Manganese in PDB 2qvw: Structure of Giardia Dicer Refined Against Twinned Data

All present enzymatic activity of Structure of Giardia Dicer Refined Against Twinned Data:
3.1.26.3;

The structure of Structure of Giardia Dicer Refined Against Twinned Data, PDB code: 2qvw was solved by J.A.Doudna, I.J.Macrae, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	155.409, 173.490, 155.453, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 26.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 39;

Binding sites:

The binding sites of Manganese atom in the Structure of Giardia Dicer Refined Against Twinned Data (pdb code 2qvw). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 39 binding sites of Manganese where determined in the Structure of Giardia Dicer Refined Against Twinned Data, PDB code: 2qvw:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 39 in the Structure of Giardia Dicer Refined Against Twinned Data


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Giardia Dicer Refined Against Twinned Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn755 b:32.4 occ:1.00 OE1 A:GLU723 2.5 26.4 1.0 OE2 A:GLU649 2.8 30.1 1.0 OD1 A:ASP720 3.0 30.8 1.0 CG A:ASP720 3.2 29.8 1.0 OD2 A:ASP720 3.2 31.3 1.0 CD A:GLU723 3.3 26.3 1.0 OE2 A:GLU723 3.5 27.5 1.0 CD A:GLU649 3.8 28.3 1.0 CA A:ASP720 4.0 28.6 1.0 CB A:ASP720 4.1 28.8 1.0 OD2 A:ASP653 4.3 28.6 1.0 CG A:GLU649 4.3 25.8 1.0 N A:ASP720 4.5 28.9 1.0 CG A:GLU723 4.5 24.8 1.0 ND2 A:ASN686 4.7 35.0 1.0 OE1 A:GLU649 4.8 28.3 1.0 C A:GLY719 4.9 29.1 1.0

Manganese binding site 2 out of 39 in the Structure of Giardia Dicer Refined Against Twinned Data


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Giardia Dicer Refined Against Twinned Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn756 b:20.1 occ:1.00 OE1 A:GLU407 2.9 26.6 1.0 OE1 A:GLU336 3.1 29.3 1.0 OD2 A:ASP404 3.6 31.1 1.0 CD A:GLU407 3.7 26.4 1.0 OE2 A:GLU407 3.7 27.4 1.0 CG B:GLU374 3.9 30.0 1.0 CD B:GLU374 4.1 32.1 1.0 OE1 B:GLU374 4.3 31.9 0.5 CD A:GLU336 4.3 28.7 1.0 CG A:ASP404 4.4 29.6 1.0 OD2 A:ASP340 4.4 31.3 1.0 OE2 B:GLU374 4.7 32.1 0.5 CA A:ASP404 4.8 27.9 1.0 CG A:GLU336 5.0 25.2 1.0

Manganese binding site 3 out of 39 in the Structure of Giardia Dicer Refined Against Twinned Data


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Giardia Dicer Refined Against Twinned Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn757 b:77.7 occ:1.00 OE2 A:GLU684 2.4 42.1 1.0 OD1 A:ASP653 2.6 28.3 1.0 CD A:GLU684 3.1 41.1 1.0 CG A:ASP653 3.2 26.6 1.0 O A:ASP653 3.5 23.9 1.0 OD2 A:ASP653 3.7 28.6 1.0 CG A:GLU684 3.7 39.1 1.0 OE2 A:GLU723 3.8 27.5 1.0 OE1 A:GLU684 4.0 42.8 1.0 CA A:ASP653 4.0 23.8 1.0 CB A:GLU684 4.1 36.8 1.0 C A:ASP653 4.1 23.7 1.0 CB A:ASP653 4.2 24.4 1.0 CD2 A:LEU656 4.3 24.5 1.0 CG A:LEU656 4.6 23.8 1.0 CB A:LEU656 4.6 23.7 1.0 N A:LYS657 4.7 24.1 1.0 O A:GLU684 4.8 36.6 1.0 CB A:LYS657 4.8 24.3 1.0 CA A:GLU684 5.0 36.6 1.0

Manganese binding site 4 out of 39 in the Structure of Giardia Dicer Refined Against Twinned Data


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Giardia Dicer Refined Against Twinned Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn758 b:68.6 occ:1.00 OE1 A:GLU673 3.6 42.1 1.0 OG A:SER399 4.2 33.8 1.0 OD1 A:ASP404 4.6 31.4 1.0 OE2 A:GLU336 4.6 30.7 1.0 CD A:GLU673 4.7 39.2 1.0 OE1 A:GLU336 5.0 29.3 1.0

Manganese binding site 5 out of 39 in the Structure of Giardia Dicer Refined Against Twinned Data


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of Giardia Dicer Refined Against Twinned Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn759 b:49.6 occ:1.00 NE2 A:HIS92 2.4 39.5 1.0 CD2 A:HIS92 3.2 38.8 1.0 CE1 A:HIS92 3.4 39.9 1.0 CG A:HIS92 4.3 38.5 1.0 ND1 A:HIS92 4.4 39.7 1.0

Manganese binding site 6 out of 39 in the Structure of Giardia Dicer Refined Against Twinned Data


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of Giardia Dicer Refined Against Twinned Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn760 b:34.3 occ:1.00 NE2 A:HIS513 3.3 46.4 1.0 OE1 D:GLU702 3.3 59.8 1.0 CD2 A:HIS513 3.7 45.2 1.0 CD D:GLU702 4.3 58.8 1.0 OE2 D:GLU702 4.4 58.9 1.0 CE1 A:HIS513 4.6 46.6 1.0 CA A:GLY519 4.9 51.1 1.0 O A:SER518 4.9 51.6 1.0

Manganese binding site 7 out of 39 in the Structure of Giardia Dicer Refined Against Twinned Data


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Structure of Giardia Dicer Refined Against Twinned Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn761 b:63.0 occ:1.00 NE2 A:HIS204 4.9 54.2 1.0

Manganese binding site 8 out of 39 in the Structure of Giardia Dicer Refined Against Twinned Data


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Structure of Giardia Dicer Refined Against Twinned Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn762 b:50.3 occ:1.00 NE2 A:HIS665 3.4 25.4 1.0 CE1 A:HIS665 3.7 26.0 1.0 NH1 A:ARG334 3.8 25.1 1.0 CD2 A:LEU335 4.1 22.1 1.0 CD2 A:HIS665 4.6 24.9 1.0 CG1 A:VAL331 4.8 23.8 1.0 CG A:LEU335 4.9 22.9 1.0 ND1 A:HIS665 4.9 25.3 1.0

Manganese binding site 9 out of 39 in the Structure of Giardia Dicer Refined Against Twinned Data


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Structure of Giardia Dicer Refined Against Twinned Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn763 b:65.2 occ:1.00 C A:HIS668 2.4 28.2 1.0 N A:PRO669 2.4 28.3 1.0 N A:THR670 2.5 28.6 1.0 CD A:PRO669 2.7 28.2 1.0 CA A:HIS668 2.7 27.9 1.0 O A:HIS668 3.0 28.4 1.0 OG1 A:THR670 3.1 28.9 1.0 CG A:PRO669 3.2 28.3 1.0 CA A:PRO669 3.2 28.4 1.0 C A:PRO669 3.3 28.6 1.0 CB A:HIS668 3.4 27.9 1.0 CA A:THR670 3.5 29.0 1.0 CB A:THR670 3.6 28.9 1.0 N A:LEU671 3.7 30.1 1.0 CG2 A:THR670 3.8 29.1 1.0 CB A:PRO669 3.9 28.5 1.0 N A:HIS668 4.0 27.7 1.0 C A:THR670 4.1 29.5 1.0 O A:LEU667 4.3 28.2 1.0 CG A:LEU671 4.4 30.0 1.0 O A:PRO669 4.5 28.7 1.0 CG A:HIS668 4.5 28.7 1.0 C A:LEU667 4.6 27.8 1.0 ND1 A:HIS668 4.7 29.9 1.0 CB A:LEU671 4.9 30.4 1.0 CA A:LEU671 4.9 30.6 1.0

Manganese binding site 10 out of 39 in the Structure of Giardia Dicer Refined Against Twinned Data


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Structure of Giardia Dicer Refined Against Twinned Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn764 b:96.1 occ:1.00 ND1 A:HIS708 3.0 71.3 1.0 CG A:HIS708 3.8 70.7 1.0 CE1 A:HIS708 3.8 71.3 1.0 CB A:HIS708 4.0 70.2 1.0 CG2 A:ILE711 4.5 68.2 1.0 CA A:HIS708 4.6 70.1 1.0 OE2 B:GLU547 4.7 56.5 1.0 NE2 A:HIS708 4.8 71.5 1.0 CD2 A:HIS708 4.8 71.2 1.0 CG2 A:VAL717 5.0 35.9 1.0

I.J.Macrae, J.A.Doudna. An Unusual Case of Pseudo-Merohedral Twinning in Orthorhombic Crystals of Dicer Acta Crystallogr.,Sect.D V. 63 993 2007.
ISSN: ISSN 0907-4449
PubMed: 17704568
DOI: 10.1107/S0907444907036128