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Zirconium in PDB 6y7p: The Complex Between the Eight-Bladed Symmetrical Designer Protein TAKO8 and 1:2 Zirconium(IV) Wells-Dawson (Zrwd)

Protein crystallography data

The structure of The Complex Between the Eight-Bladed Symmetrical Designer Protein TAKO8 and 1:2 Zirconium(IV) Wells-Dawson (Zrwd), PDB code: 6y7p was solved by L.Vandebroek, H.Noguchi, T.N.Parac-Vogt, L.Van Meervelt, A.R.D.Voet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.83 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 107.347, 72.799, 54.288, 90.00, 120.38, 90.00
R / Rfree (%) 17.8 / 21.5

Other elements in 6y7p:

The structure of The Complex Between the Eight-Bladed Symmetrical Designer Protein TAKO8 and 1:2 Zirconium(IV) Wells-Dawson (Zrwd) also contains other interesting chemical elements:

Tungsten (W) 68 atoms

Zirconium Binding Sites:

The binding sites of Zirconium atom in the The Complex Between the Eight-Bladed Symmetrical Designer Protein TAKO8 and 1:2 Zirconium(IV) Wells-Dawson (Zrwd) (pdb code 6y7p). This binding sites where shown within 5.0 Angstroms radius around Zirconium atom.
In total 4 binding sites of Zirconium where determined in the The Complex Between the Eight-Bladed Symmetrical Designer Protein TAKO8 and 1:2 Zirconium(IV) Wells-Dawson (Zrwd), PDB code: 6y7p:
Jump to Zirconium binding site number: 1; 2; 3; 4;

Zirconium binding site 1 out of 4 in 6y7p

Go back to Zirconium Binding Sites List in 6y7p
Zirconium binding site 1 out of 4 in the The Complex Between the Eight-Bladed Symmetrical Designer Protein TAKO8 and 1:2 Zirconium(IV) Wells-Dawson (Zrwd)


Mono view


Stereo pair view

A full contact list of Zirconium with other atoms in the Zr binding site number 1 of The Complex Between the Eight-Bladed Symmetrical Designer Protein TAKO8 and 1:2 Zirconium(IV) Wells-Dawson (Zrwd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zr401

b:38.2
occ:0.20
ZR1 A:ZRW401 0.0 38.2 0.2
O3L A:ZRW402 0.8 34.9 0.2
W6 A:ZRW402 2.1 32.7 0.2
O3L A:ZRW401 2.2 32.8 0.2
O1L A:ZRW401 2.2 32.4 0.2
O2L A:ZRW401 2.2 34.6 0.2
O4L A:ZRW401 2.2 31.9 0.2
O2L A:ZRW402 2.3 31.9 0.2
ZR1 A:ZRW402 2.4 38.0 0.2
O15 A:ZRW402 2.5 33.1 0.2
O6 A:ZRW402 2.7 31.6 0.2
O16 A:ZRW402 2.9 32.9 0.2
O22 A:ZRW402 3.0 32.1 0.2
O8 A:ZRW402 3.1 32.2 0.2
O4L A:ZRW402 3.2 34.5 0.2
W2 A:ZRW402 3.2 28.8 0.2
O8 A:ZRW401 3.3 31.8 0.2
O17 A:ZRW402 3.4 33.6 0.2
W5 A:ZRW402 3.5 31.0 0.2
P1 A:ZRW402 3.6 34.2 0.2
W2 A:ZRW401 3.8 34.7 0.2
W1 A:ZRW401 3.8 33.3 0.2
W6 A:ZRW401 3.9 38.6 0.2
O1L A:ZRW402 3.9 32.1 0.2
W7 A:ZRW401 3.9 30.6 0.2
O17 A:ZRW401 4.1 32.8 0.2
O27 A:ZRW402 4.1 32.5 0.2
O2 A:ZRW401 4.1 33.6 0.2
W7 A:ZRW402 4.3 35.4 0.2
O6 A:ZRW401 4.3 34.3 0.2
O23 A:ZRW402 4.3 32.4 0.2
P1 A:ZRW401 4.3 34.5 0.2
O3 A:ZRW402 4.4 32.5 0.2
O7 A:ZRW401 4.4 33.0 0.2
O16 A:ZRW401 4.5 33.7 0.2
O14 A:ZRW402 4.5 30.5 0.2
O22 A:ZRW401 4.5 31.9 0.2
O23 A:ZRW401 4.5 31.0 0.2
O2 A:ZRW402 4.6 31.8 0.2
O18 A:ZRW401 4.6 31.9 0.2
O5 A:ZRW402 4.7 30.8 0.2
W1 A:ZRW402 4.8 29.9 0.2
O13 A:ZRW402 4.8 30.9 0.2
O26 A:ZRW402 4.8 33.1 0.2
O15 A:ZRW401 4.8 34.0 0.2
O1 A:ZRW401 4.9 32.7 0.2
O19 A:ZRW401 4.9 31.4 0.2
O3 A:ZRW401 4.9 33.5 0.2
O21 A:ZRW402 4.9 30.9 0.2

Zirconium binding site 2 out of 4 in 6y7p

Go back to Zirconium Binding Sites List in 6y7p
Zirconium binding site 2 out of 4 in the The Complex Between the Eight-Bladed Symmetrical Designer Protein TAKO8 and 1:2 Zirconium(IV) Wells-Dawson (Zrwd)


Mono view


Stereo pair view

A full contact list of Zirconium with other atoms in the Zr binding site number 2 of The Complex Between the Eight-Bladed Symmetrical Designer Protein TAKO8 and 1:2 Zirconium(IV) Wells-Dawson (Zrwd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zr402

b:38.0
occ:0.20
ZR1 A:ZRW402 0.0 38.0 0.2
O3L A:ZRW402 2.2 34.9 0.2
O1L A:ZRW402 2.2 32.1 0.2
O2L A:ZRW402 2.2 31.9 0.2
O4L A:ZRW402 2.2 34.5 0.2
ZR1 A:ZRW401 2.4 38.2 0.2
O3L A:ZRW401 2.6 32.8 0.2
O8 A:ZRW402 3.3 32.2 0.2
O16 A:ZRW401 3.5 33.7 0.2
O2L A:ZRW401 3.5 34.6 0.2
W2 A:ZRW402 3.8 28.8 0.2
W1 A:ZRW402 3.8 29.9 0.2
W6 A:ZRW401 3.9 38.6 0.2
W6 A:ZRW402 3.9 32.7 0.2
O4L A:ZRW401 3.9 31.9 0.2
W7 A:ZRW402 3.9 35.4 0.2
O17 A:ZRW402 4.1 33.6 0.2
O2 A:ZRW402 4.1 31.8 0.2
O6 A:ZRW402 4.3 31.6 0.2
P1 A:ZRW402 4.3 34.2 0.2
O7 A:ZRW402 4.4 31.7 0.2
O16 A:ZRW402 4.5 32.9 0.2
O22 A:ZRW402 4.5 32.1 0.2
O23 A:ZRW402 4.5 32.4 0.2
O1L A:ZRW401 4.6 32.4 0.2
O15 A:ZRW401 4.6 34.0 0.2
O17 A:ZRW401 4.6 32.8 0.2
O18 A:ZRW402 4.6 34.7 0.2
O15 A:ZRW402 4.8 33.1 0.2
O1 A:ZRW402 4.9 31.6 0.2
O19 A:ZRW402 4.9 32.7 0.2
O3 A:ZRW402 4.9 32.5 0.2

Zirconium binding site 3 out of 4 in 6y7p

Go back to Zirconium Binding Sites List in 6y7p
Zirconium binding site 3 out of 4 in the The Complex Between the Eight-Bladed Symmetrical Designer Protein TAKO8 and 1:2 Zirconium(IV) Wells-Dawson (Zrwd)


Mono view


Stereo pair view

A full contact list of Zirconium with other atoms in the Zr binding site number 3 of The Complex Between the Eight-Bladed Symmetrical Designer Protein TAKO8 and 1:2 Zirconium(IV) Wells-Dawson (Zrwd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zr403

b:44.5
occ:0.20
ZR1 A:ZRW403 0.0 44.5 0.2
O3L A:ZRW403 2.2 39.5 0.2
O1L A:ZRW403 2.2 37.4 0.2
O2L A:ZRW403 2.2 37.4 0.2
O4L A:ZRW403 2.2 39.1 0.2
ZR1 A:ZRW404 2.4 44.8 0.2
O3L A:ZRW404 2.6 38.2 0.2
O8 A:ZRW403 3.3 37.0 0.2
O16 A:ZRW404 3.5 39.0 0.2
O2L A:ZRW404 3.6 39.6 0.2
W2 A:ZRW403 3.8 31.8 0.2
W1 A:ZRW403 3.8 34.5 0.2
W6 A:ZRW404 3.8 43.9 0.2
W6 A:ZRW403 3.9 37.5 0.2
O4L A:ZRW404 3.9 36.9 0.2
W7 A:ZRW403 3.9 39.6 0.2
O17 A:ZRW403 4.1 38.4 0.2
O2 A:ZRW403 4.1 36.5 0.2
O6 A:ZRW403 4.3 36.8 0.2
P1 A:ZRW403 4.3 38.8 0.2
O7 A:ZRW403 4.4 36.5 0.2
O16 A:ZRW403 4.5 38.1 0.2
O22 A:ZRW403 4.5 36.8 0.2
O23 A:ZRW403 4.5 37.1 0.2
O15 A:ZRW404 4.6 38.2 0.2
O1L A:ZRW404 4.6 37.8 0.2
O17 A:ZRW404 4.6 37.4 0.2
O18 A:ZRW403 4.6 38.2 0.2
O15 A:ZRW403 4.8 37.7 0.2
O1 A:ZRW403 4.9 35.6 0.2
O19 A:ZRW403 4.9 37.4 0.2
O3 A:ZRW403 4.9 37.3 0.2

Zirconium binding site 4 out of 4 in 6y7p

Go back to Zirconium Binding Sites List in 6y7p
Zirconium binding site 4 out of 4 in the The Complex Between the Eight-Bladed Symmetrical Designer Protein TAKO8 and 1:2 Zirconium(IV) Wells-Dawson (Zrwd)


Mono view


Stereo pair view

A full contact list of Zirconium with other atoms in the Zr binding site number 4 of The Complex Between the Eight-Bladed Symmetrical Designer Protein TAKO8 and 1:2 Zirconium(IV) Wells-Dawson (Zrwd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zr404

b:44.8
occ:0.20
ZR1 A:ZRW404 0.0 44.8 0.2
O3L A:ZRW403 0.8 39.5 0.2
W6 A:ZRW403 2.1 37.5 0.2
O3L A:ZRW404 2.2 38.2 0.2
O1L A:ZRW404 2.2 37.8 0.2
O2L A:ZRW404 2.2 39.6 0.2
O4L A:ZRW404 2.2 36.9 0.2
O2L A:ZRW403 2.3 37.4 0.2
ZR1 A:ZRW403 2.4 44.5 0.2
O15 A:ZRW403 2.4 37.7 0.2
O6 A:ZRW403 2.6 36.8 0.2
O16 A:ZRW403 2.9 38.1 0.2
O22 A:ZRW403 3.0 36.8 0.2
O8 A:ZRW403 3.1 37.0 0.2
W2 A:ZRW403 3.3 31.8 0.2
O8 A:ZRW404 3.3 36.8 0.2
O4L A:ZRW403 3.3 39.1 0.2
O17 A:ZRW403 3.4 38.4 0.2
W5 A:ZRW403 3.4 35.6 0.2
P1 A:ZRW403 3.7 38.8 0.2
W2 A:ZRW404 3.8 39.4 0.2
W1 A:ZRW404 3.8 37.1 0.2
W6 A:ZRW404 3.9 43.9 0.2
W7 A:ZRW404 3.9 34.0 0.2
O1L A:ZRW403 4.0 37.4 0.2
O27 A:ZRW403 4.1 36.8 0.2
O17 A:ZRW404 4.1 37.4 0.2
O2 A:ZRW404 4.1 38.4 0.2
W7 A:ZRW403 4.3 39.6 0.2
O6 A:ZRW404 4.3 38.8 0.2
P1 A:ZRW404 4.3 38.3 0.2
O23 A:ZRW403 4.4 37.1 0.2
O7 A:ZRW404 4.4 37.4 0.2
O3 A:ZRW403 4.4 37.3 0.2
O14 A:ZRW403 4.5 34.2 0.2
O16 A:ZRW404 4.5 39.0 0.2
O22 A:ZRW404 4.5 36.5 0.2
O23 A:ZRW404 4.5 35.6 0.2
O2 A:ZRW403 4.6 36.5 0.2
O18 A:ZRW404 4.6 36.7 0.2
O5 A:ZRW403 4.7 35.2 0.2
O13 A:ZRW403 4.8 34.8 0.2
O26 A:ZRW403 4.8 36.9 0.2
O15 A:ZRW404 4.8 38.2 0.2
W1 A:ZRW403 4.8 34.5 0.2
O1 A:ZRW404 4.9 36.1 0.2
O19 A:ZRW404 4.9 35.6 0.2
O3 A:ZRW404 4.9 39.8 0.2
O21 A:ZRW403 5.0 35.8 0.2

Reference:

L.Vandebroek, H.Noguchi, K.Kamata, J.R.H.Tame, T.N.Parac-Vogt, A.R.D.Voet. Shape and Size Complementarity Induced Formation of Supramolecular Protein Assemblies with Metal-Oxo Clusters Biorxiv 2020.
DOI: 10.1101/2020.11.18.388215
Page generated: Wed Dec 16 14:05:36 2020

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