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Magnesium in PDB 2nug: Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 1.7-Angstrom Resolution

Enzymatic activity of Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 1.7-Angstrom Resolution

All present enzymatic activity of Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 1.7-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 1.7-Angstrom Resolution, PDB code: 2nug 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) 29.44 / 1.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.400, 119.900, 58.900, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 22

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 1.7-Angstrom Resolution (pdb code 2nug). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 19 binding sites of Magnesium where determined in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 1.7-Angstrom Resolution, PDB code: 2nug:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 19 in 2nug

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Magnesium binding site 1 out of 19 in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 1.7-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 1.7-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg515

b:75.9
occ:1.00
 O C:HOH559 2.0 50.8 1.0
O C:HOH535 2.1 42.8 1.0
O C:HOH538 2.2 41.3 1.0
O C:HOH563 2.3 53.7 1.0
O6 C:G5 4.1 25.4 1.0
O C:HOH558 4.1 50.9 1.0
N7 C:G4 4.2 27.6 1.0
O6 C:G4 4.4 27.8 1.0
O C:HOH543 4.4 47.7 1.0
N7 C:G5 4.4 27.2 1.0
O E:HOH520 4.5 42.7 1.0
O C:HOH564 4.7 67.1 1.0
O4 C:U6 4.9 29.3 1.0
C5 C:G4 4.9 23.9 1.0
C6 C:G5 4.9 27.3 1.0
C6 C:G4 4.9 21.8 1.0
O E:HOH529 5.0 53.5 1.0

Magnesium binding site 2 out of 19 in 2nug

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Magnesium binding site 2 out of 19 in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 1.7-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 1.7-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg519

b:64.8
occ:1.00
 O C:HOH562 2.2 40.0 1.0
O C:HOH526 2.2 25.8 1.0
O C:HOH540 2.2 35.5 1.0
O C:HOH530 2.3 32.6 1.0
O C:HOH546 2.3 36.9 1.0
O F:HOH551 2.6 45.9 1.0
O C:HOH561 3.9 51.3 1.0
N4 C:C11 3.9 18.8 1.0
O6 C:G12 4.1 18.1 1.0
C5 C:C11 4.2 19.7 1.0
O D:HOH561 4.3 56.2 1.0
O C:HOH525 4.3 20.8 1.0
O F:HOH524 4.4 32.1 1.0
C4 C:C11 4.4 18.0 1.0
N7 C:G12 4.5 17.1 1.0
O B:HOH631 4.5 32.5 1.0
N6 F:A17 4.8 21.6 0.8
O C:HOH534 4.9 58.2 1.0
O D:HOH530 4.9 26.8 1.0
C6 C:G12 4.9 18.5 1.0
N6 F:A17 5.0 26.1 0.2

Magnesium binding site 3 out of 19 in 2nug

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Magnesium binding site 3 out of 19 in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 1.7-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 1.7-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg505

b:22.6
occ:0.65
 OP2 E:A17 1.9 23.0 0.7
O E:HOH512 2.0 33.1 1.0
O E:HOH509 2.1 32.0 1.0
OP2 E:G18 2.1 26.7 0.7
O E:HOH510 2.1 38.4 1.0
O E:HOH511 2.2 33.5 1.0
OP2 E:G18 2.3 48.1 0.3
P E:A17 3.2 21.4 0.7
P E:G18 3.5 27.1 0.7
OP1 E:A17 3.5 17.0 0.7
P E:G18 3.8 47.9 0.3
OP1 E:A17 3.8 20.0 0.3
OP3 E:A17 4.1 20.4 0.3
O5' E:A17 4.1 19.6 0.7
OP1 E:G18 4.1 31.0 0.7
O E:HOH508 4.1 26.2 1.0
O A:HOH522 4.3 33.4 1.0
O3' E:A17 4.3 26.2 0.7
O E:HOH524 4.3 39.6 1.0
OP3 E:A17 4.3 21.2 0.7
O E:HOH506 4.4 19.7 0.7
P E:A17 4.4 16.9 0.3
C3' E:A17 4.5 20.1 0.7
O5' E:G18 4.5 47.3 0.3
O5' E:G18 4.5 25.0 0.7
OP1 E:G18 4.6 48.8 0.3
O E:HOH519 4.7 38.7 1.0
C5' E:A17 4.7 18.2 0.7
O5' E:A17 4.8 17.3 0.3
O3' E:A17 4.8 39.7 0.3
O E:HOH507 4.8 29.8 1.0
C3' E:A17 4.9 30.7 0.3

Magnesium binding site 4 out of 19 in 2nug

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Magnesium binding site 4 out of 19 in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 1.7-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 1.7-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg514

b:52.1
occ:1.00
 O D:HOH529 2.0 38.0 1.0
O D:HOH550 2.1 58.1 1.0
O D:HOH551 2.1 50.8 1.0
O D:HOH533 2.1 34.0 1.0
O D:HOH552 2.3 43.2 1.0
O6 D:G5 3.9 30.0 1.0
O D:HOH527 3.9 38.5 1.0
O D:HOH544 3.9 51.1 1.0
N7 D:G4 3.9 28.6 1.0
N7 D:G5 4.1 24.5 1.0
O6 D:G4 4.1 28.7 1.0
O D:HOH566 4.2 40.7 1.0
C5 D:G4 4.6 26.1 1.0
C6 D:G4 4.6 26.6 1.0
C6 D:G5 4.7 22.0 1.0
C5 D:G5 4.7 24.7 1.0
O4 D:U6 4.8 28.3 1.0
O F:HOH523 4.8 41.0 1.0
C8 D:G4 4.9 26.8 1.0

Magnesium binding site 5 out of 19 in 2nug

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Magnesium binding site 5 out of 19 in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 1.7-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 1.7-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg516

b:57.4
occ:1.00
 O E:HOH526 2.0 35.0 1.0
O D:HOH562 2.2 42.6 1.0
O D:HOH522 2.2 25.4 1.0
O E:HOH513 2.3 49.7 1.0
O D:HOH531 2.4 33.7 1.0
O D:HOH535 2.4 40.5 1.0
O D:HOH536 3.8 45.1 1.0
N4 D:C11 4.0 20.9 1.0
O E:HOH535 4.1 49.5 1.0
O E:HOH515 4.2 29.2 1.0
O6 D:G12 4.2 19.2 1.0
O C:HOH541 4.2 40.4 1.0
O D:HOH525 4.3 24.3 1.0
C5 D:C11 4.4 17.5 1.0
N7 D:G12 4.5 16.9 1.0
C4 D:C11 4.5 17.4 1.0
O C:HOH532 4.7 32.6 1.0
N6 E:A17 4.8 18.8 0.7
N6 E:A17 4.8 34.5 0.3

Magnesium binding site 6 out of 19 in 2nug

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Magnesium binding site 6 out of 19 in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 1.7-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 1.7-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg511

b:25.9
occ:0.75
 OP2 F:A17 2.0 26.7 0.8
OP2 F:G18 2.1 26.9 0.8
O F:HOH519 2.1 31.4 1.0
O F:HOH518 2.2 30.7 1.0
O F:HOH517 2.2 33.9 1.0
O F:HOH520 2.3 31.2 1.0
OP2 F:G18 2.3 44.3 0.2
P F:A17 3.2 24.4 0.8
P F:G18 3.4 31.6 0.8
OP1 F:A17 3.5 24.3 0.8
P F:G18 3.9 41.9 0.2
OP1 F:A17 4.0 12.6 0.2
O5' F:A17 4.0 24.1 0.8
O B:HOH521 4.1 26.1 0.8
OP1 F:G18 4.1 32.4 0.8
O3' F:A17 4.2 29.7 0.8
O F:HOH516 4.2 24.6 1.0
O B:HOH523 4.3 32.8 1.0
OP3 F:A17 4.3 22.5 0.8
C3' F:A17 4.4 22.8 0.8
OP3 F:A17 4.4 17.5 0.2
O F:HOH522 4.5 33.1 1.0
P F:A17 4.5 10.7 0.2
O5' F:G18 4.5 43.6 0.2
O5' F:G18 4.5 28.7 0.8
O F:HOH532 4.5 49.6 1.0
C5' F:A17 4.6 23.5 0.8
O5' F:A17 4.6 16.0 0.2
O F:HOH515 4.7 30.4 1.0
OP1 F:G18 4.8 43.8 0.2
C3' F:A17 4.9 25.6 0.2
O3' F:A17 4.9 35.5 0.2

Magnesium binding site 7 out of 19 in 2nug

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Magnesium binding site 7 out of 19 in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 1.7-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 1.7-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg513

b:53.7
occ:1.00
 O F:HOH542 2.1 55.5 1.0
O F:HOH544 2.1 52.8 1.0
O F:HOH543 2.1 59.7 1.0
O F:HOH545 2.4 46.6 1.0
O F:HOH552 2.6 50.8 1.0
O6 F:G26 3.7 33.0 1.0
O F:HOH541 4.2 47.8 1.0
O4 F:U25 4.3 32.6 1.0
O F:HOH550 4.5 50.0 1.0
N4 F:C27 4.6 36.8 1.0
C6 F:G26 4.8 33.0 1.0
C4 F:U25 5.0 32.4 1.0

Magnesium binding site 8 out of 19 in 2nug

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Magnesium binding site 8 out of 19 in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 1.7-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 1.7-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:18.2
occ:1.00
 OD1 A:ASP44 2.0 14.5 1.0
O A:HOH519 2.1 21.5 0.7
OE2 A:GLU110 2.1 17.9 1.0
O A:HOH518 2.1 17.9 1.0
OP2 E:A17 2.1 24.9 0.3
O3' D:G12 2.2 17.8 1.0
O D:HOH517 2.3 19.7 1.0
CD A:GLU110 3.1 21.6 1.0
CG A:ASP44 3.1 20.1 1.0
C3' D:G12 3.5 19.1 1.0
P E:A17 3.5 16.9 0.3
OE1 A:GLU110 3.5 22.8 1.0
CB A:ASP44 3.6 15.7 1.0
O2' D:G12 3.8 16.0 1.0
OP3 E:A17 3.8 20.4 0.3
OP3 E:A17 3.8 21.2 0.7
MG A:MG502 3.9 15.9 0.3
C4' D:G12 4.0 16.5 1.0
O5' E:A17 4.1 17.3 0.3
O A:HOH523 4.1 19.0 0.7
C2' D:G12 4.1 17.4 1.0
O A:ILE75 4.2 18.6 1.0
OD2 A:ASP44 4.2 20.4 1.0
CA A:ASP44 4.2 13.8 1.0
O A:HOH531 4.2 15.8 0.3
CE2 A:PHE80 4.3 18.4 1.0
O D:HOH520 4.3 23.5 1.0
C5' E:A17 4.3 18.2 0.7
C5' E:A17 4.3 19.2 0.3
OD1 A:ASN48 4.4 17.8 1.0
CG A:GLU110 4.4 18.7 1.0
OP1 E:A17 4.6 20.0 0.3
O E:HOH506 4.6 19.7 0.7
C5' D:G12 4.6 15.1 1.0
ND2 A:ASN48 4.7 19.7 1.0
O5' E:A17 4.8 19.6 0.7
O A:HOH520 4.9 22.5 1.0
O A:ASP44 5.0 15.1 1.0
P E:A17 5.0 21.4 0.7
CG A:ASN48 5.0 19.8 1.0
CD2 A:PHE80 5.0 17.8 1.0
C A:ASP44 5.0 16.9 1.0

Magnesium binding site 9 out of 19 in 2nug

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Magnesium binding site 9 out of 19 in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 1.7-Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 1.7-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:15.9
occ:0.35
 O A:HOH531 2.0 15.8 0.3
OE2 A:GLU40 2.0 21.2 1.0
O A:HOH519 2.0 21.5 0.7
O E:HOH506 2.1 19.7 0.7
OE1 A:GLU110 2.2 22.8 1.0
OP1 E:A17 2.2 20.0 0.3
OP2 E:A17 2.3 24.9 0.3
O A:HOH520 2.3 22.5 1.0
P E:A17 2.8 16.9 0.3
CD A:GLU40 3.0 18.0 1.0
CG A:GLU40 3.3 18.3 1.0
CD A:GLU110 3.3 21.6 1.0
MG A:MG503 3.6 25.0 0.7
O A:HOH523 3.6 19.0 0.7
OE2 A:GLU110 3.7 17.9 1.0
OD1 A:ASP107 3.8 28.0 1.0
OP3 E:A17 3.9 20.4 0.3
MG A:MG501 3.9 18.2 1.0
O5' E:A17 4.0 17.3 0.3
C5' E:A17 4.0 18.2 0.7
O E:HOH508 4.1 26.2 1.0
OE1 A:GLU40 4.1 20.0 1.0
CB A:ASP44 4.1 15.7 1.0
C5' E:A17 4.1 19.2 0.3
O A:GLU40 4.2 16.7 1.0
OP3 E:A17 4.2 21.2 0.7
OP2 E:A17 4.4 23.0 0.7
O E:HOH517 4.5 25.5 1.0
OD1 A:ASP44 4.5 14.5 1.0
CG A:GLU110 4.5 18.7 1.0
CB A:GLU40 4.6 17.6 1.0
CG A:ASP44 4.7 20.1 1.0
CG A:ASP107 4.7 23.5 1.0
C A:GLU40 4.7 14.9 1.0
P E:A17 4.8 21.4 0.7
O D:HOH517 4.8 19.7 1.0
CB A:GLU110 4.8 16.4 1.0
O E:HOH507 4.8 29.8 1.0
O3' D:G12 4.8 17.8 1.0
O A:HOH522 4.9 33.4 1.0
O5' E:A17 4.9 19.6 0.7

Magnesium binding site 10 out of 19 in 2nug

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Magnesium binding site 10 out of 19 in the Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 1.7-Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Rnase III From Aquifex Aeolicus Complexed with Ds-Rna at 1.7-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:25.0
occ:0.65
 O A:HOH531 1.8 15.8 0.3
O E:HOH506 2.0 19.7 0.7
O A:HOH521 2.1 22.7 1.0
OD1 A:ASP107 2.1 28.0 1.0
O A:HOH523 2.2 19.0 0.7
O E:HOH507 2.2 29.8 1.0
O A:HOH522 2.3 33.4 1.0
CG A:ASP107 3.3 23.5 1.0
MG A:MG502 3.6 15.9 0.3
OD2 A:ASP107 3.9 30.4 1.0
OE2 A:GLU40 4.0 21.2 1.0
O A:HOH519 4.0 21.5 0.7
OP1 E:A17 4.0 20.0 0.3
OP3 E:A17 4.1 21.2 0.7
OP3 E:A17 4.1 20.4 0.3
N A:ASP107 4.2 16.6 1.0
O D:HOH520 4.2 23.5 1.0
OE1 A:GLU77 4.2 26.0 1.0
OP2 E:A17 4.2 24.9 0.3
O A:THR103 4.3 22.8 1.0
P E:A17 4.3 16.9 0.3
OE1 A:GLU110 4.3 22.8 1.0
CA A:ASP107 4.3 17.7 1.0
CB A:ASP107 4.4 17.6 1.0
OP2 E:A17 4.4 23.0 0.7
C A:GLY106 4.5 18.6 1.0
O E:HOH512 4.5 33.1 1.0
O D:HOH517 4.5 19.7 1.0
O E:HOH524 4.6 39.6 1.0
CD A:GLU40 4.7 18.0 1.0
O A:GLY106 4.8 18.1 1.0
P E:A17 4.9 21.4 0.7
O E:HOH533 4.9 60.5 1.0
CG2 A:THR103 4.9 28.6 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 00:55:15 2024

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