Manganese in PDB 2ffl: Crystal Structure of Dicer From Giardia Intestinalis

All present enzymatic activity of Crystal Structure of Dicer From Giardia Intestinalis:
3.1.26.3;

The structure of Crystal Structure of Dicer From Giardia Intestinalis, PDB code: 2ffl was solved by J.A.Doudna, I.J.Macrae, P.D.Adams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.33
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	155.515, 174.101, 152.910, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 27.5

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 Crystal Structure of Dicer From Giardia Intestinalis (pdb code 2ffl). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 39 binding sites of Manganese where determined in the Crystal Structure of Dicer From Giardia Intestinalis, PDB code: 2ffl:
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 Crystal Structure of Dicer From Giardia Intestinalis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Dicer From Giardia Intestinalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn5001 b:34.2 occ:1.00 OE2 A:GLU649 2.2 31.9 1.0 OD1 A:ASP720 2.2 32.6 1.0 OE1 A:GLU723 2.3 28.2 1.0 CD A:GLU723 3.1 28.1 1.0 CG A:ASP720 3.2 31.6 1.0 OE2 A:GLU723 3.3 29.3 1.0 CD A:GLU649 3.3 30.1 1.0 OD2 A:ASP653 3.6 30.4 1.0 OD2 A:ASP720 3.7 33.1 1.0 CG A:GLU649 3.9 27.6 1.0 OE1 A:GLU649 4.2 30.1 1.0 CB A:ASP720 4.3 30.6 1.0 CA A:ASP720 4.6 30.4 1.0 CG A:GLU723 4.6 26.6 1.0 CG A:ASP653 4.7 28.4 1.0 ND2 A:ASN686 4.8 36.8 1.0

Manganese binding site 2 out of 39 in the Crystal Structure of Dicer From Giardia Intestinalis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Dicer From Giardia Intestinalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn5002 b:21.9 occ:1.00 OE1 A:GLU407 2.0 28.4 1.0 OE1 A:GLU336 2.2 31.1 1.0 O A:HOH5039 2.5 8.8 1.0 CD A:GLU407 3.0 28.2 1.0 OD2 A:ASP404 3.2 32.9 1.0 OE2 A:GLU407 3.4 29.2 1.0 CD A:GLU336 3.5 30.5 1.0 OD2 A:ASP340 3.5 33.1 1.0 CG A:ASP404 4.0 31.4 1.0 CG A:GLU336 4.2 27.1 1.0 CG A:GLU407 4.4 27.1 1.0 OE2 A:GLU336 4.4 32.5 1.0 CG A:ASP340 4.5 31.0 1.0 OD1 A:ASP404 4.7 33.2 1.0 CB A:ASP340 4.8 28.6 1.0 CG B:GLU374 4.8 31.8 1.0 CD B:GLU374 4.9 33.9 1.0 CB A:ASP404 4.9 30.0 1.0 CB A:GLU407 4.9 26.2 1.0 CA A:ASP404 5.0 29.7 1.0 OE2 B:GLU374 5.0 34.0 0.5

Manganese binding site 3 out of 39 in the Crystal Structure of Dicer From Giardia Intestinalis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Dicer From Giardia Intestinalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn5003 b:79.6 occ:1.00 OD1 A:ASP653 2.4 30.1 1.0 OD2 A:ASP653 2.8 30.4 1.0 CG A:ASP653 2.9 28.4 1.0 OE2 A:GLU684 3.0 43.9 1.0 CD A:GLU684 3.4 42.9 1.0 OE2 A:GLU723 3.7 29.3 1.0 CG A:GLU684 3.7 41.0 1.0 O A:GLU684 4.0 38.4 1.0 OE1 A:GLU684 4.1 44.6 1.0 CB A:ASP653 4.3 26.2 1.0 O A:ASP653 4.6 25.7 1.0 CA A:ASP653 4.7 25.6 1.0 CD A:GLU723 4.7 28.1 1.0 CB A:GLU684 4.8 38.6 1.0 C A:GLU684 5.0 38.4 1.0 C A:ASP653 5.0 25.5 1.0

Manganese binding site 4 out of 39 in the Crystal Structure of Dicer From Giardia Intestinalis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Dicer From Giardia Intestinalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn5004 b:70.5 occ:1.00 OE1 A:GLU673 3.0 43.9 1.0 OE2 A:GLU336 3.5 32.5 1.0 OE2 A:GLU673 3.6 42.7 1.0 CD A:GLU673 3.7 41.0 1.0 O A:HOH5039 3.8 8.8 1.0 OD1 A:ASP404 4.0 33.2 1.0 CD A:GLU336 4.3 30.5 1.0 OE1 A:GLU336 4.3 31.1 1.0 CG A:ASP404 4.9 31.4 1.0 OG A:SER399 5.0 35.6 1.0

Manganese binding site 5 out of 39 in the Crystal Structure of Dicer From Giardia Intestinalis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Dicer From Giardia Intestinalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn5005 b:51.4 occ:1.00 NE2 A:HIS92 2.6 41.3 1.0 CE1 A:HIS92 3.5 41.7 1.0 CD2 A:HIS92 3.6 40.6 1.0 CG2 A:ILE101 4.6 51.5 1.0 OD1 A:ASN103 4.6 60.2 1.0 ND1 A:HIS92 4.6 41.5 1.0 CG A:HIS92 4.7 40.3 1.0

Manganese binding site 6 out of 39 in the Crystal Structure of Dicer From Giardia Intestinalis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Dicer From Giardia Intestinalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn5006 b:36.1 occ:1.00 NE2 A:HIS513 2.5 48.2 1.0 CD2 A:HIS513 3.5 47.0 1.0 CE1 A:HIS513 3.5 48.4 1.0 OE1 D:GLU702 4.2 61.6 1.0 OE2 D:GLU702 4.6 60.7 1.0 ND1 A:HIS513 4.6 47.6 1.0 CG A:HIS513 4.6 45.9 1.0 CD D:GLU702 4.8 60.6 1.0

Manganese binding site 7 out of 39 in the Crystal Structure of Dicer From Giardia Intestinalis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Dicer From Giardia Intestinalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn5013 b:74.2 occ:1.00 OD2 B:ASP714 2.1 57.4 1.0 OD1 A:ASP495 2.4 42.2 1.0 OE2 A:GLU491 2.8 40.9 1.0 CG B:ASP714 2.8 57.5 1.0 OD1 B:ASP714 3.0 59.2 1.0 CG A:ASP495 3.3 40.6 1.0 OD2 A:ASP495 3.6 40.6 1.0 CD A:GLU491 3.7 41.2 1.0 OE1 A:GLU491 3.8 42.9 1.0 O B:ASP714 4.1 54.0 1.0 CB B:ASP714 4.2 56.6 1.0 C B:ASP714 4.6 54.3 1.0 CB A:ASP495 4.7 39.5 1.0

Manganese binding site 8 out of 39 in the Crystal Structure of Dicer From Giardia Intestinalis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Dicer From Giardia Intestinalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn5026 b:64.9 occ:1.00 NE2 A:HIS204 2.2 56.0 1.0 CE1 A:HIS204 3.1 55.9 1.0 OD1 A:ASN202 3.1 57.1 1.0 CD2 A:HIS204 3.4 56.1 1.0 CG A:ASN202 3.6 56.2 1.0 ND2 A:ASN202 3.7 57.1 1.0 ND1 A:HIS204 4.3 55.8 1.0 CG A:HIS204 4.4 55.7 1.0 CB A:ASN202 4.8 55.4 1.0 CA A:ASN202 4.8 55.0 1.0 O A:ASN202 4.9 55.0 1.0

Manganese binding site 9 out of 39 in the Crystal Structure of Dicer From Giardia Intestinalis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Dicer From Giardia Intestinalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn5027 b:52.1 occ:1.00 NH1 A:ARG334 3.2 26.9 1.0 NE2 A:HIS665 3.2 27.2 1.0 CE1 A:HIS665 3.4 27.8 1.0 CD2 A:LEU335 4.3 23.9 1.0 CD2 A:HIS665 4.4 26.8 1.0 CZ A:ARG334 4.4 26.3 1.0 ND1 A:HIS665 4.6 27.1 1.0 CG A:LEU335 4.7 24.7 1.0 CG1 A:VAL331 4.8 25.6 1.0 CG A:ARG334 4.9 25.5 1.0

Manganese binding site 10 out of 39 in the Crystal Structure of Dicer From Giardia Intestinalis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of Dicer From Giardia Intestinalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn5029 b:67.0 occ:1.00 OG1 A:THR670 2.9 30.8 1.0 N A:THR670 3.1 30.5 1.0 CG2 A:THR670 3.4 30.9 1.0 C A:HIS668 3.4 30.0 1.0 N A:PRO669 3.4 30.1 1.0 CB A:THR670 3.5 30.7 1.0 CD A:PRO669 3.6 30.0 1.0 CA A:HIS668 3.6 29.8 1.0 CA A:THR670 3.8 30.9 1.0 CG A:PRO669 3.8 30.1 1.0 O A:HIS668 4.0 30.3 1.0 C A:PRO669 4.1 30.4 1.0 CB A:HIS668 4.1 29.7 1.0 N A:LEU671 4.2 31.9 1.0 CA A:PRO669 4.2 30.3 1.0 CG A:LEU671 4.3 31.9 1.0 CD2 A:LEU671 4.3 31.9 1.0 C A:THR670 4.3 31.3 1.0 CB A:PRO669 4.6 30.3 1.0 ND1 A:HIS668 4.6 31.8 1.0 O A:LEU667 4.7 30.0 1.0 N A:HIS668 4.8 29.5 1.0 CG A:HIS668 4.9 30.6 1.0

I.J.Macrae, K.Zhou, F.Li, A.Repic, A.N.Brooks, W.Z.Cande, P.D.Adams, J.A.Doudna. Structural Basis of Double-Stranded Rna Processing By Dicer Science V. 311 195 2006.
ISSN: ISSN 0036-8075
PubMed: 16410517
DOI: 10.1126/SCIENCE.1121638