Magnesium in PDB 3rv0: Crystal Structure of K. Polysporus DCR1 Without the C-Terminal Dsrbd

The structure of Crystal Structure of K. Polysporus DCR1 Without the C-Terminal Dsrbd, PDB code: 3rv0 was solved by K.Nakanishi, D.E.Weinberg, D.P.Bartel, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.41 / 2.29
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.037, 112.974, 135.689, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 22

The binding sites of Magnesium atom in the Crystal Structure of K. Polysporus DCR1 Without the C-Terminal Dsrbd (pdb code 3rv0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of K. Polysporus DCR1 Without the C-Terminal Dsrbd, PDB code: 3rv0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of K. Polysporus DCR1 Without the C-Terminal Dsrbd


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 K. Polysporus DCR1 Without the C-Terminal Dsrbd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1 b:45.4 occ:1.00 O A:HOH363 2.1 34.6 1.0 O A:HOH389 2.1 46.1 1.0 O A:HOH372 2.2 40.3 1.0 OE1 A:GLU224 2.2 37.8 1.0 O A:HOH379 2.3 41.1 1.0 OE2 A:GLU147 2.3 60.1 1.0 CD A:GLU224 3.2 38.3 1.0 CD A:GLU147 3.4 57.9 1.0 OE2 A:GLU224 3.4 43.1 1.0 NZ A:LYS217 3.7 79.5 1.0 OD1 A:ASP221 3.7 61.6 1.0 CG A:GLU147 3.8 41.3 1.0 O A:HOH444 3.9 45.1 1.0 O A:HOH469 4.0 54.8 1.0 O A:HOH424 4.2 52.0 1.0 OD2 A:ASP151 4.3 44.3 1.0 OD1 A:ASN184 4.4 57.8 1.0 OE1 A:GLU147 4.4 58.1 1.0 CG A:GLU224 4.5 35.5 1.0 CE A:LYS217 4.7 77.3 1.0 CG A:ASP221 4.7 56.7 1.0 CG A:ASP151 4.8 38.9 1.0 CB A:ASP151 4.9 28.3 1.0 CA A:ASP221 4.9 36.0 1.0 CB A:GLU224 4.9 29.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of K. Polysporus DCR1 Without the C-Terminal Dsrbd


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 K. Polysporus DCR1 Without the C-Terminal Dsrbd within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg3 b:49.9 occ:1.00 O B:HOH390 2.1 56.5 1.0 O B:HOH362 2.1 44.3 1.0 O B:HOH480 2.2 54.7 1.0 OE1 B:GLU224 2.2 35.4 1.0 OE2 B:GLU147 2.3 61.0 1.0 O B:HOH409 2.3 38.8 1.0 CD B:GLU224 3.2 35.3 1.0 OE2 B:GLU224 3.4 42.4 1.0 CD B:GLU147 3.4 52.0 1.0 OD1 B:ASP221 3.5 70.3 1.0 CG B:GLU147 3.8 33.4 1.0 CE B:LYS217 4.4 72.2 1.0 NZ B:LYS217 4.5 70.1 1.0 OE1 B:GLU147 4.5 63.1 1.0 OD2 B:ASP151 4.5 51.6 1.0 OD1 B:ASN184 4.5 68.2 1.0 CG B:ASP221 4.6 62.1 1.0 O B:HOH472 4.6 48.0 1.0 CG B:GLU224 4.6 28.3 1.0 CG B:ASP151 4.6 43.8 1.0 CB B:ASP151 4.8 30.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of K. Polysporus DCR1 Without the C-Terminal Dsrbd


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 K. Polysporus DCR1 Without the C-Terminal Dsrbd within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg4 b:40.1 occ:1.00 OE2 C:GLU147 2.0 36.7 1.0 OE1 C:GLU224 2.1 37.4 1.0 O C:HOH370 2.1 33.7 1.0 O C:HOH361 2.2 34.4 1.0 O C:HOH383 2.2 28.6 1.0 CD C:GLU224 3.1 41.5 1.0 CD C:GLU147 3.2 42.2 1.0 OE2 C:GLU224 3.4 36.4 1.0 OD1 C:ASP221 3.6 53.1 1.0 CG C:GLU147 3.7 42.6 1.0 OD2 C:ASP151 4.0 54.2 1.0 OD1 C:ASN184 4.1 53.5 1.0 OE1 C:GLU147 4.2 36.0 1.0 ND2 C:ASN184 4.4 50.7 1.0 CG C:GLU224 4.4 36.3 1.0 CG C:ASP221 4.6 56.5 1.0 CG C:ASP151 4.7 41.5 1.0 CG C:ASN184 4.7 47.6 1.0 CA C:ASP221 4.8 47.6 1.0 CB C:GLU224 4.8 25.4 1.0 CB C:ASP151 4.9 37.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of K. Polysporus DCR1 Without the C-Terminal Dsrbd


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 K. Polysporus DCR1 Without the C-Terminal Dsrbd within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2 b:56.8 occ:1.00 O D:HOH374 2.2 61.7 1.0 O D:HOH392 2.2 53.6 1.0 OE2 D:GLU147 2.2 76.4 1.0 O D:HOH465 2.2 55.9 1.0 OE1 D:GLU224 2.3 50.0 1.0 OD1 D:ASP221 2.8 46.2 1.0 CD D:GLU147 3.3 63.5 1.0 CD D:GLU224 3.3 42.9 1.0 OE2 D:GLU224 3.6 48.2 1.0 CG D:GLU147 3.7 33.2 1.0 CG D:ASP221 3.8 49.4 1.0 O D:HOH474 3.9 58.0 1.0 OD1 D:ASP151 4.2 57.5 1.0 OE1 D:GLU147 4.4 63.9 1.0 OD2 D:ASP221 4.5 54.5 1.0 CB D:ASP151 4.6 32.4 1.0 CA D:ASP221 4.6 44.0 1.0 CG D:GLU224 4.7 35.0 1.0 CB D:ASP221 4.7 35.0 1.0 CG D:ASP151 4.7 50.2 1.0

D.E.Weinberg, K.Nakanishi, D.J.Patel, D.P.Bartel. The Inside-Out Mechanism of Dicers From Budding Yeasts. Cell(Cambridge,Mass.) V. 146 262 2011.
ISSN: ISSN 0092-8674
PubMed: 21784247
DOI: 10.1016/J.CELL.2011.06.021