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Yttrium in PDB 4yhu: Yeast PRP3 C-Terminal Fragment 296-469

Protein crystallography data

The structure of Yeast PRP3 C-Terminal Fragment 296-469, PDB code: 4yhu was solved by S.Liu, M.C.Wahl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 87.663, 161.205, 105.214, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 26.2

Yttrium Binding Sites:

The binding sites of Yttrium atom in the Yeast PRP3 C-Terminal Fragment 296-469 (pdb code 4yhu). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 4 binding sites of Yttrium where determined in the Yeast PRP3 C-Terminal Fragment 296-469, PDB code: 4yhu:
Jump to Yttrium binding site number: 1; 2; 3; 4;

Yttrium binding site 1 out of 4 in 4yhu

Go back to Yttrium Binding Sites List in 4yhu
Yttrium binding site 1 out of 4 in the Yeast PRP3 C-Terminal Fragment 296-469


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Yeast PRP3 C-Terminal Fragment 296-469 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y501

b:61.9
occ:1.00
O A:HOH603 2.2 19.5 1.0
OD1 A:ASP405 2.3 61.0 1.0
OD2 A:ASP418 2.5 61.2 1.0
OD1 A:ASP418 2.5 65.7 1.0
O A:HOH606 2.5 40.3 1.0
OD2 A:ASP405 2.5 56.5 1.0
CG A:ASP418 2.7 62.8 1.0
CG A:ASP405 2.8 59.1 1.0
CB A:ASP418 4.2 60.7 1.0
CB A:ASP405 4.3 58.7 1.0
CA A:ASP418 4.6 58.4 1.0
N A:MET419 4.6 56.1 1.0
N A:HIS420 4.6 58.0 1.0
CB A:HIS420 4.7 63.4 1.0
O A:ASN403 4.7 55.9 1.0
C A:ASP418 4.9 56.7 1.0
N A:ASP405 5.0 56.9 1.0
CA A:HIS420 5.0 60.2 1.0

Yttrium binding site 2 out of 4 in 4yhu

Go back to Yttrium Binding Sites List in 4yhu
Yttrium binding site 2 out of 4 in the Yeast PRP3 C-Terminal Fragment 296-469


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Yeast PRP3 C-Terminal Fragment 296-469 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y502

b:0.7
occ:1.00
OE1 A:GLU386 2.5 77.6 1.0
OE2 A:GLU386 3.0 78.8 1.0
CD A:GLU386 3.1 74.7 1.0
O A:HOH620 4.1 31.4 1.0
O A:HOH625 4.5 63.3 1.0
CG A:GLU386 4.6 66.8 1.0
CE2 B:PHE354 4.8 66.4 1.0
CE B:MET358 5.0 73.0 1.0

Yttrium binding site 3 out of 4 in 4yhu

Go back to Yttrium Binding Sites List in 4yhu
Yttrium binding site 3 out of 4 in the Yeast PRP3 C-Terminal Fragment 296-469


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of Yeast PRP3 C-Terminal Fragment 296-469 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y501

b:0.8
occ:1.00
OD1 B:ASP405 2.4 91.4 1.0
OD2 B:ASP405 3.1 83.7 1.0
CG B:ASP405 3.1 85.4 1.0
OD1 B:ASP418 3.1 0.6 1.0
O B:HOH616 3.4 77.7 1.0
O B:HOH629 4.0 28.8 1.0
CG B:ASP418 4.4 0.2 1.0
CB B:ASP405 4.6 82.6 1.0
N B:MET419 4.8 84.0 1.0
O B:ASN403 4.8 72.4 0.5
O B:ASN403 4.8 72.4 0.5
N B:HIS420 4.9 89.6 1.0

Yttrium binding site 4 out of 4 in 4yhu

Go back to Yttrium Binding Sites List in 4yhu
Yttrium binding site 4 out of 4 in the Yeast PRP3 C-Terminal Fragment 296-469


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 4 of Yeast PRP3 C-Terminal Fragment 296-469 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Y501

b:0.4
occ:1.00
OD2 C:ASP405 2.5 0.7 1.0
CG C:ASP405 3.5 0.4 1.0
CB C:ASP405 3.9 0.8 1.0
N C:ASP405 4.2 0.7 1.0
O C:ASN403 4.4 0.7 1.0
ND2 C:ASN403 4.4 0.4 1.0
OD1 C:ASP405 4.5 0.9 1.0
C C:GLU404 4.5 0.9 1.0
CA C:ASP405 4.6 0.5 1.0
CA C:GLU404 4.7 0.3 1.0
C C:ASN403 5.0 0.9 1.0

Reference:

S.Liu, S.Mozaffari-Jovin, J.Wollenhaupt, K.F.Santos, M.Theuser, S.Dunin-Horkawicz, P.Fabrizio, J.M.Bujnicki, R.Luhrmann, M.C.Wahl. A Composite Double-/Single-Stranded Rna-Binding Region in Protein PRP3 Supports Tri-Snrnp Stability and Splicing. Elife V. 4 07320 2015.
ISSN: ESSN 2050-084X
PubMed: 26161500
DOI: 10.7554/ELIFE.07320
Page generated: Mon Jan 25 16:07:20 2021

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