Atomistry » Magnesium » PDB 2e75-2ein » 2eb1
Atomistry »
  Magnesium »
    PDB 2e75-2ein »
      2eb1 »

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

Go back to Magnesium Binding Sites List in 2eb1
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

Go back to Magnesium Binding Sites List in 2eb1
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

Go back to Magnesium Binding Sites List in 2eb1
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

Go back to Magnesium Binding Sites List in 2eb1
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

Go back to Magnesium Binding Sites List in 2eb1
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

Go back to Magnesium Binding Sites List in 2eb1
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy