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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

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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

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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

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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

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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

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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

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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

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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

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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

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