Yttrium in PDB 1fs8: Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate Complex

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate Complex, PDB code: 1fs8 was solved by O.Einsle, P.Stach, A.Messerschmidt, J.Simon, A.Kroeger, R.Huber, P.M.H.Kroneck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.60
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	119.010, 119.010, 186.525, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 20.6

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate Complex also contains other interesting chemical elements:

Iron	(Fe)	5 atoms
Calcium	(Ca)	1 atom

The binding sites of Yttrium atom in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate Complex (pdb code 1fs8). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 4 binding sites of Yttrium where determined in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate Complex, PDB code: 1fs8:
Jump to Yttrium binding site number: 1; 2; 3; 4;

Yttrium binding site 1 out of 4 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate Complex


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Y652 b:19.6 occ:1.00 O A:HOH1022 2.2 18.9 1.0 OE1 A:GLU52 2.3 18.3 1.0 O A:HOH1025 2.3 21.9 1.0 O A:HOH822 2.3 16.8 1.0 O A:HOH1023 2.4 20.9 1.0 O A:HOH1024 2.4 25.5 1.0 CD A:GLU52 3.4 17.4 1.0 OE2 A:GLU52 3.8 18.7 1.0 O A:ACT659 4.1 31.7 1.0 CD A:ARG55 4.4 25.9 1.0 O A:HOH1033 4.5 34.2 1.0 OXT A:ACT659 4.5 26.9 1.0 O A:GLU52 4.6 18.6 1.0 O A:GLU45 4.6 18.1 1.0 NH1 A:ARG55 4.6 29.4 1.0 CG A:GLU52 4.6 16.8 1.0 C A:ACT659 4.7 34.2 1.0 CB A:GLU52 4.8 18.1 1.0 O A:HOH671 4.9 20.9 1.0 CA A:GLU52 4.9 17.9 1.0

Yttrium binding site 2 out of 4 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate Complex


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Y653 b:29.9 occ:1.00 O1A A:HEM510 2.3 21.4 1.0 O1A A:HEM511 2.3 26.1 1.0 O A:PRO99 2.3 16.0 1.0 O A:HOH1047 2.4 31.9 1.0 O A:HOH1048 2.4 33.6 1.0 O A:HOH1046 2.4 36.2 1.0 O A:HOH833 2.4 30.9 1.0 O A:HOH1049 2.5 42.1 1.0 CGA A:HEM511 3.4 26.0 1.0 CGA A:HEM510 3.4 22.7 1.0 C A:PRO99 3.5 16.2 1.0 O2A A:HEM510 4.1 29.1 1.0 CA A:ARG100 4.1 15.3 1.0 O2A A:HEM511 4.1 26.6 1.0 N A:ARG100 4.2 15.8 1.0 O A:HOH1276 4.3 52.4 1.0 O A:HOH1190 4.3 40.4 1.0 O A:HOH1057 4.5 32.0 1.0 O A:HOH1191 4.5 49.1 1.0 CBA A:HEM511 4.5 19.8 1.0 CA A:PRO99 4.5 14.6 1.0 CBA A:HEM510 4.6 15.6 1.0 CAA A:HEM510 4.6 14.8 1.0 O A:HOH1044 4.6 51.2 1.0 N A:PRO99 4.7 15.5 1.0 O A:HOH682 4.7 40.4 1.0 CB A:PRO99 4.8 16.9 1.0 O A:HOH681 4.8 22.4 1.0 CB A:ARG100 4.8 17.2 1.0 CD A:PRO99 4.8 18.0 1.0 O A:HOH1040 4.9 39.1 1.0

Yttrium binding site 3 out of 4 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate Complex


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Y654 b:25.9 occ:0.50 O2A A:HEM512 2.2 18.1 1.0 OE2 A:GLU408 2.3 15.3 1.0 O4 A:SO4658 2.6 44.0 1.0 O1 A:SO4658 3.0 43.3 1.0 CGA A:HEM512 3.3 32.1 1.0 S A:SO4658 3.4 40.9 1.0 CD A:GLU408 3.4 15.6 1.0 O1A A:HEM512 4.0 36.7 1.0 CG A:GLU408 4.1 13.8 1.0 NZ A:LYS344 4.2 19.1 1.0 CBA A:HEM512 4.2 24.2 1.0 O2 A:SO4658 4.4 32.4 1.0 OE1 A:GLU408 4.4 16.9 1.0 O3 A:SO4658 4.5 39.2 1.0 CB A:PRO407 5.0 16.5 1.0

Yttrium binding site 4 out of 4 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate Complex


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 4 of Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Y655 b:33.2 occ:1.00 O A:HOH1290 2.4 34.6 1.0 OE1 A:GLN304 2.4 42.6 1.0 O2 A:SO4657 2.4 41.7 1.0 O A:HOH1289 2.5 38.3 1.0 O A:HOH1229 2.5 37.1 1.0 CD A:GLN304 3.3 45.7 1.0 S A:SO4657 3.8 49.1 1.0 NE2 A:GLN304 3.8 43.0 1.0 O3 A:SO4657 4.2 48.9 1.0 O A:HOH1123 4.4 46.0 1.0 CB A:GLN304 4.5 39.0 1.0 CG A:GLN304 4.5 38.9 1.0 O1 A:SO4657 4.6 43.5 1.0 O4 A:SO4657 4.8 44.6 1.0

O.Einsle, P.Stach, A.Messerschmidt, J.Simon, A.Kroger, R.Huber, P.M.Kroneck. Cytochrome C Nitrite Reductase From Wolinella Succinogenes. Structure at 1.6 A Resolution, Inhibitor Binding, and Heme-Packing Motifs. J.Biol.Chem. V. 275 39608 2000.
ISSN: ISSN 0021-9258
PubMed: 10984487
DOI: 10.1074/JBC.M006188200