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Yttrium in PDB 2e80: Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Substrate Nitrite

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

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

Protein crystallography data

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Substrate Nitrite, PDB code: 2e80 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) 50.00 / 1.60
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 118.984, 118.984, 186.731, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 21

Other elements in 2e80:

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Substrate Nitrite 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 Substrate Nitrite (pdb code 2e80). 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 Substrate Nitrite, PDB code: 2e80:
Jump to Yttrium binding site number: 1; 2; 3;

Yttrium binding site 1 out of 3 in 2e80

Go back to Yttrium Binding Sites List in 2e80
Yttrium binding site 1 out of 3 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Substrate Nitrite


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 Substrate Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y801

b:23.0
occ:1.00
 OE1 A:GLU52 2.3 20.0 1.0
O A:HOH1901 2.4 23.7 1.0
O A:HOH1713 2.4 20.8 1.0
O A:HOH1902 2.4 24.8 1.0
O A:HOH1903 2.4 25.5 1.0
O A:HOH1900 2.4 18.9 1.0
CD A:GLU52 3.4 21.9 1.0
OE2 A:GLU52 3.8 23.3 1.0
CD A:ARG55 4.2 40.2 1.0
O A:HOH1909 4.3 42.1 1.0
NH1 A:ARG55 4.5 37.7 1.0
O A:GLU52 4.5 23.6 1.0
O A:GLU45 4.6 22.3 1.0
OH A:TYR56 4.6 32.5 1.0
O A:HOH1524 4.6 29.9 1.0
CG A:GLU52 4.6 23.5 1.0
CB A:GLU52 4.8 22.1 1.0
CA A:GLU52 4.9 22.3 1.0

Yttrium binding site 2 out of 3 in 2e80

Go back to Yttrium Binding Sites List in 2e80
Yttrium binding site 2 out of 3 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Substrate Nitrite


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 Substrate Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y802

b:25.2
occ:1.00
 O1A A:HEM1511 2.3 25.2 1.0
O1A A:HEM1510 2.3 24.7 1.0
O A:PRO99 2.3 19.7 1.0
O A:HOH1724 2.3 31.7 1.0
O A:HOH1922 2.3 31.7 1.0
OXT A:ACT706 2.6 39.8 1.0
O A:HOH1921 2.6 28.1 1.0
O A:ACT706 2.7 40.8 1.0
C A:ACT706 3.0 42.0 1.0
CGA A:HEM1511 3.4 26.5 1.0
C A:PRO99 3.5 19.7 1.0
CGA A:HEM1510 3.5 28.7 1.0
O2A A:HEM1511 3.9 23.8 1.0
O A:HOH1574 4.0 53.4 1.0
CA A:ARG100 4.1 18.6 1.0
O2A A:HEM1510 4.2 34.2 1.0
N A:ARG100 4.3 20.1 1.0
O A:HOH2034 4.3 48.6 1.0
CH3 A:ACT706 4.5 41.8 1.0
CA A:PRO99 4.5 19.8 1.0
CBA A:HEM1511 4.6 24.6 1.0
CAA A:HEM1510 4.6 19.4 1.0
CBA A:HEM1510 4.6 23.1 1.0
O A:HOH1919 4.6 40.6 1.0
N A:PRO99 4.6 18.6 1.0
CD A:PRO99 4.8 19.9 1.0
O A:HOH2033 4.8 55.5 1.0
CB A:PRO99 4.8 21.5 1.0
O A:HOH1916 4.9 37.8 1.0
CB A:ARG100 4.9 21.7 1.0

Yttrium binding site 3 out of 3 in 2e80

Go back to Yttrium Binding Sites List in 2e80
Yttrium binding site 3 out of 3 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Substrate Nitrite


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 Substrate Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y803

b:37.7
occ:0.50
 OE2 A:GLU408 2.4 24.1 1.0
O1A A:HEM1512 2.5 37.5 1.0
O A:ACT705 2.6 42.4 1.0
OXT A:ACT705 2.8 42.2 1.0
C A:ACT705 3.1 42.4 1.0
CGA A:HEM1512 3.4 37.3 1.0
CD A:GLU408 3.5 24.6 1.0
CG A:GLU408 4.0 22.1 1.0
NZ A:LYS344 4.1 23.6 1.0
CBA A:HEM1512 4.2 26.7 1.0
O2A A:HEM1512 4.2 34.3 1.0
OE1 A:GLU408 4.5 26.6 1.0
CH3 A:ACT705 4.6 36.1 1.0
O A:HOH2059 4.6 33.7 1.0
CB A:PRO407 4.8 20.8 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: Tue Aug 19 18:37:21 2025

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