Atomistry » Terbium » PDB 1m9s-6zv9 » 6rqa
Atomistry »
  Terbium »
    PDB 1m9s-6zv9 »
      6rqa »

Terbium in PDB 6rqa: Crystal Structure of the Iminosuccinate Reductase of Paracoccus Denitrificans in Complex with Nad+

Protein crystallography data

The structure of Crystal Structure of the Iminosuccinate Reductase of Paracoccus Denitrificans in Complex with Nad+, PDB code: 6rqa was solved by J.Zarzycki, F.Severi, L.Schada Von Borzyskowski, T.J.Erb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.40 / 2.56
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.386, 72.407, 164.266, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 22.5

Terbium Binding Sites:

The binding sites of Terbium atom in the Crystal Structure of the Iminosuccinate Reductase of Paracoccus Denitrificans in Complex with Nad+ (pdb code 6rqa). This binding sites where shown within 5.0 Angstroms radius around Terbium atom.
In total 3 binding sites of Terbium where determined in the Crystal Structure of the Iminosuccinate Reductase of Paracoccus Denitrificans in Complex with Nad+, PDB code: 6rqa:
Jump to Terbium binding site number: 1; 2; 3;

Terbium binding site 1 out of 3 in 6rqa

Go back to Terbium Binding Sites List in 6rqa
Terbium binding site 1 out of 3 in the Crystal Structure of the Iminosuccinate Reductase of Paracoccus Denitrificans in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 1 of Crystal Structure of the Iminosuccinate Reductase of Paracoccus Denitrificans in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb402

b:0.7
occ:1.00
OD2 A:ASP48 2.3 96.3 1.0
OD1 A:ASP48 2.7 94.9 1.0
CG A:ASP48 2.9 85.5 1.0
CB A:ASP48 4.4 65.2 1.0

Terbium binding site 2 out of 3 in 6rqa

Go back to Terbium Binding Sites List in 6rqa
Terbium binding site 2 out of 3 in the Crystal Structure of the Iminosuccinate Reductase of Paracoccus Denitrificans in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 2 of Crystal Structure of the Iminosuccinate Reductase of Paracoccus Denitrificans in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb403

b:0.1
occ:1.00
OE2 A:GLU163 2.3 0.6 1.0
OE1 A:GLU163 2.8 0.6 1.0
CD A:GLU163 2.9 0.6 1.0
CG A:GLU163 4.4 0.6 1.0

Terbium binding site 3 out of 3 in 6rqa

Go back to Terbium Binding Sites List in 6rqa
Terbium binding site 3 out of 3 in the Crystal Structure of the Iminosuccinate Reductase of Paracoccus Denitrificans in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 3 of Crystal Structure of the Iminosuccinate Reductase of Paracoccus Denitrificans in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb402

b:43.2
occ:0.95
TB B:7MT402 0.0 43.2 0.9
N23 B:7MT402 2.4 59.4 0.9
N17 B:7MT402 2.5 45.8 0.9
N06 B:7MT402 2.6 52.5 0.9
N09 B:7MT402 2.6 44.0 0.9
N02 B:7MT402 2.7 46.8 0.9
O26 B:7MT402 2.8 57.8 0.9
OD1 B:ASP48 2.8 38.4 1.0
OD2 B:ASP48 2.9 47.4 1.0
O27 B:7MT402 2.9 46.7 0.9
CG B:ASP48 3.2 48.6 1.0
C11 B:7MT402 3.2 44.3 0.9
C22 B:7MT402 3.3 57.4 0.9
C30 B:7MT402 3.3 49.1 0.9
C10 B:7MT402 3.3 58.0 0.9
C29 B:7MT402 3.3 44.7 0.9
C01 B:7MT402 3.3 34.3 0.9
C08 B:7MT402 3.4 45.7 0.9
C16 B:7MT402 3.5 50.9 0.9
C24 B:7MT402 3.5 53.6 0.9
C05 B:7MT402 3.5 49.6 0.9
C03 B:7MT402 3.6 33.8 0.9
C18 B:7MT402 3.6 56.8 0.9
C07 B:7MT402 3.6 55.4 0.9
C04 B:7MT402 3.7 51.3 0.9
O B:HOH527 4.4 32.4 1.0
C19 B:7MT402 4.6 47.1 0.9
C21 B:7MT402 4.6 52.0 0.9
C13 B:7MT402 4.7 60.9 0.9
CB B:ASP48 4.7 42.2 1.0
O25 B:7MT402 4.7 55.5 0.9
ND2 B:ASN74 4.7 39.0 1.0
C15 B:7MT402 4.8 48.5 0.9
O28 B:7MT402 4.8 64.6 0.9
O B:HOH533 4.8 50.0 1.0
N B:ASP48 4.9 28.2 1.0

Reference:

L.Schada Von Borzyskowski, F.Severi, K.Kruger, L.Hermann, A.Gilardet, F.Sippel, B.Pommerenke, P.Claus, N.S.Cortina, T.Glatter, S.Zauner, J.Zarzycki, B.M.Fuchs, E.Bremer, U.G.Maier, R.I.Amann, T.J.Erb. Marine Proteobacteria Metabolize Glycolate Via the Beta-Hydroxyaspartate Cycle. Nature V. 575 500 2019.
ISSN: ESSN 1476-4687
PubMed: 31723261
DOI: 10.1038/S41586-019-1748-4
Page generated: Wed Dec 16 02:27:23 2020

Last articles

Tb in 6TVY
Si in 6Y7O
Rh in 6WRM
Rh in 6WRL
Ni in 6Y8Z
Ni in 6Y8Y
Na in 6ZXZ
Na in 7ACG
Na in 6YLS
Na in 6Y8Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy