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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

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