Atomistry » Magnesium » PDB 2mtk-2o52 » 2nuf
Atomistry »
  Magnesium »
    PDB 2mtk-2o52 »
      2nuf »

Magnesium in PDB 2nuf: Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution

Enzymatic activity of Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution

All present enzymatic activity of Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution:
3.1.26.3;

Protein crystallography data

The structure of Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution, PDB code: 2nuf was solved by J.H.Gan, G.Shaw, J.E.Tropea, D.S.Waugh, D.L.Court, X.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.76 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.100, 51.100, 113.400, 90.00, 104.90, 90.00
R / Rfree (%) 22.2 / 28.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution (pdb code 2nuf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution, PDB code: 2nuf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2nuf

Go back to Magnesium Binding Sites List in 2nuf
Magnesium binding site 1 out of 8 in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution


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 Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:62.0
occ:1.00
 OP1 C:C1 2.0 56.1 1.0
OP2 C:A2 2.4 57.5 1.0
O C:HOH223 3.1 48.0 1.0
P C:C1 3.2 64.8 1.0
OP3 C:C1 3.4 61.4 1.0
P C:A2 3.8 58.9 1.0
O A:HOH278 4.0 38.6 1.0
O5' C:C1 4.1 56.3 1.0
OP2 C:C1 4.3 58.1 1.0
C3' C:C1 4.4 50.8 1.0
O3' C:C1 4.4 51.7 1.0
OP1 C:A2 4.7 55.9 1.0
O5' C:A2 4.8 57.2 1.0
C5' C:A2 4.8 51.2 1.0
C5' C:C1 4.9 48.7 1.0

Magnesium binding site 2 out of 8 in 2nuf

Go back to Magnesium Binding Sites List in 2nuf
Magnesium binding site 2 out of 8 in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution


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 Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg206

b:54.2
occ:1.00
 OP1 D:C1 1.9 54.7 1.0
OP2 D:A2 2.1 57.7 1.0
O D:HOH210 2.6 44.9 1.0
P D:C1 3.3 57.2 1.0
P D:A2 3.3 60.1 1.0
O B:HOH232 3.6 47.9 1.0
OP3 D:C1 3.8 61.2 1.0
OP1 D:A2 3.9 60.5 1.0
MG D:MG208 4.0 75.6 1.0
O3' D:C1 4.0 53.3 1.0
O5' D:C1 4.1 54.9 1.0
C3' D:C1 4.2 50.7 1.0
OP2 D:C1 4.4 53.7 1.0
O5' D:A2 4.5 58.7 1.0
C5' D:C1 4.7 52.8 1.0
C5' D:A2 4.7 50.4 1.0

Magnesium binding site 3 out of 8 in 2nuf

Go back to Magnesium Binding Sites List in 2nuf
Magnesium binding site 3 out of 8 in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution


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 Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg208

b:75.6
occ:1.00
 OP1 D:A2 2.2 60.5 1.0
OE2 B:GLU40 2.8 60.5 1.0
P D:A2 3.0 60.1 1.0
OE1 B:GLU40 3.1 66.5 1.0
O3' D:C1 3.2 53.3 1.0
CD B:GLU40 3.3 59.9 1.0
OP2 D:A2 3.6 57.7 1.0
OP1 D:C1 3.9 54.7 1.0
MG D:MG206 4.0 54.2 1.0
O B:HOH232 4.1 47.9 1.0
OD2 B:ASP44 4.3 65.0 1.0
C3' D:C1 4.4 50.7 1.0
O5' D:A2 4.4 58.7 1.0
C5' D:C1 4.7 52.8 1.0
MG B:MG223 4.7 57.7 1.0
CG B:GLU40 4.7 55.4 1.0
O B:HOH248 4.7 48.6 1.0
OE1 A:GLU64 4.8 92.1 1.0
C4' D:C1 4.9 50.0 1.0

Magnesium binding site 4 out of 8 in 2nuf

Go back to Magnesium Binding Sites List in 2nuf
Magnesium binding site 4 out of 8 in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution


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 Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg222

b:54.8
occ:1.00
 OE2 A:GLU110 2.1 59.7 1.0
OD2 A:ASP44 3.0 67.3 1.0
OD1 A:ASP44 3.1 76.5 1.0
CD A:GLU110 3.3 59.4 1.0
CG A:ASP44 3.3 69.8 1.0
O C:HOH207 3.7 55.6 1.0
OE1 A:GLU110 3.8 65.7 1.0
O A:ILE75 4.0 50.0 1.0
MG A:MG223 4.0 54.7 1.0
OP2 C:C1 4.1 58.1 1.0
CE2 A:PHE80 4.4 40.8 1.0
CG A:GLU110 4.5 53.9 1.0
OE2 A:GLU40 4.7 61.5 1.0
CB A:ASP44 4.7 61.1 1.0
O A:HOH273 4.9 40.6 1.0
CD2 A:PHE80 5.0 43.6 1.0

Magnesium binding site 5 out of 8 in 2nuf

Go back to Magnesium Binding Sites List in 2nuf
Magnesium binding site 5 out of 8 in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution


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 Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg223

b:54.7
occ:1.00
 OD1 A:ASP107 2.2 57.5 1.0
OE2 A:GLU40 2.4 61.5 1.0
OE1 A:GLU110 2.7 65.7 1.0
CD A:GLU40 3.0 52.0 1.0
CG A:ASP107 3.4 58.0 1.0
CG A:GLU40 3.5 50.8 1.0
O A:HOH278 3.5 38.6 1.0
CD A:GLU110 3.6 59.4 1.0
OE1 A:GLU40 3.8 51.8 1.0
OE2 A:GLU110 3.8 59.7 1.0
OD2 A:ASP44 3.9 67.3 1.0
MG A:MG222 4.0 54.8 1.0
OP2 C:C1 4.0 58.1 1.0
OD2 A:ASP107 4.1 62.7 1.0
CB A:ASP107 4.4 49.4 1.0
CA A:ASP107 4.5 49.6 1.0
O C:HOH207 4.6 55.6 1.0
OP1 C:C1 4.6 56.1 1.0
O A:HOH276 4.8 51.4 1.0
N A:ASP107 5.0 47.8 1.0
P C:C1 5.0 64.8 1.0
O A:HOH277 5.0 26.7 1.0
MG A:MG224 5.0 47.5 1.0

Magnesium binding site 6 out of 8 in 2nuf

Go back to Magnesium Binding Sites List in 2nuf
Magnesium binding site 6 out of 8 in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution


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 Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg224

b:47.5
occ:1.00
 O A:HOH276 2.0 51.4 1.0
O A:HOH279 2.1 35.0 1.0
O A:HOH278 2.2 38.6 1.0
OE1 A:GLU40 2.3 51.8 1.0
O A:HOH277 2.4 26.7 1.0
OP1 C:A2 2.5 55.9 1.0
CD A:GLU40 3.1 52.0 1.0
OE2 A:GLU40 3.3 61.5 1.0
P C:A2 3.6 58.9 1.0
O3' C:C1 3.6 51.7 1.0
CA A:PHE41 4.0 41.0 1.0
CD1 A:PHE41 4.1 46.8 1.0
N A:PHE41 4.1 41.1 1.0
OE2 B:GLU64 4.2 83.1 1.0
CB A:PHE41 4.3 43.6 1.0
OP2 C:A2 4.4 57.5 1.0
CG A:GLU40 4.5 50.8 1.0
C A:GLU40 4.5 41.8 1.0
O A:GLU37 4.6 45.1 1.0
CG A:PHE41 4.7 41.6 1.0
O A:GLU40 4.7 40.7 1.0
O5' C:A2 4.8 57.2 1.0
OD2 A:ASP44 4.8 67.3 1.0
CB A:GLU40 4.8 46.2 1.0
C3' C:C1 5.0 50.8 1.0
MG A:MG223 5.0 54.7 1.0

Magnesium binding site 7 out of 8 in 2nuf

Go back to Magnesium Binding Sites List in 2nuf
Magnesium binding site 7 out of 8 in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg222

b:71.2
occ:1.00
 O B:HOH248 2.0 48.6 1.0
OD1 B:ASP44 2.5 63.9 1.0
OE2 B:GLU110 2.7 45.5 1.0
CG B:ASP44 3.4 59.8 1.0
OD2 B:ASP44 3.5 65.0 1.0
OP2 D:C1 3.5 53.7 1.0
CD B:GLU110 3.7 43.9 1.0
O C:HOH222 3.8 49.1 1.0
MG B:MG223 3.8 57.7 1.0
OE1 B:GLU110 4.0 41.0 1.0
O B:ILE75 4.3 51.1 1.0
CB B:ASP44 4.8 54.0 1.0
C5' D:C1 4.9 52.8 1.0
P D:C1 4.9 57.2 1.0
OE2 B:GLU40 4.9 60.5 1.0
CE2 B:PHE80 5.0 49.3 1.0

Magnesium binding site 8 out of 8 in 2nuf

Go back to Magnesium Binding Sites List in 2nuf
Magnesium binding site 8 out of 8 in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 2.5-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg223

b:57.7
occ:1.00
 O B:HOH248 2.0 48.6 1.0
O B:HOH232 2.2 47.9 1.0
OD1 B:ASP107 2.3 51.6 1.0
OE1 B:GLU110 2.8 41.0 1.0
OE2 B:GLU40 3.1 60.5 1.0
CD B:GLU40 3.4 59.9 1.0
CG B:ASP107 3.4 56.5 1.0
OE1 B:GLU40 3.7 66.5 1.0
CD B:GLU110 3.7 43.9 1.0
MG B:MG222 3.8 71.2 1.0
OP2 D:C1 3.9 53.7 1.0
OE2 B:GLU110 3.9 45.5 1.0
OD2 B:ASP107 4.0 63.9 1.0
CG B:GLU40 4.1 55.4 1.0
CA B:ASP107 4.5 49.0 1.0
CB B:ASP107 4.6 49.7 1.0
OP1 D:C1 4.6 54.7 1.0
OD1 B:ASP44 4.6 63.9 1.0
OD2 B:ASP44 4.7 65.0 1.0
MG D:MG208 4.7 75.6 1.0
N B:ASP107 4.8 47.8 1.0
P D:C1 4.8 57.2 1.0

Reference:

J.Gan, G.Shaw, J.E.Tropea, D.S.Waugh, D.L.Court, X.Ji. A Stepwise Model For Double-Stranded Rna Processing By Ribonuclease III. Mol.Microbiol. V. 67 143 2007.
ISSN: ISSN 0950-382X
PubMed: 18047582
DOI: 10.1111/J.1365-2958.2007.06032.X
Page generated: Wed Aug 14 00:54:51 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