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Yttrium in PDB 3sag: Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site

Protein crystallography data

The structure of Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site, PDB code: 3sag was solved by K.Januszyk, Q.Liu, C.D.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.70 / 2.70
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 138.800, 138.800, 60.300, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 26.2

Other elements in 3sag:

The structure of Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Yttrium Binding Sites:

The binding sites of Yttrium atom in the Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site (pdb code 3sag). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 3 binding sites of Yttrium where determined in the Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site, PDB code: 3sag:
Jump to Yttrium binding site number: 1; 2; 3;

Yttrium binding site 1 out of 3 in 3sag

Go back to Yttrium Binding Sites List in 3sag
Yttrium binding site 1 out of 3 in the Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y1

b:63.9
occ:1.00
OE2 A:GLU489 2.2 75.7 1.0
OE1 A:GLU489 2.4 75.8 1.0
OD2 A:ASP488 2.5 72.5 1.0
CD A:GLU489 2.6 75.4 1.0
O A:HOH116 2.7 51.6 1.0
O A:HOH104 2.8 39.6 1.0
O A:HOH73 2.9 40.6 1.0
CG A:ASP488 3.3 70.8 1.0
OD1 A:ASP488 3.3 69.2 1.0
CG A:GLU489 4.1 73.5 1.0
O A:HOH178 4.2 58.3 1.0
N A:GLU489 4.6 72.1 1.0
CB A:ASP488 4.8 70.7 1.0
O A:HOH611 4.9 57.0 1.0

Yttrium binding site 2 out of 3 in 3sag

Go back to Yttrium Binding Sites List in 3sag
Yttrium binding site 2 out of 3 in the Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y3

b:71.8
occ:1.00
OD1 A:ASP440 2.3 70.6 1.0
O A:HOH28 2.6 58.4 1.0
O A:HOH632 2.9 58.7 1.0
O A:HOH630 2.9 81.2 1.0
OD1 A:ASP404 2.9 87.0 1.0
CG A:ASP440 3.0 68.4 1.0
OD2 A:ASP440 3.1 70.9 1.0
CG A:ASP404 3.7 87.3 1.0
OD2 A:ASP404 3.8 89.8 1.0
O A:HOH631 4.0 64.0 1.0
CB A:ASP440 4.5 64.8 1.0
CE1 A:TYR436 4.7 58.3 1.0
O A:TYR436 4.7 50.9 1.0
O A:ASN416 4.7 79.0 1.0
CB A:SER415 4.7 80.3 1.0
CZ A:TYR436 4.8 58.6 1.0
CD1 A:LEU407 4.9 63.8 1.0
O A:HOH80 4.9 53.9 1.0
OH A:TYR436 4.9 58.9 1.0
CB A:ASP404 4.9 84.8 1.0
NE2 A:GLN420 5.0 77.5 1.0
OG A:SER415 5.0 81.1 1.0
CA A:ASP440 5.0 61.9 1.0

Yttrium binding site 3 out of 3 in 3sag

Go back to Yttrium Binding Sites List in 3sag
Yttrium binding site 3 out of 3 in the Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y2

b:65.6
occ:1.00
OE2 B:GLU489 1.6 63.8 1.0
O B:HOH128 1.7 20.8 1.0
CD B:GLU489 2.6 63.6 1.0
OD1 B:ASP488 2.7 64.2 1.0
OE1 B:GLU489 2.9 63.8 1.0
O B:HOH43 2.9 38.4 1.0
CG B:ASP488 3.5 62.8 1.0
OD2 B:ASP488 3.6 60.6 1.0
CG B:GLU489 4.0 64.6 1.0
O B:HOH610 4.6 39.8 1.0
OE1 B:GLN511 4.6 59.7 1.0
O B:HOH76 4.8 53.5 1.0
N B:GLU489 4.9 67.4 1.0
CB B:ASP488 4.9 64.5 1.0

Reference:

K.Januszyk, Q.Liu, C.D.Lima. Activities of Human RRP6 and Structure of the Human RRP6 Catalytic Domain. Rna V. 17 1566 2011.
ISSN: ISSN 1355-8382
PubMed: 21705430
DOI: 10.1261/RNA.2763111
Page generated: Mon Jan 25 16:07:20 2021

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