Atomistry » Yttrium » PDB 1dde-3ph5 » 1fs7
Atomistry »
  Yttrium »
    PDB 1dde-3ph5 »
      1fs7 »

Yttrium in PDB 1fs7: Cytochrome C Nitrite Reductase From Wolinella Succinogenes

Protein crystallography data

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes, PDB code: 1fs7 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 / 1.60
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 119.822, 119.822, 186.025, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 20.7

Other elements in 1fs7:

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes 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 (pdb code 1fs7). 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, PDB code: 1fs7:
Jump to Yttrium binding site number: 1; 2; 3;

Yttrium binding site 1 out of 3 in 1fs7

Go back to Yttrium Binding Sites List in 1fs7
Yttrium binding site 1 out of 3 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y652

b:21.8
occ:1.00
OE1 A:GLU52 2.2 16.5 1.0
O A:HOH947 2.4 22.4 1.0
O A:HOH951 2.4 21.0 1.0
O A:HOH814 2.4 23.7 1.0
O A:HOH948 2.4 27.3 1.0
O A:HOH946 2.5 20.8 1.0
CD A:GLU52 3.4 19.4 1.0
OE2 A:GLU52 3.8 21.3 1.0
O A:ACT655 4.0 32.7 1.0
O A:HOH988 4.4 30.2 1.0
O A:HOH987 4.4 33.8 1.0
CD A:ARG55 4.4 25.1 1.0
OXT A:ACT655 4.5 25.7 1.0
O A:GLU45 4.6 20.0 1.0
O A:GLU52 4.6 22.2 1.0
CG A:GLU52 4.6 20.0 1.0
NH1 A:ARG55 4.7 30.1 1.0
C A:ACT655 4.7 31.8 1.0
CB A:GLU52 4.7 19.5 1.0
CA A:GLU52 4.8 20.7 1.0
O A:HOH677 4.9 23.0 1.0

Yttrium binding site 2 out of 3 in 1fs7

Go back to Yttrium Binding Sites List in 1fs7
Yttrium binding site 2 out of 3 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y653

b:25.5
occ:1.00
O1A A:HEM511 2.3 26.7 1.0
O1A A:HEM510 2.3 21.6 1.0
O A:HOH875 2.3 26.4 1.0
O A:PRO99 2.3 18.1 1.0
O A:HOH821 2.4 27.9 1.0
O A:HOH954 2.5 26.5 1.0
OXT A:ACT656 2.5 34.9 1.0
O A:ACT656 2.5 38.0 1.0
C A:ACT656 2.9 38.4 1.0
CGA A:HEM510 3.4 20.8 1.0
C A:PRO99 3.5 19.1 1.0
CGA A:HEM511 3.5 27.8 1.0
O2A A:HEM510 4.0 24.2 1.0
CA A:ARG100 4.1 17.9 1.0
O2A A:HEM511 4.1 25.8 1.0
N A:ARG100 4.2 18.6 1.0
O A:HOH1207 4.3 33.5 1.0
CH3 A:ACT656 4.4 36.4 1.0
O A:HOH1154 4.4 42.6 1.0
CA A:PRO99 4.5 18.1 1.0
CBA A:HEM511 4.6 20.9 1.0
N A:PRO99 4.6 17.2 1.0
O A:HOH953 4.6 30.7 1.0
CBA A:HEM510 4.6 21.5 1.0
CAA A:HEM510 4.7 17.8 1.0
CB A:PRO99 4.7 20.2 1.0
CD A:PRO99 4.8 18.7 1.0
O A:HOH688 4.8 44.9 1.0
CB A:ARG100 4.9 18.7 1.0

Yttrium binding site 3 out of 3 in 1fs7

Go back to Yttrium Binding Sites List in 1fs7
Yttrium binding site 3 out of 3 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y654

b:38.7
occ:0.50
OE2 A:GLU408 2.4 24.8 1.0
O A:ACT657 2.6 38.2 1.0
O1A A:HEM512 2.6 44.9 1.0
OXT A:ACT657 2.9 39.9 1.0
C A:ACT657 3.1 38.0 1.0
CGA A:HEM512 3.4 40.2 1.0
CD A:GLU408 3.6 23.1 1.0
O2A A:HEM512 3.9 38.2 1.0
CG A:GLU408 4.1 18.1 1.0
NZ A:LYS344 4.2 23.0 1.0
CBA A:HEM512 4.2 29.6 1.0
CH3 A:ACT657 4.6 34.2 1.0
OE1 A:GLU408 4.6 25.9 1.0
CB A:PRO407 4.8 19.4 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

Last articles

Zn in 7M6U
Zn in 7NNG
Zn in 7NEE
Zn in 7NEU
Zn in 7M3K
Zn in 7KWD
Zn in 7KYH
Zn in 7KNG
Zn in 7KY2
Zn in 7KYF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy