Full-Length 3'-Exonuclease

The structure of Crystal Structure of Full-Length 3'-Exonuclease, PDB code: 1zbu was solved by Y.Cheng, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 3.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	215.843, 215.843, 114.468, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 22.5

The binding sites of Magnesium atom in the Crystal Structure of Full-Length 3'-Exonuclease (pdb code 1zbu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Full-Length 3'-Exonuclease, PDB code: 1zbu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structure of Full-Length 3'-Exonuclease


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 Full-Length 3'-Exonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1000 b:32.9 occ:1.00 O1P A:AMP1002 2.4 41.1 1.0 OD1 A:ASP134 2.5 36.1 1.0 CG A:ASP134 3.2 30.3 1.0 OD2 A:ASP234 3.5 28.5 1.0 OD2 A:ASP134 3.5 34.2 1.0 O5' A:AMP1002 3.6 39.3 1.0 OD1 A:ASP234 3.6 31.9 1.0 P A:AMP1002 3.6 41.0 1.0 MG A:MG1001 3.7 42.6 1.0 C5' A:AMP1002 3.7 35.7 1.0 O A:PHE135 3.8 19.7 1.0 CG A:ASP234 3.9 28.1 1.0 CB A:ASP134 4.5 24.9 1.0 O3P A:AMP1002 4.6 40.9 1.0 N A:PHE135 4.6 21.0 1.0 O2P A:AMP1002 4.7 40.1 1.0 O A:ASP230 4.7 23.9 1.0 CA A:ASP134 4.7 24.1 1.0 C A:ASP134 4.8 22.6 1.0 C A:PHE135 4.9 19.4 1.0 OD2 A:ASP230 5.0 25.3 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of Full-Length 3'-Exonuclease


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 Full-Length 3'-Exonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:42.6 occ:1.00 O1P A:AMP1002 2.3 41.1 1.0 OE2 A:GLU136 2.4 25.5 1.0 O2P A:AMP1002 2.7 40.1 1.0 OD1 A:ASP134 2.8 36.1 1.0 P A:AMP1002 3.0 41.0 1.0 OD2 A:ASP134 3.0 34.2 1.0 CG A:ASP134 3.1 30.3 1.0 CG A:ASP298 3.4 27.9 1.0 CD A:GLU136 3.4 22.9 1.0 OD1 A:ASP298 3.5 32.9 1.0 O A:PHE135 3.6 19.7 1.0 CB A:ASP298 3.6 25.0 1.0 MG A:MG1000 3.7 32.9 1.0 OD2 A:ASP298 3.8 28.8 1.0 OE1 A:GLU136 3.9 23.7 1.0 O5' A:AMP1002 4.0 39.3 1.0 C5' A:AMP1002 4.1 35.7 1.0 CA A:GLY295 4.1 26.3 1.0 O3P A:AMP1002 4.2 40.9 1.0 CA A:HIS293 4.5 29.3 1.0 CB A:ASP134 4.5 24.9 1.0 O A:ASP134 4.5 22.4 1.0 N A:GLY295 4.6 26.6 1.0 C A:PHE135 4.6 19.4 1.0 CG A:GLU136 4.6 21.0 1.0 C A:HIS293 4.7 28.8 1.0 O A:CYS294 4.8 26.9 1.0 C A:CYS294 4.8 27.2 1.0 C A:ASP134 4.8 22.6 1.0 O A:HIS293 4.8 28.7 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of Full-Length 3'-Exonuclease


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 Full-Length 3'-Exonuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2000 b:52.1 occ:1.00 O1P B:AMP2002 2.3 64.7 1.0 OD2 B:ASP134 2.5 30.2 1.0 O5' B:AMP2002 3.1 63.3 1.0 C5' B:AMP2002 3.2 61.1 1.0 P B:AMP2002 3.4 64.7 1.0 MG B:MG2001 3.5 42.2 1.0 OD2 B:ASP234 3.6 26.2 1.0 O B:PHE135 3.6 19.1 1.0 CG B:ASP134 3.6 25.4 1.0 OD1 B:ASP234 3.8 30.6 1.0 CG B:ASP234 4.1 26.7 1.0 OD1 B:ASP134 4.1 29.4 1.0 O2P B:AMP2002 4.3 64.4 1.0 O3P B:AMP2002 4.5 65.1 1.0 C4' B:AMP2002 4.6 59.9 1.0 N B:PHE135 4.7 19.7 1.0 C B:PHE135 4.7 18.8 1.0 C B:ASP134 4.8 20.8 1.0 CB B:ASP134 4.9 22.1 1.0 CA B:ASP134 4.9 21.6 1.0 O4' B:AMP2002 5.0 60.0 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of Full-Length 3'-Exonuclease


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 Full-Length 3'-Exonuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2001 b:42.2 occ:1.00 OE2 B:GLU136 2.5 22.8 1.0 OD2 B:ASP298 2.6 29.9 1.0 O1P B:AMP2002 2.7 64.7 1.0 OD2 B:ASP134 2.7 30.2 1.0 CG B:ASP134 3.0 25.4 1.0 OD1 B:ASP134 3.2 29.4 1.0 O2P B:AMP2002 3.3 64.4 1.0 CG B:ASP298 3.5 27.0 1.0 P B:AMP2002 3.5 64.7 1.0 CB B:ASP298 3.5 24.7 1.0 MG B:MG2000 3.5 52.1 1.0 CD B:GLU136 3.6 22.4 1.0 O B:PHE135 4.0 19.1 1.0 CB B:ASP134 4.0 22.1 1.0 O B:ASP134 4.0 21.0 1.0 CA B:GLY295 4.2 29.8 1.0 OE1 B:GLU136 4.2 23.4 1.0 C5' B:AMP2002 4.4 61.1 1.0 O5' B:AMP2002 4.4 63.3 1.0 C B:ASP134 4.5 20.8 1.0 CA B:HIS293 4.6 35.2 1.0 O B:CYS294 4.6 31.4 1.0 N B:GLY295 4.6 30.9 1.0 OD1 B:ASP298 4.7 29.0 1.0 O B:GLY295 4.7 28.8 1.0 CG B:GLU136 4.7 20.3 1.0 C B:CYS294 4.8 31.8 1.0 C B:HIS293 4.8 34.6 1.0 O3P B:AMP2002 4.8 65.1 1.0 C B:PHE135 4.8 18.8 1.0 CA B:ASP134 4.8 21.6 1.0 C B:GLY295 4.9 29.0 1.0 O B:HIS293 4.9 34.7 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of Full-Length 3'-Exonuclease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Full-Length 3'-Exonuclease within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg3000 b:54.4 occ:1.00 OD2 C:ASP134 2.2 30.1 1.0 OD2 C:ASP234 2.5 29.9 1.0 O C:PHE135 2.9 18.5 1.0 O1P C:AMP3002 3.0 59.4 1.0 CG C:ASP234 3.3 29.2 1.0 OD1 C:ASP234 3.3 32.5 1.0 CG C:ASP134 3.4 26.9 1.0 C5' C:AMP3002 3.5 55.4 1.0 N C:PHE135 3.5 19.0 1.0 MG C:MG3001 3.9 40.1 1.0 C C:PHE135 3.9 18.4 1.0 C C:ASP134 3.9 20.1 1.0 O5' C:AMP3002 4.0 58.3 1.0 P C:AMP3002 4.2 59.6 1.0 CA C:PHE135 4.2 18.1 1.0 CB C:ASP134 4.2 22.0 1.0 OD1 C:ASP134 4.3 31.9 1.0 CA C:ASP134 4.3 21.2 1.0 O C:ASP134 4.6 19.8 1.0 CE2 C:PHE238 4.6 18.2 1.0 C4' C:AMP3002 4.7 52.9 1.0 CB C:ASP234 4.7 27.2 1.0 CB C:PHE135 4.8 17.1 1.0 CD2 C:PHE238 4.8 17.8 1.0 O2P C:AMP3002 4.9 58.9 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of Full-Length 3'-Exonuclease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Full-Length 3'-Exonuclease within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg3001 b:40.1 occ:1.00 OE2 C:GLU136 2.3 24.4 1.0 O1P C:AMP3002 2.7 59.4 1.0 OD1 C:ASP298 2.7 28.5 1.0 O2P C:AMP3002 2.7 58.9 1.0 OD1 C:ASP134 3.0 31.9 1.0 OD2 C:ASP134 3.1 30.1 1.0 P C:AMP3002 3.2 59.6 1.0 CD C:GLU136 3.4 23.6 1.0 CG C:ASP134 3.4 26.9 1.0 CG C:ASP298 3.5 27.0 1.0 CB C:ASP298 3.6 24.6 1.0 O C:PHE135 3.8 18.5 1.0 MG C:MG3000 3.9 54.4 1.0 OE1 C:GLU136 3.9 25.2 1.0 O5' C:AMP3002 4.2 58.3 1.0 CA C:HIS293 4.3 28.8 1.0 CA C:GLY295 4.3 25.1 1.0 C5' C:AMP3002 4.3 55.4 1.0 O3P C:AMP3002 4.4 59.5 1.0 O C:ASP134 4.5 19.8 1.0 N C:GLY295 4.5 26.1 1.0 CG C:GLU136 4.5 21.1 1.0 C C:HIS293 4.5 28.5 1.0 O C:CYS294 4.6 26.6 1.0 C C:CYS294 4.6 26.8 1.0 C C:PHE135 4.7 18.4 1.0 OD2 C:ASP298 4.7 29.7 1.0 N C:CYS294 4.8 28.0 1.0 N C:HIS293 4.8 29.0 1.0 C C:ASP134 4.9 20.1 1.0 CB C:ASP134 4.9 22.0 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of Full-Length 3'-Exonuclease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Full-Length 3'-Exonuclease within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg4000 b:60.1 occ:1.00 MG D:MG4001 2.6 59.4 1.0 O1P D:AMP4002 2.8 90.9 1.0 O D:ASP230 2.8 27.7 1.0 OD1 D:ASP134 3.1 29.9 1.0 OD2 D:ASP230 3.3 31.4 1.0 CZ2 D:TRP233 3.5 39.9 1.0 OD2 D:ASP234 3.5 31.3 1.0 CB D:ASP230 3.6 27.1 1.0 CE2 D:TRP233 3.6 40.8 1.0 CG D:ASP230 3.7 28.9 1.0 CH2 D:TRP233 3.8 39.5 1.0 C D:ASP230 3.8 27.2 1.0 OD1 D:ASP234 3.9 28.1 1.0 CG D:ASP234 4.1 29.4 1.0 CD2 D:TRP233 4.1 39.9 1.0 NE1 D:TRP233 4.1 40.8 1.0 CG D:ASP134 4.2 24.9 1.0 P D:AMP4002 4.2 90.9 1.0 CZ3 D:TRP233 4.2 40.1 1.0 CA D:ASP230 4.2 26.6 1.0 CE3 D:TRP233 4.4 40.5 1.0 N D:ASP230 4.6 25.6 1.0 OD2 D:ASP134 4.6 27.3 1.0 O5' D:AMP4002 4.7 89.7 1.0 OD1 D:ASP230 4.7 30.7 1.0 O3P D:AMP4002 4.8 90.9 1.0 CD1 D:TRP233 4.8 40.0 1.0 CG D:TRP233 4.8 37.4 1.0 N D:GLY231 4.9 27.6 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of Full-Length 3'-Exonuclease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Full-Length 3'-Exonuclease within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg4001 b:59.4 occ:1.00 O1P D:AMP4002 2.1 90.9 1.0 OD1 D:ASP134 2.4 29.9 1.0 MG D:MG4000 2.6 60.1 1.0 O D:PHE135 2.9 18.7 1.0 CG D:ASP134 3.3 24.9 1.0 P D:AMP4002 3.4 90.9 1.0 C5' D:AMP4002 3.5 87.5 1.0 OD1 D:ASP234 3.5 28.1 1.0 OD2 D:ASP134 3.7 27.3 1.0 O5' D:AMP4002 3.7 89.7 1.0 O2P D:AMP4002 3.9 91.1 1.0 C D:PHE135 4.0 18.5 1.0 N D:PHE135 4.1 19.5 1.0 C D:ASP134 4.2 20.6 1.0 OE2 D:GLU136 4.2 22.8 1.0 CG D:ASP234 4.3 29.4 1.0 OD2 D:ASP234 4.5 31.3 1.0 CB D:ASP134 4.5 21.9 1.0 CA D:ASP134 4.6 21.3 1.0 O D:ASP134 4.6 21.0 1.0 CA D:PHE135 4.6 18.6 1.0 O3P D:AMP4002 4.6 90.9 1.0 CZ3 D:TRP233 4.8 40.1 1.0 CH2 D:TRP233 4.9 39.5 1.0 C4' D:AMP4002 4.9 85.9 1.0

Y.Cheng, D.J.Patel. Structural Basis For 3'-End Specific Recognition of Histone Mrna Stem-Loop By 3'-Exonuclease, A Human Nuclease That Also Targets Sirna To Be Published.