Magnesium in PDB 8yii: Dmdcr-2/Loqspd/SLM2 in Dicing State

All present enzymatic activity of Dmdcr-2/Loqspd/SLM2 in Dicing State:
3.1.21.1; 3.1.26.3; 3.6.1.3;

The binding sites of Magnesium atom in the Dmdcr-2/Loqspd/SLM2 in Dicing State (pdb code 8yii). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Dmdcr-2/Loqspd/SLM2 in Dicing State, PDB code: 8yii:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Dmdcr-2/Loqspd/SLM2 in Dicing State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dmdcr-2/Loqspd/SLM2 in Dicing State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1802 b:77.5 occ:1.00 OP1 C:U84 2.0 47.8 1.0 OD1 A:ASP1368 2.1 67.9 1.0 OE2 A:GLU1213 2.2 57.0 1.0 OE1 A:GLU1371 2.6 73.4 1.0 OE2 A:GLU1371 2.6 58.6 1.0 CD A:GLU1371 2.8 65.8 1.0 CD A:GLU1213 3.1 47.4 1.0 NZ A:LYS1364 3.1 55.7 1.0 CG A:ASP1368 3.2 61.8 1.0 P C:U84 3.5 54.7 1.0 CG A:GLU1213 3.6 38.9 1.0 OE1 A:GLU1213 4.0 53.2 1.0 OD2 A:ASP1368 4.1 57.7 1.0 CA A:ASP1368 4.1 55.0 1.0 CB A:ASP1368 4.1 56.1 1.0 O3' C:G83 4.1 48.4 1.0 ND2 A:ASN1250 4.2 69.8 1.0 CG A:GLU1371 4.2 56.8 1.0 N A:ASP1368 4.3 53.1 1.0 O5' C:U84 4.3 40.7 1.0 OP2 C:U84 4.4 47.3 1.0 OD1 A:ASN1250 4.4 80.2 1.0 C5' C:U84 4.5 44.7 1.0 CE A:LYS1364 4.6 65.1 1.0 C A:ALA1367 4.7 46.5 1.0 CB A:GLU1371 4.7 52.2 1.0 CG A:ASN1250 4.7 72.8 1.0 O A:ALA1367 4.8 49.6 1.0

Magnesium binding site 2 out of 5 in the Dmdcr-2/Loqspd/SLM2 in Dicing State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dmdcr-2/Loqspd/SLM2 in Dicing State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1803 b:50.6 occ:1.00 OP1 C:G23 1.9 44.7 1.0 OE2 A:GLU1617 2.0 73.7 1.0 OE1 A:GLU1617 2.2 65.3 1.0 CD A:GLU1617 2.4 66.4 1.0 OE2 A:GLU1472 2.5 56.1 1.0 OD1 A:ASP1614 2.7 56.6 1.0 P C:G23 3.3 48.4 1.0 CD A:GLU1472 3.5 55.2 1.0 CG A:ASP1614 3.8 57.2 1.0 CG A:GLU1617 3.8 52.2 1.0 CG A:GLU1472 3.9 41.3 1.0 O3' C:A22 3.9 42.9 1.0 CA A:ASP1614 4.1 42.6 1.0 ND2 A:ASN1509 4.2 64.7 1.0 OP2 C:G23 4.2 49.3 1.0 N A:ASP1614 4.3 33.9 1.0 CB A:ASP1614 4.4 52.7 1.0 O5' C:G23 4.4 51.5 1.0 CB A:GLU1617 4.5 52.7 1.0 O A:GLY1613 4.5 60.0 1.0 C A:GLY1613 4.5 47.0 1.0 OE1 A:GLU1472 4.6 69.7 1.0 C5' C:G23 4.7 46.6 1.0 OD2 A:ASP1614 4.8 53.5 1.0 CB A:ASN1476 4.9 46.9 1.0 OD1 A:ASN1476 4.9 64.6 1.0

Magnesium binding site 3 out of 5 in the Dmdcr-2/Loqspd/SLM2 in Dicing State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dmdcr-2/Loqspd/SLM2 in Dicing State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1804 b:122.0 occ:1.00 OG1 A:THR35 2.1 116.5 1.0 O3B A:ADP1801 2.5 128.4 1.0 O2A A:ADP1801 2.5 135.1 1.0 O2B A:ADP1801 3.0 132.0 1.0 PA A:ADP1801 3.1 139.5 1.0 PB A:ADP1801 3.2 132.2 1.0 O1A A:ADP1801 3.3 134.8 1.0 CB A:THR35 3.3 116.5 1.0 O3A A:ADP1801 3.6 134.6 1.0 NE2 A:GLN73 4.2 119.0 1.0 CG2 A:THR35 4.2 115.4 1.0 N A:THR35 4.3 116.4 1.0 CA A:THR35 4.4 117.2 1.0 NZ A:LYS34 4.4 126.4 1.0 O1B A:ADP1801 4.6 128.6 1.0 O5' A:ADP1801 4.7 129.9 1.0 OE1 A:GLN73 4.7 118.3 1.0 CD A:GLN73 4.9 118.2 1.0 NE2 A:GLN72 4.9 115.1 1.0

Magnesium binding site 4 out of 5 in the Dmdcr-2/Loqspd/SLM2 in Dicing State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dmdcr-2/Loqspd/SLM2 in Dicing State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1805 b:37.7 occ:1.00 OE1 A:GLU1213 2.0 53.2 1.0 OE1 A:GLU1210 2.0 54.5 1.0 OP1 C:C85 2.7 56.2 1.0 CD A:GLU1210 2.8 52.9 1.0 CD A:GLU1213 3.0 47.4 1.0 OE2 A:GLU1210 3.0 53.9 1.0 OE2 A:GLU1213 3.5 57.0 1.0 P C:C85 3.6 50.5 1.0 OP2 C:C85 3.6 61.2 1.0 OD2 A:ASP1368 4.2 57.7 1.0 CG A:GLU1210 4.2 53.1 1.0 CG A:GLU1213 4.3 38.9 1.0 CB A:GLU1213 4.4 42.9 1.0 O A:GLU1210 4.5 37.4 1.0 CB A:GLU1210 4.6 52.9 1.0 CG A:ASP1368 4.6 61.8 1.0 CA A:GLU1210 4.6 51.1 1.0 O3' C:U84 4.7 38.9 1.0 O5' C:C85 4.8 44.3 1.0 OD1 A:ASP1368 4.9 67.9 1.0

Magnesium binding site 5 out of 5 in the Dmdcr-2/Loqspd/SLM2 in Dicing State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Dmdcr-2/Loqspd/SLM2 in Dicing State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1806 b:52.6 occ:1.00 NE2 A:GLN1469 2.1 49.2 1.0 OE1 A:GLU1472 2.1 69.7 1.0 CD A:GLU1472 3.1 55.2 1.0 OP1 C:G24 3.1 70.7 1.0 OP2 C:G24 3.1 60.9 1.0 CD A:GLN1469 3.3 51.6 1.0 OE2 A:GLU1472 3.3 56.1 1.0 P C:G24 3.6 69.4 1.0 CG A:GLN1469 3.7 44.4 1.0 OE1 A:GLN1469 4.4 60.7 1.0 OD2 A:ASP1614 4.4 53.5 1.0 CG A:GLU1472 4.5 41.3 1.0 O5' C:G24 4.5 51.3 1.0 O A:GLN1469 4.5 52.7 1.0 CG A:ASP1614 4.6 57.2 1.0 CB A:GLU1472 4.8 32.2 1.0 OD1 A:ASP1614 4.8 56.6 1.0 OE2 A:GLU1237 4.9 80.1 1.0 CA A:GLN1469 4.9 51.1 1.0 CB A:GLN1469 4.9 47.1 1.0 O3' C:G23 4.9 49.0 1.0

N.Cao, S.Su, J.Wang, J.Ma, H.-W.Wang. Structural Basic of Endo-Sirna Processing By Drosophila Dcr-2 and Loqs-Pd To Be Published.