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Yttrium in PDB 1fs9: Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex

Protein crystallography data

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex, PDB code: 1fs9 was solved by O.Einsle, P.Stach, A.Messerschmidt, J.Simon, A.Kroeger, R.Huber, 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 (°) 119.532, 119.532, 186.056, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 20.8

Other elements in 1fs9:

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide 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 Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex (pdb code 1fs9). 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-Azide Complex, PDB code: 1fs9:
Jump to Yttrium binding site number: 1; 2; 3;

Yttrium binding site 1 out of 3 in 1fs9

Go back to Yttrium Binding Sites List in 1fs9
Yttrium binding site 1 out of 3 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex


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-Azide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y514

b:28.1
occ:1.00
O A:HOH811 2.3 27.5 1.0
OE1 A:GLU52 2.3 26.9 1.0
O A:HOH812 2.3 29.7 1.0
O A:HOH674 2.4 27.1 1.0
O A:HOH816 2.4 22.8 1.0
O A:HOH813 2.4 26.4 1.0
CD A:GLU52 3.4 27.7 1.0
OE2 A:GLU52 3.8 26.0 1.0
O A:HOH521 3.9 40.7 1.0
O A:HOH852 4.4 43.9 1.0
CD A:ARG55 4.4 34.5 1.0
O A:HOH851 4.4 41.4 1.0
O A:HOH520 4.4 32.9 1.0
NH1 A:ARG55 4.5 31.6 1.0
O A:GLU45 4.6 27.1 1.0
O A:GLU52 4.6 27.1 1.0
CG A:GLU52 4.6 26.1 1.0
CB A:GLU52 4.8 23.8 1.0
CA A:GLU52 4.9 25.6 1.0
O A:HOH532 4.9 26.7 1.0

Yttrium binding site 2 out of 3 in 1fs9

Go back to Yttrium Binding Sites List in 1fs9
Yttrium binding site 2 out of 3 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex


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-Azide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y515

b:27.2
occ:1.00
O1A A:HEM510 2.3 30.0 1.0
O A:PRO99 2.3 21.4 1.0
O1A A:HEM511 2.3 29.4 1.0
O A:HOH683 2.3 26.1 1.0
O A:HOH739 2.4 29.8 1.0
O A:HOH820 2.4 30.9 1.0
O A:HOH907 2.5 36.1 1.0
O A:HOH819 2.5 29.3 1.0
CGA A:HEM511 3.4 31.3 1.0
CGA A:HEM510 3.5 35.6 1.0
C A:PRO99 3.5 24.6 1.0
O2A A:HEM511 3.9 28.2 1.0
O2A A:HEM510 4.0 29.4 1.0
CA A:ARG100 4.1 23.1 1.0
O A:HOH905 4.2 35.2 1.0
N A:ARG100 4.3 23.3 1.0
O A:HOH908 4.3 58.2 1.0
CG A:PRO99 4.5 33.5 1.0
CA A:PRO99 4.5 25.3 1.0
CBA A:HEM511 4.5 28.5 1.0
N A:PRO99 4.6 25.1 1.0
O A:HOH818 4.6 49.4 1.0
CBA A:HEM510 4.6 29.2 1.0
CAA A:HEM510 4.7 19.8 1.0
CD A:PRO99 4.8 25.9 1.0
O A:HOH543 4.8 35.0 1.0
O A:HOH542 4.8 23.3 1.0
CB A:PRO99 4.9 28.8 1.0
CB A:ARG100 5.0 23.8 1.0

Yttrium binding site 3 out of 3 in 1fs9

Go back to Yttrium Binding Sites List in 1fs9
Yttrium binding site 3 out of 3 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex


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-Azide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y516

b:67.0
occ:0.50
O A:HOH866 2.5 51.6 1.0
OE1 A:GLU408 3.0 43.8 1.0
CGA A:HEM512 3.6 53.9 1.0
O2A A:HEM512 3.6 51.1 1.0
O1A A:HEM512 3.8 56.5 1.0
CD A:GLU408 3.9 30.5 1.0
CG A:GLU408 4.0 26.0 1.0
CBA A:HEM512 4.1 47.8 1.0
CG A:PRO407 4.2 28.9 1.0
NZ A:LYS344 4.5 24.3 1.0
O A:HOH831 4.6 40.6 1.0
O A:HOH921 4.9 34.5 1.0
OE2 A:GLU408 5.0 44.2 1.0

Reference:

O.Einsle, P.Stach, A.Messerschmidt, J.Simon, A.Kroger, R.Huber, P.M.Kroneck. Cytochrome C Nitrite Reductase From Wolinella Succinogenes. Structure at 1.6 A Resolution, Inhibitor Binding, and Heme-Packing Motifs. J.Biol.Chem. V. 275 39608 2000.
ISSN: ISSN 0021-9258
PubMed: 10984487
DOI: 10.1074/JBC.M006188200
Page generated: Wed Dec 16 02:40:44 2020

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