Yttrium in PDB 3bng: W. Succinogenes Nrfa Y218F

All present enzymatic activity of W. Succinogenes Nrfa Y218F:
1.7.2.2;

The structure of W. Succinogenes Nrfa Y218F, PDB code: 3bng was solved by P.Lukat, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.45 / 1.50
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	120.030, 120.030, 186.276, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 21.5

The structure of W. Succinogenes Nrfa Y218F also contains other interesting chemical elements:

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

The binding sites of Yttrium atom in the W. Succinogenes Nrfa Y218F (pdb code 3bng). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 4 binding sites of Yttrium where determined in the W. Succinogenes Nrfa Y218F, PDB code: 3bng:
Jump to Yttrium binding site number: 1; 2; 3; 4;

Yttrium binding site 1 out of 4 in the W. Succinogenes Nrfa Y218F


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of W. Succinogenes Nrfa Y218F within 5.0Å range: probe atom residue distance (Å) B Occ A:Y509 b:22.5 occ:1.00 OE1 A:GLU52 2.3 19.3 1.0 O A:HOH793 2.3 19.3 1.0 O A:HOH670 2.3 20.6 1.0 O A:HOH792 2.4 24.4 1.0 O A:HOH794 2.4 23.8 1.0 O A:HOH797 2.4 21.6 1.0 CD A:GLU52 3.4 20.3 1.0 OE2 A:GLU52 3.9 20.8 1.0 O A:ACT3 4.0 33.4 1.0 CD A:ARG55 4.4 25.7 1.0 O A:HOH826 4.4 31.5 1.0 O A:HOH825 4.5 38.1 1.0 O A:GLU52 4.6 20.4 1.0 OXT A:ACT3 4.6 31.6 1.0 O A:GLU45 4.6 21.8 1.0 CG A:GLU52 4.7 19.5 1.0 NH1 A:ARG55 4.7 26.1 1.0 C A:ACT3 4.8 33.3 1.0 CB A:GLU52 4.8 18.1 1.0 CA A:GLU52 4.9 18.8 1.0 O A:HOH536 4.9 22.2 1.0

Yttrium binding site 2 out of 4 in the W. Succinogenes Nrfa Y218F


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of W. Succinogenes Nrfa Y218F within 5.0Å range: probe atom residue distance (Å) B Occ A:Y510 b:20.6 occ:0.50 O A:HOH1078 2.0 26.0 1.0 O A:HOH677 2.2 22.9 0.5 O A:HOH726 2.3 32.1 1.0 O1A A:HEM515 2.3 23.7 1.0 O1A A:HEM516 2.3 28.0 1.0 O A:PRO99 2.4 18.6 1.0 O A:HOH800 2.7 33.9 1.0 CGA A:HEM516 3.5 26.0 1.0 CGA A:HEM515 3.5 21.7 1.0 C A:PRO99 3.6 16.9 1.0 O2A A:HEM516 4.1 28.1 1.0 O2A A:HEM515 4.1 26.3 1.0 CA A:ARG100 4.2 17.4 1.0 N A:ARG100 4.4 17.4 1.0 O A:HOH949 4.4 44.0 1.0 O A:HOH983 4.4 50.1 1.0 CA A:PRO99 4.6 17.2 1.0 CBA A:HEM516 4.6 23.4 1.0 O A:HOH799 4.6 35.9 1.0 CAA A:HEM515 4.6 17.2 1.0 N A:PRO99 4.6 17.1 1.0 CBA A:HEM515 4.6 19.1 1.0 CB A:PRO99 4.6 16.9 1.0 O A:ACT5 4.7 57.3 1.0 CD A:PRO99 4.7 16.8 1.0 O A:HOH1149 4.7 38.3 1.0 CH3 A:ACT5 4.9 57.3 1.0 C A:ACT5 4.9 57.4 1.0 CB A:ALA98 5.0 17.9 1.0 CB A:ARG100 5.0 18.6 1.0

Yttrium binding site 3 out of 4 in the W. Succinogenes Nrfa Y218F


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of W. Succinogenes Nrfa Y218F within 5.0Å range: probe atom residue distance (Å) B Occ A:Y511 b:21.4 occ:0.50 O A:HOH1076 2.1 37.1 1.0 OE2 A:GLU334 2.2 31.9 1.0 OD1 A:ASP323 2.3 32.0 1.0 O4 A:SO42 2.5 96.3 1.0 OD2 A:ASP323 2.6 34.6 1.0 CG A:ASP323 2.8 32.4 1.0 CD A:GLU334 3.3 29.6 1.0 O A:HOH1116 3.8 34.5 1.0 S A:SO42 3.9 84.4 1.0 OE1 A:GLU334 4.1 29.4 1.0 CG A:GLU334 4.1 28.8 1.0 CB A:ASP323 4.3 31.1 1.0 O A:HOH1094 4.4 34.8 1.0 O2 A:SO42 4.4 96.2 1.0 O1 A:SO42 4.5 95.9 1.0 CG A:MET327 4.7 28.1 1.0 O3 A:SO42 4.8 96.0 1.0 CA A:ASP323 4.9 31.4 1.0

Yttrium binding site 4 out of 4 in the W. Succinogenes Nrfa Y218F


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 4 of W. Succinogenes Nrfa Y218F within 5.0Å range: probe atom residue distance (Å) B Occ A:Y512 b:35.9 occ:0.50 O1A A:HEM517 2.1 26.1 1.0 OE2 A:GLU408 2.1 19.9 1.0 CGA A:HEM517 3.2 27.9 1.0 CD A:GLU408 3.3 14.5 1.0 O2A A:HEM517 3.9 36.3 1.0 CG A:GLU408 4.0 16.9 1.0 O2 A:SO41 4.1 21.7 0.6 NZ A:LYS344 4.2 21.5 1.0 CBA A:HEM517 4.2 28.2 1.0 O A:HOH727 4.2 29.8 1.0 OE1 A:GLU408 4.3 19.9 1.0 CG A:PRO407 5.0 17.7 1.0

P.Lukat, M.Rudolf, P.Stach, A.Messerschmidt, P.M.H.Kroneck, J.Simon, O.Einsle. Binding and Reduction of Sulfite By Cytochrome C Nitrite Reductase Biochemistry V. 47 2080 2008.
ISSN: ISSN 0006-2960
PubMed: 18201106
DOI: 10.1021/BI7021415