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Yttrium in PDB 3bnf: W. Succinogenes Nrfa Sulfite Complex

Enzymatic activity of W. Succinogenes Nrfa Sulfite Complex

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

Protein crystallography data

The structure of W. Succinogenes Nrfa Sulfite Complex, PDB code: 3bnf 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) 22.31 / 1.70
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 119.500, 119.500, 186.674, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 28

Other elements in 3bnf:

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

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

Yttrium Binding Sites:

The binding sites of Yttrium atom in the W. Succinogenes Nrfa Sulfite Complex (pdb code 3bnf). 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 Sulfite Complex, PDB code: 3bnf:
Jump to Yttrium binding site number: 1; 2; 3;

Yttrium binding site 1 out of 3 in 3bnf

Go back to Yttrium Binding Sites List in 3bnf
Yttrium binding site 1 out of 3 in the W. Succinogenes Nrfa 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 Sulfite Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y2

b:29.3
occ:1.00
OE1 A:GLU52 2.3 22.1 1.0
O A:HOH777 2.3 26.8 1.0
O A:HOH781 2.3 28.7 1.0
O A:HOH776 2.4 29.6 1.0
O A:HOH659 2.4 25.1 1.0
O A:HOH778 2.5 33.1 1.0
CD A:GLU52 3.4 26.6 1.0
O A:ACT6 3.5 40.3 1.0
OE2 A:GLU52 3.8 26.6 1.0
O A:HOH814 4.3 37.1 1.0
CD A:ARG55 4.4 30.0 1.0
O A:GLU45 4.5 26.4 1.0
O A:HOH813 4.5 35.5 1.0
O A:GLU52 4.5 28.0 1.0
C A:ACT6 4.5 40.9 1.0
CG A:GLU52 4.6 24.5 1.0
OXT A:ACT6 4.7 40.7 1.0
CB A:GLU52 4.7 24.3 1.0
NH1 A:ARG55 4.8 26.7 1.0
CA A:GLU52 4.8 24.3 1.0
O A:HOH525 4.9 30.1 1.0

Yttrium binding site 2 out of 3 in 3bnf

Go back to Yttrium Binding Sites List in 3bnf
Yttrium binding site 2 out of 3 in the W. Succinogenes Nrfa 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 Sulfite Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y3

b:54.2
occ:0.50
O1A A:HEM510 2.4 30.6 1.0
O A:HOH1069 2.5 39.6 1.0
O A:PRO99 2.7 24.8 1.0
O1A A:HEM511 2.9 40.7 1.0
O A:HOH784 3.0 38.7 1.0
O A:HOH666 3.3 51.3 1.0
CGA A:HEM510 3.4 28.2 1.0
CGA A:HEM511 3.6 38.3 1.0
C A:PRO99 3.7 24.6 1.0
O2A A:HEM511 3.8 41.0 1.0
O2A A:HEM510 3.9 31.1 1.0
O A:HOH536 4.1 49.3 1.0
CA A:ARG100 4.1 22.9 1.0
O A:HOH783 4.3 34.7 1.0
N A:ARG100 4.3 25.0 1.0
O A:HOH937 4.4 31.9 1.0
O A:HOH1062 4.4 54.4 1.0
CAA A:HEM510 4.4 21.8 1.0
CBA A:HEM510 4.5 20.7 1.0
O A:HOH1082 4.6 43.2 1.0
CA A:PRO99 4.7 24.6 1.0
CB A:PRO99 4.7 26.1 1.0
CBA A:HEM511 4.7 31.2 1.0
N A:PRO99 4.8 23.5 1.0
CB A:ARG100 4.8 23.0 1.0
CD A:PRO99 4.9 23.8 1.0
C A:ARG100 4.9 23.4 1.0

Yttrium binding site 3 out of 3 in 3bnf

Go back to Yttrium Binding Sites List in 3bnf
Yttrium binding site 3 out of 3 in the W. Succinogenes Nrfa 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 Sulfite Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y4

b:32.7
occ:0.50
OE2 A:GLU408 2.3 20.9 1.0
O1A A:HEM512 2.3 30.1 1.0
O A:ACT5 3.0 46.8 1.0
OXT A:ACT5 3.1 46.8 1.0
CGA A:HEM512 3.2 36.8 1.0
CD A:GLU408 3.5 24.1 1.0
C A:ACT5 3.5 46.3 1.0
O2A A:HEM512 3.8 40.9 1.0
NZ A:LYS344 4.1 24.5 1.0
CG A:GLU408 4.1 20.3 1.0
CBA A:HEM512 4.2 30.1 1.0
OE1 A:GLU408 4.4 23.1 1.0

Reference:

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
Page generated: Wed Dec 16 02:40:51 2020

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