Yttrium in PDB 1fs7: Cytochrome C Nitrite Reductase From Wolinella Succinogenes

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes, PDB code: 1fs7 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 (°)	119.822, 119.822, 186.025, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.7

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes 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 (pdb code 1fs7). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 3 binding sites of Yttrium where determined in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes, PDB code: 1fs7:
Jump to Yttrium binding site number: 1; 2; 3;

Yttrium binding site 1 out of 3 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Y652 b:21.8 occ:1.00 OE1 A:GLU52 2.2 16.5 1.0 O A:HOH947 2.4 22.4 1.0 O A:HOH951 2.4 21.0 1.0 O A:HOH814 2.4 23.7 1.0 O A:HOH948 2.4 27.3 1.0 O A:HOH946 2.5 20.8 1.0 CD A:GLU52 3.4 19.4 1.0 OE2 A:GLU52 3.8 21.3 1.0 O A:ACT655 4.0 32.7 1.0 O A:HOH988 4.4 30.2 1.0 O A:HOH987 4.4 33.8 1.0 CD A:ARG55 4.4 25.1 1.0 OXT A:ACT655 4.5 25.7 1.0 O A:GLU45 4.6 20.0 1.0 O A:GLU52 4.6 22.2 1.0 CG A:GLU52 4.6 20.0 1.0 NH1 A:ARG55 4.7 30.1 1.0 C A:ACT655 4.7 31.8 1.0 CB A:GLU52 4.7 19.5 1.0 CA A:GLU52 4.8 20.7 1.0 O A:HOH677 4.9 23.0 1.0

Yttrium binding site 2 out of 3 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Y653 b:25.5 occ:1.00 O1A A:HEM511 2.3 26.7 1.0 O1A A:HEM510 2.3 21.6 1.0 O A:HOH875 2.3 26.4 1.0 O A:PRO99 2.3 18.1 1.0 O A:HOH821 2.4 27.9 1.0 O A:HOH954 2.5 26.5 1.0 OXT A:ACT656 2.5 34.9 1.0 O A:ACT656 2.5 38.0 1.0 C A:ACT656 2.9 38.4 1.0 CGA A:HEM510 3.4 20.8 1.0 C A:PRO99 3.5 19.1 1.0 CGA A:HEM511 3.5 27.8 1.0 O2A A:HEM510 4.0 24.2 1.0 CA A:ARG100 4.1 17.9 1.0 O2A A:HEM511 4.1 25.8 1.0 N A:ARG100 4.2 18.6 1.0 O A:HOH1207 4.3 33.5 1.0 CH3 A:ACT656 4.4 36.4 1.0 O A:HOH1154 4.4 42.6 1.0 CA A:PRO99 4.5 18.1 1.0 CBA A:HEM511 4.6 20.9 1.0 N A:PRO99 4.6 17.2 1.0 O A:HOH953 4.6 30.7 1.0 CBA A:HEM510 4.6 21.5 1.0 CAA A:HEM510 4.7 17.8 1.0 CB A:PRO99 4.7 20.2 1.0 CD A:PRO99 4.8 18.7 1.0 O A:HOH688 4.8 44.9 1.0 CB A:ARG100 4.9 18.7 1.0

Yttrium binding site 3 out of 3 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Y654 b:38.7 occ:0.50 OE2 A:GLU408 2.4 24.8 1.0 O A:ACT657 2.6 38.2 1.0 O1A A:HEM512 2.6 44.9 1.0 OXT A:ACT657 2.9 39.9 1.0 C A:ACT657 3.1 38.0 1.0 CGA A:HEM512 3.4 40.2 1.0 CD A:GLU408 3.6 23.1 1.0 O2A A:HEM512 3.9 38.2 1.0 CG A:GLU408 4.1 18.1 1.0 NZ A:LYS344 4.2 23.0 1.0 CBA A:HEM512 4.2 29.6 1.0 CH3 A:ACT657 4.6 34.2 1.0 OE1 A:GLU408 4.6 25.9 1.0 CB A:PRO407 4.8 19.4 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