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Magnesium in PDB 2eb1: Crystal Structure of the C-Terminal Rnase III Domain of Human Dicer

Enzymatic activity of Crystal Structure of the C-Terminal Rnase III Domain of Human Dicer

All present enzymatic activity of Crystal Structure of the C-Terminal Rnase III Domain of Human Dicer:
3.1.26.3;

Protein crystallography data

The structure of Crystal Structure of the C-Terminal Rnase III Domain of Human Dicer, PDB code: 2eb1 was solved by D.Takeshita, S.Zenno, W.C.Lee, K.Nagata, K.Saigo, M.Tanokura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 88.602, 199.743, 119.640, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 23.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the C-Terminal Rnase III Domain of Human Dicer (pdb code 2eb1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the C-Terminal Rnase III Domain of Human Dicer, PDB code: 2eb1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2eb1

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Magnesium binding site 1 out of 6 in the Crystal Structure of the C-Terminal Rnase III Domain of Human Dicer


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 the C-Terminal Rnase III Domain of Human Dicer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:23.9
occ:1.00
 O A:HOH507 1.9 38.4 1.0
OE1 A:GLU47 2.1 35.1 1.0
OE2 A:GLU155 2.2 39.7 1.0
O A:HOH562 2.2 61.2 1.0
O A:HOH514 2.2 40.7 1.0
OD2 A:ASP152 2.2 43.5 1.0
CD A:GLU47 3.1 35.2 1.0
CD A:GLU155 3.1 36.9 1.0
CG A:ASP152 3.3 34.4 1.0
CG A:GLU47 3.4 31.6 1.0
OE1 A:GLU155 3.4 39.1 1.0
OD1 A:ASP152 4.1 37.8 1.0
CB A:ASP152 4.2 31.6 1.0
CA A:ASP152 4.2 30.8 1.0
OE2 A:GLU47 4.2 36.1 1.0
O A:HOH531 4.4 46.4 1.0
OD1 A:ASP51 4.5 48.1 1.0
CG A:GLU155 4.5 34.0 1.0
O A:HOH560 4.5 55.5 1.0
O A:HOH561 4.6 53.1 1.0
OD1 A:ASN84 4.6 49.7 1.0
N A:ASP152 4.8 31.3 1.0
CB A:GLU155 4.9 30.7 1.0
CB A:GLU47 5.0 30.0 1.0

Magnesium binding site 2 out of 6 in 2eb1

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Magnesium binding site 2 out of 6 in the Crystal Structure of the C-Terminal Rnase III Domain of Human Dicer


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 the C-Terminal Rnase III Domain of Human Dicer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:39.5
occ:1.00
 O A:HOH533 2.0 44.2 1.0
O A:HOH563 2.1 51.6 1.0
OD2 A:ASP51 2.3 48.6 1.0
O A:HOH553 2.4 54.7 1.0
O A:HOH526 2.4 41.4 1.0
CG A:ASP51 3.2 42.0 1.0
OD1 A:ASP51 3.6 48.1 1.0
O A:HOH535 3.9 48.7 1.0
OD1 A:ASP55 4.0 54.6 1.0
O A:ASP51 4.0 30.1 1.0
CB A:ASP55 4.2 34.5 1.0
O A:HOH559 4.2 68.6 1.0
C A:ASP51 4.2 31.9 1.0
OD1 C:ASP55 4.3 15.0 1.0
CG A:ASP55 4.4 42.9 1.0
CB A:ASP51 4.5 33.5 1.0
N A:ALA52 4.6 30.9 1.0
CA A:ALA52 4.8 30.6 1.0
CA A:ASP51 4.8 32.5 1.0

Magnesium binding site 3 out of 6 in 2eb1

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Magnesium binding site 3 out of 6 in the Crystal Structure of the C-Terminal Rnase III Domain of Human Dicer


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 the C-Terminal Rnase III Domain of Human Dicer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:25.1
occ:1.00
 O B:HOH513 1.9 37.6 1.0
OE1 B:GLU47 2.1 33.7 1.0
OE1 B:GLU155 2.1 37.7 1.0
OD1 B:ASP152 2.3 48.1 1.0
O B:HOH571 2.3 50.8 1.0
O B:HOH521 2.3 40.9 1.0
CD B:GLU155 3.1 39.0 1.0
CD B:GLU47 3.1 34.3 1.0
OE2 B:GLU155 3.3 43.4 1.0
CG B:ASP152 3.4 37.1 1.0
CG B:GLU47 3.4 31.1 1.0
OD1 B:ASP51 4.2 50.3 1.0
OD2 B:ASP152 4.2 40.7 1.0
CB B:ASP152 4.3 34.8 1.0
OE2 B:GLU47 4.3 32.5 1.0
CA B:ASP152 4.4 33.9 1.0
O B:HOH566 4.5 48.9 1.0
CG B:GLU155 4.5 35.1 1.0
O B:HOH552 4.7 50.5 1.0
OD1 B:ASN84 4.9 54.5 1.0
CB B:GLU155 4.9 31.2 1.0
N B:ASP152 4.9 33.2 1.0
CB B:GLU47 5.0 30.4 1.0

Magnesium binding site 4 out of 6 in 2eb1

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Magnesium binding site 4 out of 6 in the Crystal Structure of the C-Terminal Rnase III Domain of Human Dicer


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 the C-Terminal Rnase III Domain of Human Dicer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg506

b:38.0
occ:1.00
 O B:HOH543 1.9 44.2 1.0
O B:HOH565 2.0 62.6 1.0
OD2 B:ASP51 2.1 49.8 1.0
O B:HOH572 2.3 62.4 1.0
O B:HOH520 2.4 47.5 1.0
CG B:ASP51 3.1 42.6 1.0
OD1 B:ASP51 3.5 50.3 1.0
OD2 B:ASP55 3.8 51.8 1.0
O B:ASP51 3.9 31.3 1.0
O B:HOH554 4.1 48.8 1.0
C B:ASP51 4.2 32.4 1.0
CB B:ASP55 4.3 35.8 1.0
CB B:ASP51 4.4 35.9 1.0
CG B:ASP55 4.4 44.3 1.0
N B:ALA52 4.5 30.3 1.0
CA B:ALA52 4.7 29.8 1.0
CA B:ASP51 4.8 33.1 1.0

Magnesium binding site 5 out of 6 in 2eb1

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Magnesium binding site 5 out of 6 in the Crystal Structure of the C-Terminal Rnase III Domain of Human Dicer


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 the C-Terminal Rnase III Domain of Human Dicer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:21.8
occ:1.00
 O C:HOH508 1.7 34.0 1.0
OE1 C:GLU47 2.0 33.6 1.0
O C:HOH571 2.1 62.7 1.0
OE1 C:GLU155 2.1 34.6 1.0
O C:HOH529 2.2 39.8 1.0
OD1 C:ASP152 2.4 42.3 1.0
CD C:GLU47 3.1 32.1 1.0
CD C:GLU155 3.1 34.9 1.0
OE2 C:GLU155 3.4 38.9 1.0
CG C:ASP152 3.4 33.3 1.0
CG C:GLU47 3.5 28.0 1.0
O C:HOH565 3.7 61.6 1.0
OD2 C:ASP152 4.2 39.2 1.0
CA C:ASP152 4.2 30.2 1.0
OE2 C:GLU47 4.2 33.8 1.0
CB C:ASP152 4.2 30.0 1.0
O C:HOH561 4.3 61.7 1.0
O C:HOH562 4.5 54.4 1.0
OD1 C:ASP51 4.5 44.7 1.0
CG C:GLU155 4.5 29.8 1.0
ND2 C:ASN84 4.7 45.4 1.0
N C:ASP152 4.8 29.6 1.0
O C:HOH560 4.8 44.3 1.0
CB C:GLU155 4.9 29.5 1.0

Magnesium binding site 6 out of 6 in 2eb1

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Magnesium binding site 6 out of 6 in the Crystal Structure of the C-Terminal Rnase III Domain of Human Dicer


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 the C-Terminal Rnase III Domain of Human Dicer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg504

b:32.1
occ:1.00
 O C:HOH535 1.8 42.1 1.0
OD2 C:ASP51 2.0 42.1 1.0
O A:HOH559 2.1 68.6 1.0
O A:HOH508 2.1 42.5 1.0
O C:HOH572 2.2 56.4 1.0
CG C:ASP51 3.0 38.7 1.0
OD1 C:ASP51 3.3 44.7 1.0
OD1 A:ASP55 3.5 54.6 1.0
OD1 C:ASP55 3.6 15.0 1.0
O C:ASP51 3.9 29.1 1.0
O C:HOH526 4.1 44.8 1.0
C C:ASP51 4.1 29.1 1.0
CB C:ASP51 4.3 32.9 1.0
CB C:ASP55 4.4 15.0 1.0
CG C:ASP55 4.4 15.0 1.0
N C:ALA52 4.4 28.9 1.0
O A:HOH563 4.4 51.6 1.0
CA C:ALA52 4.6 29.2 1.0
CG A:ASP55 4.7 42.9 1.0
CA C:ASP51 4.7 30.5 1.0
OD2 A:ASP55 4.9 50.0 1.0
NH2 A:ARG78 4.9 43.6 1.0
CZ A:ARG78 5.0 46.8 1.0

Reference:

D.Takeshita, S.Zenno, W.C.Lee, K.Nagata, K.Saigo, M.Tanokura. Homodimeric Structure and Double-Stranded Rna Cleavage Activity of the C-Terminal Rnase III Domain of Human Dicer J.Mol.Biol. V. 374 106 2007.
ISSN: ISSN 0022-2836
PubMed: 17920623
DOI: 10.1016/J.JMB.2007.08.069
Page generated: Tue Aug 13 22:43:52 2024

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