Atomistry » Magnesium » PDB 1qsi-1rc5 » 1rc5
Atomistry »
  Magnesium »
    PDB 1qsi-1rc5 »
      1rc5 »

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

Go back to Magnesium Binding Sites List in 1rc5
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

Go back to Magnesium Binding Sites List in 1rc5
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

Go back to Magnesium Binding Sites List in 1rc5
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

Go back to Magnesium Binding Sites List in 1rc5
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy