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:
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: Thu Oct 31 15:44:19 2024
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