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Yttrium in PDB 4wfd: Structure of the RRP6-RRP47-MTR4 Interaction

Enzymatic activity of Structure of the RRP6-RRP47-MTR4 Interaction

All present enzymatic activity of Structure of the RRP6-RRP47-MTR4 Interaction:
3.6.4.13;

Protein crystallography data

The structure of Structure of the RRP6-RRP47-MTR4 Interaction, PDB code: 4wfd was solved by B.Schuch, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.42 / 2.40
Space group P 3 1 2
Cell size a, b, c (Å), α, β, γ (°) 142.745, 142.745, 63.450, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 24.3

Yttrium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Yttrium atom in the Structure of the RRP6-RRP47-MTR4 Interaction (pdb code 4wfd). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 22 binding sites of Yttrium where determined in the Structure of the RRP6-RRP47-MTR4 Interaction, PDB code: 4wfd:
Jump to Yttrium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Yttrium binding site 1 out of 22 in 4wfd

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Yttrium binding site 1 out of 22 in the Structure of the RRP6-RRP47-MTR4 Interaction


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Structure of the RRP6-RRP47-MTR4 Interaction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y201

b:69.5
occ:1.00
O A:LEU58 2.2 47.5 1.0
OD2 A:ASP61 2.4 67.2 1.0
CB A:ASP61 2.5 58.7 1.0
CG A:ASP61 2.7 72.3 1.0
C A:LEU58 3.4 46.9 1.0
O A:HOH314 3.6 62.2 1.0
CA A:ASP61 3.7 54.4 1.0
OD1 A:ASP61 3.9 79.3 1.0
N A:ASP61 4.0 48.2 1.0
CA A:LEU58 4.1 47.2 1.0
N A:SER59 4.4 46.2 1.0
C A:SER59 4.6 54.9 1.0
C A:ILE60 4.6 56.0 1.0
CA A:SER59 4.7 46.0 1.0
O A:SER59 4.7 63.3 1.0
CB A:LEU58 4.8 47.2 1.0
N A:ILE60 4.9 58.1 1.0
C A:ASP61 5.0 68.9 1.0

Yttrium binding site 2 out of 22 in 4wfd

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Yttrium binding site 2 out of 22 in the Structure of the RRP6-RRP47-MTR4 Interaction


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Structure of the RRP6-RRP47-MTR4 Interaction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y202

b:0.7
occ:1.00
OD2 A:ASP97 2.5 60.2 1.0
O A:HOH324 3.0 67.9 1.0
OD1 A:ASP97 3.1 72.8 1.0
CG A:ASP97 3.1 67.6 1.0
OD1 A:ASP93 3.1 86.7 1.0
O A:HOH313 3.2 57.0 1.0
OD2 A:ASP93 3.2 79.3 1.0
CG A:ASP93 3.6 77.5 1.0
O A:HOH303 4.1 62.1 1.0
CB A:ASP97 4.5 60.6 1.0
O A:HOH306 4.8 63.4 1.0

Yttrium binding site 3 out of 22 in 4wfd

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Yttrium binding site 3 out of 22 in the Structure of the RRP6-RRP47-MTR4 Interaction


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of Structure of the RRP6-RRP47-MTR4 Interaction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y203

b:0.9
occ:1.00
Y A:YT3204 3.4 78.0 1.0
CG A:ASP76 3.5 68.3 1.0
OD2 A:ASP76 3.6 69.8 1.0
CB A:ASP76 3.6 76.7 1.0
Y A:YT3206 3.6 98.3 0.3
OD1 A:ASP76 3.9 69.1 1.0
OD1 A:ASP73 4.7 0.1 1.0
CA A:ASP76 4.9 81.3 1.0

Yttrium binding site 4 out of 22 in 4wfd

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Yttrium binding site 4 out of 22 in the Structure of the RRP6-RRP47-MTR4 Interaction


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 4 of Structure of the RRP6-RRP47-MTR4 Interaction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y204

b:78.0
occ:1.00
Y A:YT3203 3.4 0.9 1.0
Y A:YT3205 3.6 90.5 1.0
OD1 A:ASP73 4.5 0.1 1.0

Yttrium binding site 5 out of 22 in 4wfd

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Yttrium binding site 5 out of 22 in the Structure of the RRP6-RRP47-MTR4 Interaction


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 5 of Structure of the RRP6-RRP47-MTR4 Interaction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y205

b:90.5
occ:1.00
OD1 A:ASP73 3.1 0.1 1.0
OD2 A:ASP73 3.4 73.8 1.0
CG A:ASP73 3.6 88.8 1.0
Y A:YT3204 3.6 78.0 1.0

Yttrium binding site 6 out of 22 in 4wfd

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Yttrium binding site 6 out of 22 in the Structure of the RRP6-RRP47-MTR4 Interaction


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 6 of Structure of the RRP6-RRP47-MTR4 Interaction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y206

b:98.3
occ:0.33
OD2 A:ASP76 2.2 69.8 1.0
OD1 A:ASP76 2.4 69.1 1.0
CG A:ASP76 2.5 68.3 1.0
Y A:YT3203 3.6 0.9 1.0
CB A:ASP76 3.9 76.7 1.0
OD1 A:ASP73 4.8 0.1 1.0
CA A:ASP76 5.0 81.3 1.0

Yttrium binding site 7 out of 22 in 4wfd

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Yttrium binding site 7 out of 22 in the Structure of the RRP6-RRP47-MTR4 Interaction


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 7 of Structure of the RRP6-RRP47-MTR4 Interaction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y207

b:56.7
occ:1.00
O B:HOH301 2.0 52.2 1.0
OE2 B:GLU26 2.1 53.4 1.0
OE1 A:GLU55 2.3 74.9 1.0
OE1 B:GLU26 2.3 53.3 1.0
CD B:GLU26 2.5 52.8 1.0
CD A:GLU55 3.0 66.8 1.0
OE2 A:GLU55 3.6 64.4 1.0
CG A:GLU55 3.8 60.2 1.0
CG B:GLU26 4.0 55.6 1.0
O B:HOH302 4.5 52.2 1.0
OG1 B:THR29 4.5 47.2 1.0
NZ B:LYS22 4.7 58.9 1.0
CB A:GLU55 4.8 61.0 1.0
CB B:GLU26 4.9 50.0 1.0
CE B:LYS22 5.0 61.8 1.0

Yttrium binding site 8 out of 22 in 4wfd

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Yttrium binding site 8 out of 22 in the Structure of the RRP6-RRP47-MTR4 Interaction


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 8 of Structure of the RRP6-RRP47-MTR4 Interaction within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Y101

b:78.8
occ:1.00
OD1 C:ASP8 2.2 0.6 1.0
CG C:ASP8 3.3 0.4 1.0
OD2 C:ASP5 3.4 98.4 1.0
OE1 C:GLU11 3.6 91.6 1.0
OD2 C:ASP8 4.0 0.4 1.0
CG C:ASP5 4.3 0.9 1.0
CB C:ASP5 4.3 0.5 1.0
CD C:GLU11 4.3 95.2 1.0
CB C:ASP8 4.4 94.5 1.0
OE2 C:GLU11 4.4 0.2 1.0
CA C:ASP8 4.4 77.3 1.0
N C:ASP8 4.6 72.0 1.0

Yttrium binding site 9 out of 22 in 4wfd

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Yttrium binding site 9 out of 22 in the Structure of the RRP6-RRP47-MTR4 Interaction


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 9 of Structure of the RRP6-RRP47-MTR4 Interaction within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Y201

b:52.2
occ:1.00
OD1 D:ASP61 2.0 77.2 1.0
O D:LEU58 2.5 77.7 1.0
CG D:ASP61 2.7 75.2 1.0
OD2 D:ASP61 3.0 85.0 1.0
OE1 D:GLU62 3.1 73.9 1.0
N D:GLU62 3.2 75.6 1.0
C D:LEU58 3.6 46.6 1.0
CA D:GLU62 3.6 86.3 1.0
C D:ASP61 3.7 90.9 1.0
CB D:GLU62 3.7 89.2 1.0
CB D:ASP61 3.9 75.4 1.0
CD D:GLU62 4.1 87.7 1.0
CA D:ASP61 4.1 75.1 1.0
N D:ASP61 4.1 73.9 1.0
CA D:LEU58 4.1 39.3 1.0
O D:ASP61 4.4 0.5 1.0
CG D:GLU62 4.5 75.1 1.0
N D:SER59 4.7 40.1 1.0
C D:SER59 4.7 40.7 1.0
C D:ILE60 4.7 39.8 1.0
O D:SER59 4.7 47.2 1.0
CB D:LEU58 4.8 39.6 1.0
O D:ILE57 4.9 62.7 1.0
CA D:SER59 5.0 40.8 1.0

Yttrium binding site 10 out of 22 in 4wfd

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Yttrium binding site 10 out of 22 in the Structure of the RRP6-RRP47-MTR4 Interaction


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 10 of Structure of the RRP6-RRP47-MTR4 Interaction within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Y202

b:69.5
occ:1.00
OD2 D:ASP97 2.7 76.0 1.0
OD2 D:ASP93 2.9 84.1 1.0
OD1 D:ASP93 3.0 87.9 1.0
OD1 D:ASP97 3.0 88.8 1.0
CG D:ASP97 3.2 77.2 1.0
CG D:ASP93 3.3 83.3 1.0
O D:HOH305 4.5 52.2 1.0
O D:HOH312 4.6 52.2 1.0
O D:HOH313 4.6 52.2 1.0
CB D:ASP97 4.7 70.2 1.0
CB D:ASP93 4.8 63.8 1.0
O D:ASP93 4.9 64.1 1.0

Reference:

B.Schuch, M.Feigenbutz, D.L.Makino, S.Falk, C.Basquin, P.Mitchell, E.Conti. The Exosome-Binding Factors RRP6 and RRP47 Form A Composite Surface For Recruiting the MTR4 Helicase. Embo J. 2014.
ISSN: ESSN 1460-2075
PubMed: 25319414
DOI: 10.15252/EMBJ.201488757
Page generated: Wed Dec 16 02:41:15 2020

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