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Magnesium in PDB 4oog: Crystal Structure of Yeast Rnase III (RNT1P) Complexed with the Product of Dsrna Processing

Enzymatic activity of Crystal Structure of Yeast Rnase III (RNT1P) Complexed with the Product of Dsrna Processing

All present enzymatic activity of Crystal Structure of Yeast Rnase III (RNT1P) Complexed with the Product of Dsrna Processing:
3.1.26.3;

Protein crystallography data

The structure of Crystal Structure of Yeast Rnase III (RNT1P) Complexed with the Product of Dsrna Processing, PDB code: 4oog was solved by Y.-H.Liang, X.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.72 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 157.972, 183.804, 61.289, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Yeast Rnase III (RNT1P) Complexed with the Product of Dsrna Processing (pdb code 4oog). 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 Yeast Rnase III (RNT1P) Complexed with the Product of Dsrna Processing, PDB code: 4oog:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4oog

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Magnesium binding site 1 out of 4 in the Crystal Structure of Yeast Rnase III (RNT1P) Complexed with the Product of Dsrna Processing


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 Yeast Rnase III (RNT1P) Complexed with the Product of Dsrna Processing within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:53.2
occ:1.00
 O C:HOH702 2.0 56.1 1.0
OE2 C:GLU320 2.0 52.1 1.0
O C:HOH701 2.0 63.2 1.0
O3' D:C34 2.0 57.6 1.0
OD2 C:ASP245 2.0 64.2 1.0
CD C:GLU320 3.0 65.4 1.0
CG C:ASP245 3.1 53.5 1.0
C3' D:C34 3.4 50.0 1.0
OE1 C:GLU320 3.4 52.2 1.0
MG C:MG602 3.6 58.4 1.0
CB C:ASP245 3.7 53.2 1.0
O C:HOH703 3.9 58.5 1.0
O2' D:C34 4.0 61.8 1.0
C4' D:C34 4.1 58.6 1.0
OD1 C:ASN278 4.1 57.5 1.0
OD1 C:ASP245 4.2 68.6 1.0
C2' D:C34 4.2 53.2 1.0
CG C:GLU320 4.3 55.5 1.0
O C:HOH704 4.3 56.6 1.0
O C:VAL276 4.3 53.9 1.0
CA C:ASP245 4.4 52.2 1.0
C5' D:C34 4.6 43.4 1.0
CD1 C:ILE281 4.9 57.1 1.0
CG C:ASN278 5.0 62.1 1.0
OD1 C:ASN249 5.0 67.0 1.0

Magnesium binding site 2 out of 4 in 4oog

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Magnesium binding site 2 out of 4 in the Crystal Structure of Yeast Rnase III (RNT1P) Complexed with the Product of Dsrna Processing


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 Yeast Rnase III (RNT1P) Complexed with the Product of Dsrna Processing within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:58.4
occ:1.00
 O C:HOH703 2.0 58.5 1.0
O C:HOH704 2.0 56.6 1.0
OE1 C:GLU320 2.0 52.2 1.0
OE2 C:GLU241 2.0 61.1 1.0
CD C:GLU320 3.0 65.4 1.0
CD C:GLU241 3.1 64.0 1.0
OE2 C:GLU320 3.5 52.1 1.0
CG C:GLU241 3.6 56.7 1.0
MG C:MG601 3.6 53.2 1.0
OD1 C:ASP317 3.7 74.6 1.0
O C:HOH708 3.9 68.2 1.0
NZ C:LYS313 3.9 67.0 1.0
OE1 C:GLU241 4.2 52.0 1.0
CG C:GLU320 4.3 55.5 1.0
O C:HOH702 4.4 56.1 1.0
OD1 C:ASN278 4.5 57.5 1.0
CB C:ASP245 4.5 53.2 1.0
OD2 C:ASP245 4.6 64.2 1.0
O C:GLU241 4.6 59.0 1.0
CG C:ASP317 4.6 77.7 1.0
O3' D:C34 4.7 57.6 1.0
CB C:GLU320 4.8 52.1 1.0
CA C:ASP317 4.9 57.3 1.0
CB C:GLU241 4.9 44.8 1.0
CG C:ASP245 4.9 53.5 1.0
CE C:LYS313 4.9 74.1 1.0

Magnesium binding site 3 out of 4 in 4oog

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Magnesium binding site 3 out of 4 in the Crystal Structure of Yeast Rnase III (RNT1P) Complexed with the Product of Dsrna Processing


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 Yeast Rnase III (RNT1P) Complexed with the Product of Dsrna Processing within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:63.9
occ:1.00
 O C:HOH707 2.0 52.4 1.0
O C:HOH706 2.0 48.5 1.0
O C:HOH705 2.0 52.8 1.0
OE1 C:GLU241 2.0 52.0 1.0
O C:HOH708 2.0 68.2 1.0
OE1 C:GLU238 2.0 61.8 1.0
CD C:GLU241 3.0 64.0 1.0
CD C:GLU238 3.1 58.6 1.0
OE2 C:GLU241 3.4 61.1 1.0
OE2 C:GLU238 3.6 61.6 1.0
CG C:GLU241 4.3 56.7 1.0
CG C:GLU238 4.4 60.8 1.0
CB C:GLU241 4.4 44.8 1.0
OD2 C:ASP317 4.5 72.1 1.0
O C:GLU238 4.6 62.0 1.0
CB C:GLU238 4.6 57.7 1.0
CA C:GLU238 4.7 55.9 1.0
CG C:ASP317 4.8 77.7 1.0
O C:HOH704 4.9 56.6 1.0

Magnesium binding site 4 out of 4 in 4oog

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Magnesium binding site 4 out of 4 in the Crystal Structure of Yeast Rnase III (RNT1P) Complexed with the Product of Dsrna Processing


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 Yeast Rnase III (RNT1P) Complexed with the Product of Dsrna Processing within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:75.7
occ:1.00
 O D:HOH227 2.0 61.0 1.0
O D:HOH226 2.0 47.2 1.0
O6 D:G27 2.0 53.5 1.0
O D:HOH228 2.0 61.9 1.0
O D:HOH229 2.0 51.7 1.0
C6 D:G27 2.9 55.5 1.0
C5 D:G27 3.5 52.6 1.0
N7 D:G27 3.6 50.8 1.0
O4 D:U26 4.0 61.9 1.0
N1 D:G27 4.0 57.8 1.0
N7 D:G28 4.1 53.9 1.0
N4 D:C6 4.1 57.5 1.0
O6 D:G28 4.3 53.0 1.0
C4 D:U26 4.7 55.2 1.0
O4 D:U5 4.8 53.5 1.0
C8 D:G27 4.8 63.9 1.0
C4 D:G27 4.8 53.0 1.0
C5 D:G28 4.9 61.2 1.0
C6 D:G28 4.9 59.7 1.0

Reference:

Y.H.Liang, M.Lavoie, M.A.Comeau, S.Abou Elela, X.Ji. Structure of A Eukaryotic Rnase III Postcleavage Complex Reveals A Double-Ruler Mechanism For Substrate Selection. Mol.Cell V. 54 431 2014.
ISSN: ISSN 1097-2765
PubMed: 24703949
DOI: 10.1016/J.MOLCEL.2014.03.006
Page generated: Tue Aug 20 00:56:19 2024

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