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Thorium in PDB 5kid: Tightening the Recognition of Tetravalent Zr and Th Complexes By the Siderophore-Binding Mammalian Protein Siderocalin For Theranostic Applications

Protein crystallography data

The structure of Tightening the Recognition of Tetravalent Zr and Th Complexes By the Siderophore-Binding Mammalian Protein Siderocalin For Theranostic Applications, PDB code: 5kid was solved by P.B.Rupert, R.K.Strong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.15
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 115.547, 115.547, 118.028, 90.00, 90.00, 90.00
R / Rfree (%) 23.2 / 26.3

Other elements in 5kid:

The structure of Tightening the Recognition of Tetravalent Zr and Th Complexes By the Siderophore-Binding Mammalian Protein Siderocalin For Theranostic Applications also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Thorium Binding Sites:

The binding sites of Thorium atom in the Tightening the Recognition of Tetravalent Zr and Th Complexes By the Siderophore-Binding Mammalian Protein Siderocalin For Theranostic Applications (pdb code 5kid). This binding sites where shown within 5.0 Angstroms radius around Thorium atom.
In total 3 binding sites of Thorium where determined in the Tightening the Recognition of Tetravalent Zr and Th Complexes By the Siderophore-Binding Mammalian Protein Siderocalin For Theranostic Applications, PDB code: 5kid:
Jump to Thorium binding site number: 1; 2; 3;

Thorium binding site 1 out of 3 in 5kid

Go back to Thorium Binding Sites List in 5kid
Thorium binding site 1 out of 3 in the Tightening the Recognition of Tetravalent Zr and Th Complexes By the Siderophore-Binding Mammalian Protein Siderocalin For Theranostic Applications


Mono view


Stereo pair view

A full contact list of Thorium with other atoms in the Th binding site number 1 of Tightening the Recognition of Tetravalent Zr and Th Complexes By the Siderophore-Binding Mammalian Protein Siderocalin For Theranostic Applications within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Th201

b:0.8
occ:0.75
O9 A:7K9202 2.5 40.9 0.8
O8 A:7K9202 2.6 43.5 0.8
C27 A:7K9202 3.3 40.3 0.8
C28 A:7K9202 3.4 45.0 0.8
OH A:TYR106 4.2 46.8 1.0
NZ A:LYS134 4.2 53.8 1.0
NZ A:LYS125 4.3 55.0 1.0
CE2 A:TYR106 4.6 46.1 1.0
C26 A:7K9202 4.6 40.4 0.8
C10 A:7K9202 4.7 43.3 0.8
CZ A:TYR106 4.9 47.1 1.0
CE A:LYS125 5.0 52.6 1.0
N2 A:7K9202 5.0 53.8 0.8

Thorium binding site 2 out of 3 in 5kid

Go back to Thorium Binding Sites List in 5kid
Thorium binding site 2 out of 3 in the Tightening the Recognition of Tetravalent Zr and Th Complexes By the Siderophore-Binding Mammalian Protein Siderocalin For Theranostic Applications


Mono view


Stereo pair view

A full contact list of Thorium with other atoms in the Th binding site number 2 of Tightening the Recognition of Tetravalent Zr and Th Complexes By the Siderophore-Binding Mammalian Protein Siderocalin For Theranostic Applications within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Th300

b:0.9
occ:0.75
O8 B:7K9301 2.6 76.3 0.8
O9 B:7K9301 3.1 72.4 0.8
C28 B:7K9301 3.6 71.3 0.8
C27 B:7K9301 3.7 70.5 0.8
NZ B:LYS125 4.1 59.8 1.0
OH B:TYR106 4.2 64.9 1.0
NZ B:LYS134 4.3 65.0 1.0
CE2 B:TYR106 4.5 61.8 1.0
C10 B:7K9301 4.8 67.3 0.8
N2 B:7K9301 4.8 66.8 0.8
CZ B:TYR106 4.9 62.0 1.0
CE B:LYS125 4.9 59.0 1.0
CD B:LYS125 5.0 57.7 1.0

Thorium binding site 3 out of 3 in 5kid

Go back to Thorium Binding Sites List in 5kid
Thorium binding site 3 out of 3 in the Tightening the Recognition of Tetravalent Zr and Th Complexes By the Siderophore-Binding Mammalian Protein Siderocalin For Theranostic Applications


Mono view


Stereo pair view

A full contact list of Thorium with other atoms in the Th binding site number 3 of Tightening the Recognition of Tetravalent Zr and Th Complexes By the Siderophore-Binding Mammalian Protein Siderocalin For Theranostic Applications within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Th201

b:0.8
occ:0.75
O9 C:7K9202 2.6 44.1 0.8
O8 C:7K9202 2.6 46.8 0.8
C27 C:7K9202 3.4 42.6 0.8
C28 C:7K9202 3.5 43.8 0.8
NZ C:LYS134 3.9 52.5 1.0
NZ C:LYS125 4.6 46.8 1.0
OH C:TYR106 4.7 47.3 1.0
C26 C:7K9202 4.8 44.2 0.8
C10 C:7K9202 4.8 42.7 0.8

Reference:

I.Captain, G.J.Deblonde, P.B.Rupert, D.D.An, M.C.Illy, E.Rostan, C.Y.Ralston, R.K.Strong, R.J.Abergel. Engineered Recognition of Tetravalent Zirconium and Thorium By Chelator-Protein Systems: Toward Flexible Radiotherapy and Imaging Platforms. Inorg Chem V. 55 11930 2016.
ISSN: ISSN 1520-510X
PubMed: 27802058
DOI: 10.1021/ACS.INORGCHEM.6B02041
Page generated: Wed Dec 16 02:28:19 2020

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