Yttrium in PDB 3bnj: W. Succinogenes Nrfa Y218F Sulfite Complex

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

The structure of W. Succinogenes Nrfa Y218F Sulfite Complex, PDB code: 3bnj 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)	40.39 / 1.30
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	119.353, 119.470, 184.789, 89.76, 89.90, 90.22
R / Rfree (%)	18.1 / 20.8

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

Yttrium binding site 1 out of 3 in the W. Succinogenes Nrfa Y218F Sulfite Complex


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 Sulfite Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Y510 b:16.4 occ:0.70 OE1 A:GLU52 2.2 18.5 1.0 O A:HOH787 2.3 23.3 1.0 O A:HOH786 2.3 18.4 1.0 O A:HOH790 2.3 22.1 1.0 O A:HOH785 2.3 22.1 1.0 O A:HOH665 2.3 20.1 1.0 CD A:GLU52 3.4 17.9 1.0 OE2 A:GLU52 3.8 20.8 1.0 O A:ACT512 4.1 26.7 1.0 O A:HOH825 4.3 31.2 1.0 CD A:ARG55 4.4 23.2 1.0 O A:HOH824 4.4 31.3 1.0 O A:GLU45 4.5 20.6 1.0 O A:GLU52 4.5 19.7 1.0 OXT A:ACT512 4.6 24.5 1.0 CG A:GLU52 4.6 17.1 1.0 NH1 A:ARG55 4.7 25.1 1.0 CB A:GLU52 4.7 17.3 1.0 C A:ACT512 4.8 26.1 1.0 CA A:GLU52 4.8 17.9 1.0 O A:HOH530 4.9 22.2 1.0

Yttrium binding site 2 out of 3 in the W. Succinogenes Nrfa Y218F Sulfite Complex


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 Sulfite Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Y2 b:29.5 occ:0.30 O A:HOH1086 1.9 28.5 1.0 O A:HOH672 2.2 43.1 1.0 O1A A:HEM516 2.3 28.3 1.0 O1A A:HEM515 2.3 23.6 1.0 O A:PRO99 2.4 18.1 1.0 O A:HOH793 2.9 32.7 1.0 CGA A:HEM516 3.5 25.6 1.0 C A:PRO99 3.5 17.2 1.0 CGA A:HEM515 3.5 21.4 1.0 O A:HOH1082 3.8 35.9 1.0 O2A A:HEM516 4.0 29.5 1.0 CA A:ARG100 4.0 16.7 1.0 O A:HOH955 4.2 31.1 1.0 N A:ARG100 4.2 16.1 1.0 O2A A:HEM515 4.3 26.1 1.0 O A:HOH792 4.3 31.6 1.0 CAA A:HEM515 4.4 16.4 1.0 OG A:SER70 4.5 19.4 0.5 O A:HOH541 4.5 40.4 1.0 CA A:PRO99 4.5 16.6 1.0 CBA A:HEM515 4.6 17.8 1.0 O A:HOH1099 4.6 39.9 1.0 CB A:PRO99 4.6 17.7 1.0 N A:PRO99 4.7 16.2 1.0 CBA A:HEM516 4.7 20.8 1.0 CD A:PRO99 4.8 17.1 1.0 CB A:ARG100 4.8 17.7 1.0 CG A:PRO99 4.9 17.2 1.0 C A:ARG100 5.0 15.8 1.0

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


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 Sulfite Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Y3 b:54.1 occ:0.50 O1A A:HEM517 2.1 24.3 1.0 OE2 A:GLU408 2.4 19.1 1.0 CGA A:HEM517 3.1 31.1 1.0 O A:HOH800 3.3 74.8 1.0 CD A:GLU408 3.6 20.3 1.0 O2A A:HEM517 3.8 32.9 1.0 NZ A:LYS344 4.0 24.1 1.0 CBA A:HEM517 4.1 28.2 1.0 O2 A:SO4509 4.2 22.0 0.5 CG A:GLU408 4.2 18.8 1.0 OE1 A:GLU408 4.5 19.8 1.0 CG A:PRO407 4.9 19.7 1.0 CAA A:HEM517 4.9 25.1 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