Sodium in PDB 1j70: Crystal Structure of Yeast Atp Sulfurylase

All present enzymatic activity of Crystal Structure of Yeast Atp Sulfurylase:
2.7.7.4;

The structure of Crystal Structure of Yeast Atp Sulfurylase, PDB code: 1j70 was solved by D.J.Lalor, T.Schnyder, V.Saridakis, D.E.Pilloff, A.Dong, H.Tang, T.S.Leyh, E.F.Pai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.84 / 2.30
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	230.850, 230.850, 69.710, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 26.7

The binding sites of Sodium atom in the Crystal Structure of Yeast Atp Sulfurylase (pdb code 1j70). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Yeast Atp Sulfurylase, PDB code: 1j70:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Yeast Atp Sulfurylase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Yeast Atp Sulfurylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1765 b:40.8 occ:1.00 OH A:TYR144 2.7 36.5 1.0 N A:ARG40 3.3 35.6 1.0 CE1 A:TYR144 3.5 40.4 1.0 CD A:PRO39 3.6 39.6 1.0 CZ A:TYR144 3.6 39.3 1.0 CB A:PRO39 3.7 39.0 1.0 N A:PRO39 3.8 37.0 1.0 CB A:ARG40 3.8 31.5 1.0 OG1 A:THR38 3.9 34.4 1.0 CB A:THR38 4.0 35.0 1.0 CG A:PRO39 4.1 39.0 1.0 CA A:PRO39 4.1 36.0 1.0 CA A:ARG40 4.2 36.8 1.0 C A:PRO39 4.2 34.5 1.0 C A:THR38 4.4 41.2 1.0 CG1 A:VAL148 4.5 33.5 1.0 CA A:THR38 4.8 39.7 1.0 CD1 A:TYR144 4.9 38.7 1.0 CE2 A:TYR144 4.9 38.0 1.0 CD1 A:LEU227 5.0 40.7 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Yeast Atp Sulfurylase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Yeast Atp Sulfurylase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1759 b:40.8 occ:1.00 OH C:TYR144 2.9 23.7 1.0 N C:ARG40 3.2 19.2 1.0 CG2 C:THR38 3.4 12.8 1.0 CB C:ARG40 3.5 23.6 1.0 CD C:PRO39 3.5 24.2 1.0 CB C:PRO39 3.6 21.5 1.0 CE1 C:TYR144 3.7 24.5 1.0 CZ C:TYR144 3.7 24.8 1.0 N C:PRO39 3.8 29.5 1.0 CA C:ARG40 3.9 20.1 1.0 CG C:PRO39 4.0 19.1 1.0 C C:PRO39 4.0 25.9 1.0 CA C:PRO39 4.0 27.2 1.0 CB C:THR38 4.4 20.1 1.0 C C:THR38 4.4 22.1 1.0 OG1 C:THR38 4.5 22.4 1.0 CD1 C:LEU227 4.7 27.0 1.0 CG1 C:VAL148 4.7 18.5 1.0 CG C:ARG40 4.8 20.9 1.0 CA C:THR38 4.9 21.6 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Yeast Atp Sulfurylase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Yeast Atp Sulfurylase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1763 b:40.8 occ:1.00 N C:HIS433 3.3 29.2 1.0 N C:ASN434 3.4 36.0 1.0 CE1 C:HIS433 3.5 33.8 1.0 ND1 C:HIS433 3.6 36.1 1.0 NE2 C:HIS433 3.7 33.4 1.0 ND2 C:ASN457 3.7 23.3 1.0 CA C:GLU432 3.7 33.5 1.0 CB C:ASN457 3.8 22.7 1.0 CG C:HIS433 3.9 33.4 1.0 CD2 C:HIS433 3.9 32.8 1.0 C C:GLU432 3.9 33.5 1.0 O C:HOH2536 4.0 40.0 1.0 CA C:ASN434 4.1 36.9 1.0 CB C:GLU432 4.2 38.5 1.0 CA C:HIS433 4.3 30.2 1.0 C C:HIS433 4.3 31.6 1.0 N C:ASN457 4.3 26.2 1.0 CG C:ASN457 4.3 26.2 1.0 CG C:GLU432 4.4 46.4 1.0 O C:ASN457 4.5 28.1 1.0 OD1 C:ASN434 4.5 41.5 1.0 O C:PHE431 4.5 28.2 1.0 CA C:ASN457 4.6 26.7 1.0 CD C:PRO456 4.6 18.8 1.0 CB C:HIS433 4.7 32.5 1.0 CG C:ASN434 4.8 43.3 1.0 C C:ASN457 4.9 27.4 1.0 N C:GLU432 5.0 30.2 1.0

D.J.Lalor, T.Schnyder, V.Saridakis, D.E.Pilloff, A.Dong, H.Tang, T.S.Leyh, E.F.Pai. Structural and Functional Analysis of A Truncated Form of Saccharomyces Cerevisiae Atp Sulfurylase: C-Terminal Domain Essential For Oligomer Formation But Not For Activity. Protein Eng. V. 16 1071 2003.
ISSN: ISSN 0269-2139
PubMed: 14983089
DOI: 10.1093/PROTEIN/GZG133