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Magnesium in PDB 1rc5: Crystal Structure of Mg(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.30 Angstrom Resolution

Enzymatic activity of Crystal Structure of Mg(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.30 Angstrom Resolution

All present enzymatic activity of Crystal Structure of Mg(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.30 Angstrom Resolution:
3.1.26.3;

Protein crystallography data

The structure of Crystal Structure of Mg(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.30 Angstrom Resolution, PDB code: 1rc5 was solved by J.Blaszczyk, J.Gan, X.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.742, 140.856, 49.746, 90.00, 117.29, 90.00
R / Rfree (%) 21.5 / 25.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mg(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.30 Angstrom Resolution (pdb code 1rc5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Mg(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.30 Angstrom Resolution, PDB code: 1rc5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1rc5

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Magnesium binding site 1 out of 4 in the Crystal Structure of Mg(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.30 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 Mg(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.30 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg761

b:19.9
occ:1.00
 OE2 A:GLU40 2.0 14.8 1.0
O A:HOH1136 2.1 27.2 1.0
OE1 A:GLU110 2.2 30.2 1.0
O A:HOH1056 2.4 24.1 1.0
OD1 A:ASP107 2.6 34.1 1.0
O A:HOH1004 2.6 11.9 1.0
CD A:GLU40 3.1 12.2 1.0
CD A:GLU110 3.1 25.6 1.0
OE2 A:GLU110 3.3 26.4 1.0
CG A:GLU40 3.6 14.7 1.0
CG A:ASP107 3.6 33.0 1.0
O A:HOH1064 3.8 28.3 1.0
OE1 A:GLU40 4.2 17.0 1.0
CA A:ASP107 4.2 27.6 1.0
O B:HOH1054 4.2 25.3 1.0
CB A:ASP107 4.4 30.4 1.0
CG A:GLU110 4.4 22.1 1.0
OD2 A:ASP44 4.4 29.9 1.0
OD2 A:ASP107 4.5 36.9 1.0
N A:ASP107 4.8 21.5 1.0
O A:HOH1408 4.8 77.6 1.0
O A:HOH1481 4.8 44.6 1.0
O A:HOH1037 4.9 42.6 1.0

Magnesium binding site 2 out of 4 in 1rc5

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Magnesium binding site 2 out of 4 in the Crystal Structure of Mg(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.30 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 Mg(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.30 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg762

b:19.3
occ:1.00
 OE1 B:GLU310 2.0 27.8 1.0
OD1 B:ASP307 2.2 30.3 1.0
O B:HOH1007 2.5 28.8 1.0
OE1 B:GLU240 2.5 43.0 1.0
O B:HOH1319 2.8 36.4 1.0
CD B:GLU310 2.9 29.6 1.0
O B:HOH1245 3.1 44.6 1.0
OE2 B:GLU310 3.2 26.8 1.0
CG B:ASP307 3.4 22.1 1.0
CD B:GLU240 3.7 41.9 1.0
OD2 B:ASP307 4.1 26.4 1.0
OE2 B:GLU240 4.2 39.6 1.0
CG B:GLU310 4.3 24.5 1.0
CA B:ASP307 4.4 28.6 1.0
O B:HOH1255 4.4 40.0 1.0
OD2 B:ASP244 4.4 22.7 1.0
CB B:ASP307 4.5 24.9 1.0
CE D:LYS633 4.6 63.5 1.0
NZ D:LYS633 4.6 71.0 1.0
O B:HOH1288 4.8 77.4 1.0
N B:ASP307 4.8 34.9 1.0
CB B:GLU310 4.8 18.0 1.0
CG D:LYS633 4.8 56.2 1.0
CG B:GLU240 4.9 36.4 1.0

Magnesium binding site 3 out of 4 in 1rc5

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Magnesium binding site 3 out of 4 in the Crystal Structure of Mg(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.30 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 Mg(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.30 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg763

b:15.9
occ:1.00
 OE2 C:GLU440 2.1 17.7 1.0
OE1 C:GLU510 2.5 14.9 1.0
O C:HOH1008 2.5 18.6 1.0
OD1 C:ASP507 2.6 20.8 1.0
O C:HOH1015 2.8 40.1 1.0
O C:HOH1039 2.8 19.5 1.0
CD C:GLU440 3.1 14.8 1.0
OE2 C:GLU510 3.2 24.2 1.0
CD C:GLU510 3.2 11.3 1.0
CG C:GLU440 3.4 14.4 1.0
CG C:ASP507 3.6 26.3 1.0
O C:HOH1471 3.8 34.2 1.0
OD2 C:ASP444 4.0 17.1 1.0
O C:HOH1062 4.1 24.2 1.0
OE1 C:GLU440 4.2 11.9 1.0
CA C:ASP507 4.3 19.6 1.0
CB C:ASP507 4.3 26.7 1.0
O C:HOH1270 4.3 18.0 1.0
OD2 C:ASP507 4.4 33.6 1.0
O C:HOH1152 4.6 28.3 1.0
O C:HOH1234 4.6 76.3 1.0
O C:HOH1081 4.7 68.2 1.0
CG C:GLU510 4.7 14.7 1.0
O C:HOH1304 4.8 29.0 1.0
N C:ASP507 4.9 20.3 1.0
CB C:GLU440 4.9 15.3 1.0

Magnesium binding site 4 out of 4 in 1rc5

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Magnesium binding site 4 out of 4 in the Crystal Structure of Mg(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.30 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 Mg(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.30 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg764

b:24.2
occ:1.00
 OD1 D:ASP707 2.0 38.0 1.0
OE1 D:GLU710 2.2 15.1 1.0
O D:HOH1123 2.3 20.6 1.0
OE1 D:GLU640 2.3 38.0 1.0
O D:HOH1302 3.0 48.2 1.0
CD D:GLU640 3.1 34.1 1.0
CG D:ASP707 3.1 33.2 1.0
OE2 D:GLU640 3.2 33.7 1.0
O D:HOH1305 3.3 55.2 1.0
CD D:GLU710 3.3 24.1 1.0
OE2 D:GLU710 3.8 23.5 1.0
OD2 D:ASP707 3.9 35.5 1.0
CB D:ASP707 4.1 23.8 1.0
O D:HOH1020 4.2 23.6 1.0
CA D:ASP707 4.2 27.0 1.0
O D:HOH1420 4.3 27.0 1.0
CG D:GLU710 4.5 23.9 1.0
CG D:GLU640 4.6 32.8 1.0
N D:ASP707 4.7 29.2 1.0
CB D:GLU710 4.9 27.6 1.0

Reference:

J.Blaszczyk, J.Gan, J.E.Tropea, D.L.Court, D.S.Waugh, X.Ji. Noncatalytic Assembly of Ribonuclease III with Double-Stranded Rna. Structure V. 12 457 2004.
ISSN: ISSN 0969-2126
PubMed: 15016361
DOI: 10.1016/J.STR.2004.02.004
Page generated: Tue Aug 13 12:07:09 2024

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