Manganese in PDB 1d8h: X-Ray Crystal Structure of Yeast Rna Triphosphatase in Complex with Sulfate and Manganese Ions.

All present enzymatic activity of X-Ray Crystal Structure of Yeast Rna Triphosphatase in Complex with Sulfate and Manganese Ions.:
3.1.3.33;

The structure of X-Ray Crystal Structure of Yeast Rna Triphosphatase in Complex with Sulfate and Manganese Ions., PDB code: 1d8h was solved by C.D.Lima, L.K.Wang, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.436, 118.723, 85.138, 90.00, 108.06, 90.00
R / Rfree (%)	22.9 / 31

The binding sites of Manganese atom in the X-Ray Crystal Structure of Yeast Rna Triphosphatase in Complex with Sulfate and Manganese Ions. (pdb code 1d8h). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the X-Ray Crystal Structure of Yeast Rna Triphosphatase in Complex with Sulfate and Manganese Ions., PDB code: 1d8h:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the X-Ray Crystal Structure of Yeast Rna Triphosphatase in Complex with Sulfate and Manganese Ions.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Crystal Structure of Yeast Rna Triphosphatase in Complex with Sulfate and Manganese Ions. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn550 b:51.8 occ:1.00 O A:HOH620 2.1 28.4 1.0 OE2 A:GLU496 2.5 35.3 1.0 OE2 A:GLU307 2.6 37.1 1.0 OE2 A:GLU305 2.8 33.3 1.0 O A:HOH767 2.9 39.4 1.0 O4 A:SO4601 3.0 38.3 1.0 CD A:GLU305 3.5 29.1 1.0 O A:HOH629 3.6 35.5 1.0 CD A:GLU307 3.6 37.9 1.0 CD A:GLU496 3.6 38.1 1.0 CG A:GLU305 3.9 30.4 1.0 CG A:GLU496 4.1 36.0 1.0 S A:SO4601 4.1 46.7 1.0 OE1 A:GLU307 4.2 40.2 1.0 OE1 A:GLU305 4.2 33.5 1.0 OD1 A:ASP471 4.5 41.5 1.0 NZ A:LYS409 4.6 42.2 1.0 O1 A:SO4601 4.6 40.3 1.0 OE1 A:GLU496 4.7 44.0 1.0 OE2 A:GLU494 4.8 45.0 1.0 O A:HOH705 4.8 42.9 1.0 CB A:GLU307 4.8 14.1 1.0 CG A:GLU307 4.8 29.9 1.0 O3 A:SO4601 4.9 51.5 1.0 OE1 A:GLU433 4.9 46.6 1.0 CD A:GLU494 5.0 44.3 1.0

Manganese binding site 2 out of 3 in the X-Ray Crystal Structure of Yeast Rna Triphosphatase in Complex with Sulfate and Manganese Ions.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Crystal Structure of Yeast Rna Triphosphatase in Complex with Sulfate and Manganese Ions. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn550 b:39.5 occ:1.00 O B:HOH618 2.0 22.5 1.0 OE2 B:GLU307 2.3 26.2 1.0 OE2 B:GLU496 2.3 35.0 1.0 OE2 B:GLU305 2.7 37.9 1.0 O B:HOH641 2.9 26.4 1.0 O B:HOH713 3.1 33.3 1.0 CD B:GLU496 3.2 36.0 1.0 CD B:GLU305 3.3 39.3 1.0 CD B:GLU307 3.5 34.0 1.0 CG B:GLU496 3.6 35.5 1.0 CG B:GLU305 3.9 38.8 1.0 OE1 B:GLU305 4.0 39.3 1.0 O B:HOH652 4.1 37.8 1.0 OE1 B:GLU307 4.1 37.1 1.0 OD1 B:ASP471 4.2 47.4 1.0 OE1 B:GLU496 4.2 40.5 1.0 O1 B:SO4602 4.5 31.9 1.0 O4 B:SO4602 4.5 45.2 1.0 CG B:GLU307 4.6 28.4 1.0 NZ B:LYS409 4.7 47.2 1.0 CB B:GLU307 4.8 25.1 1.0 OE1 B:GLU494 4.8 47.9 1.0 CD B:GLU494 4.8 41.5 1.0 OE2 B:GLU494 4.8 40.5 1.0 S B:SO4602 4.8 38.3 1.0 O2 B:SO4602 4.9 44.3 1.0

Manganese binding site 3 out of 3 in the X-Ray Crystal Structure of Yeast Rna Triphosphatase in Complex with Sulfate and Manganese Ions.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Crystal Structure of Yeast Rna Triphosphatase in Complex with Sulfate and Manganese Ions. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn550 b:53.1 occ:1.00 O C:HOH614 2.3 40.1 1.0 OE2 C:GLU496 2.5 38.9 1.0 OE2 C:GLU307 2.5 40.2 1.0 O C:HOH763 2.6 49.0 1.0 OE2 C:GLU305 2.8 34.8 1.0 O3 C:SO4603 3.1 54.4 1.0 CD C:GLU307 3.3 40.2 1.0 CD C:GLU496 3.3 41.3 1.0 CD C:GLU305 3.3 34.7 1.0 OE1 C:GLU307 3.4 43.5 1.0 O C:HOH630 3.6 37.2 1.0 CG C:GLU496 3.6 37.1 1.0 CG C:GLU305 3.9 33.7 1.0 O C:HOH778 4.0 47.5 1.0 OD1 C:ASP471 4.1 45.8 1.0 OE1 C:GLU305 4.1 39.0 1.0 OE2 C:GLU494 4.2 40.3 1.0 S C:SO4603 4.4 54.1 1.0 O2 C:SO4603 4.5 56.6 1.0 OE1 C:GLU496 4.5 44.9 1.0 CD C:GLU494 4.5 40.1 1.0 NZ C:LYS409 4.6 42.4 1.0 CG C:GLU307 4.7 33.8 1.0 OE1 C:GLU494 4.8 44.4 1.0 CB C:GLU307 4.9 25.9 1.0

C.D.Lima, L.K.Wang, S.Shuman. Structure and Mechanism of Yeast Rna Triphosphatase: An Essential Component of the Mrna Capping Apparatus. Cell(Cambridge,Mass.) V. 99 533 1999.
ISSN: ISSN 0092-8674
PubMed: 10589681
DOI: 10.1016/S0092-8674(00)81541-X