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Yttrium in PDB 2e81: Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Intermediate Hydroxylamine

Enzymatic activity of Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Intermediate Hydroxylamine

All present enzymatic activity of Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Intermediate Hydroxylamine:
1.7.2.2;

Protein crystallography data

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Intermediate Hydroxylamine, PDB code: 2e81 was solved by O.Einsle, 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 / 2.00
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 119.891, 119.891, 186.224, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.3

Other elements in 2e81:

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Intermediate Hydroxylamine 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 Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Intermediate Hydroxylamine (pdb code 2e81). 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 with Bound Intermediate Hydroxylamine, PDB code: 2e81:
Jump to Yttrium binding site number: 1; 2; 3;

Yttrium binding site 1 out of 3 in 2e81

Go back to Yttrium Binding Sites List in 2e81
Yttrium binding site 1 out of 3 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Intermediate Hydroxylamine


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 with Bound Intermediate Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y801

b:34.7
occ:1.00
 OE1 A:GLU52 2.3 32.6 1.0
O A:HOH1839 2.3 32.5 1.0
O A:HOH1833 2.4 33.8 1.0
O A:HOH1834 2.4 30.5 1.0
O A:HOH1683 2.4 28.5 1.0
O A:HOH1835 2.4 31.7 1.0
CD A:GLU52 3.4 33.0 1.0
OE2 A:GLU52 3.8 32.9 1.0
O A:HOH1528 3.9 51.9 1.0
O A:HOH1882 4.4 46.1 1.0
O A:HOH1883 4.5 55.2 1.0
CD A:ARG55 4.5 42.1 1.0
O A:HOH1527 4.6 35.1 1.0
O A:GLU45 4.6 30.4 1.0
O A:GLU52 4.6 33.4 1.0
CG A:GLU52 4.6 30.7 1.0
NH1 A:ARG55 4.7 38.1 1.0
CB A:GLU52 4.8 30.4 1.0
CA A:GLU52 4.9 33.3 1.0

Yttrium binding site 2 out of 3 in 2e81

Go back to Yttrium Binding Sites List in 2e81
Yttrium binding site 2 out of 3 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Intermediate Hydroxylamine


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 with Bound Intermediate Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y802

b:70.8
occ:1.00
 O1A A:HEM1511 2.4 45.6 1.0
O A:HOH1752 2.5 42.8 1.0
O A:PRO99 2.5 29.9 1.0
O1A A:HEM1510 2.6 44.0 1.0
O A:HOH1843 2.7 62.9 1.0
O A:HOH1693 2.9 57.4 1.0
O A:HOH1842 3.0 54.4 1.0
CGA A:HEM1511 3.5 41.8 1.0
C A:PRO99 3.6 30.0 1.0
CGA A:HEM1510 3.7 40.1 1.0
O2A A:HEM1511 4.1 43.1 1.0
CA A:ARG100 4.2 29.0 1.0
O2A A:HEM1510 4.3 43.1 1.0
N A:ARG100 4.4 29.2 1.0
CG A:PRO99 4.5 33.6 1.0
N A:PRO99 4.6 27.9 1.0
CA A:PRO99 4.7 29.6 1.0
O A:HOH1841 4.7 49.2 1.0
O A:HOH1518 4.7 54.9 1.0
O A:HOH1550 4.7 47.9 1.0
CAA A:HEM1510 4.7 24.8 1.0
CBA A:HEM1511 4.7 36.5 1.0
CD A:PRO99 4.7 30.4 1.0
CBA A:HEM1510 4.8 33.6 1.0
CB A:ALA98 4.9 24.2 1.0

Yttrium binding site 3 out of 3 in 2e81

Go back to Yttrium Binding Sites List in 2e81
Yttrium binding site 3 out of 3 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Intermediate Hydroxylamine


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 with Bound Intermediate Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y803

b:99.1
occ:0.50
 O A:HOH1899 2.7 58.6 1.0
OE2 A:GLU408 2.8 41.0 1.0
O1A A:HEM1512 3.3 56.0 1.0
CGA A:HEM1512 3.4 53.2 1.0
O2A A:HEM1512 3.6 53.5 1.0
CD A:GLU408 3.9 35.4 1.0
CBA A:HEM1512 4.1 46.9 1.0
NZ A:LYS344 4.1 33.9 1.0
CG A:GLU408 4.2 32.8 1.0
CG A:PRO407 4.2 32.9 1.0

Reference:

O.Einsle, A.Messerschmidt, R.Huber, P.M.H.Kroneck, F.Neese. Mechanism of the Six-Electron Reduction of Nitrite to Ammonia By Cytochrome C Nitrite Reductase J.Am.Chem.Soc. V. 124 11737 2002.
ISSN: ISSN 0002-7863
PubMed: 12296741
DOI: 10.1021/JA0206487
Page generated: Sat Oct 12 20:28:40 2024

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