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Sodium in PDB 6su0: Crystal Structure of Dimethylated Rslex in Complex with Cucurbit[7]Uril

Protein crystallography data

The structure of Crystal Structure of Dimethylated Rslex in Complex with Cucurbit[7]Uril, PDB code: 6su0 was solved by F.Guagnini, S.Engilberge, P.B.Crowley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.32 / 1.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 54.638, 94.534, 149.649, 90.00, 90.06, 90.00
R / Rfree (%) 24.7 / 31.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Dimethylated Rslex in Complex with Cucurbit[7]Uril (pdb code 6su0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Dimethylated Rslex in Complex with Cucurbit[7]Uril, PDB code: 6su0:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6su0

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Sodium binding site 1 out of 6 in the Crystal Structure of Dimethylated Rslex in Complex with Cucurbit[7]Uril


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Dimethylated Rslex in Complex with Cucurbit[7]Uril within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:24.1
occ:1.00
O03 K:QQ7201 2.9 14.2 1.0
O05 K:QQ7201 3.1 13.7 1.0
C13 K:QQ7201 3.7 23.9 1.0
C11 K:QQ7201 3.8 17.3 1.0
C16 K:QQ7201 4.1 13.3 1.0
N07 K:QQ7201 4.2 21.7 1.0
N10 K:QQ7201 4.4 12.8 1.0
O K:HOH315 4.7 26.8 1.0
O K:HOH301 4.8 26.9 1.0

Sodium binding site 2 out of 6 in 6su0

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Sodium binding site 2 out of 6 in the Crystal Structure of Dimethylated Rslex in Complex with Cucurbit[7]Uril


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Dimethylated Rslex in Complex with Cucurbit[7]Uril within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:20.7
occ:1.00
O12 J:QQ7201 3.0 16.5 1.0
O09 J:QQ7201 3.2 12.8 1.0
C26 J:QQ7201 4.0 24.0 1.0
C29 J:QQ7201 4.0 13.7 1.0
O J:HOH319 4.0 30.0 1.0
C25 J:QQ7201 4.2 16.4 1.0
O J:HOH327 4.4 31.0 1.0
N21 J:QQ7201 4.5 21.5 1.0
N19 J:QQ7201 4.6 17.9 1.0

Sodium binding site 3 out of 6 in 6su0

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Sodium binding site 3 out of 6 in the Crystal Structure of Dimethylated Rslex in Complex with Cucurbit[7]Uril


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Dimethylated Rslex in Complex with Cucurbit[7]Uril within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:19.7
occ:1.00
O09 C:QQ7204 2.9 14.5 1.0
O08 C:QQ7204 3.2 11.7 1.0
C40 C:QQ7204 3.7 28.5 1.0
C25 C:QQ7204 3.9 17.0 1.0
O C:HOH329 4.0 46.6 1.0
O C:HOH324 4.1 32.4 1.0
C20 C:QQ7204 4.1 17.0 1.0
N18 C:QQ7204 4.2 21.8 1.0
N16 C:QQ7204 4.4 22.7 1.0

Sodium binding site 4 out of 6 in 6su0

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Sodium binding site 4 out of 6 in the Crystal Structure of Dimethylated Rslex in Complex with Cucurbit[7]Uril


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Dimethylated Rslex in Complex with Cucurbit[7]Uril within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na203

b:22.8
occ:1.00
O04 C:QQ7204 2.9 15.2 1.0
O01 C:QQ7204 3.1 14.1 1.0
C03 C:QQ7204 3.7 32.4 1.0
C10 C:QQ7204 3.8 19.8 1.0
C05 C:QQ7204 4.1 13.9 1.0
N05 C:QQ7204 4.2 27.9 1.0
N03 C:QQ7204 4.4 21.0 1.0
O C:HOH324 4.7 32.4 1.0
O C:HOH307 4.8 23.4 1.0

Sodium binding site 5 out of 6 in 6su0

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Sodium binding site 5 out of 6 in the Crystal Structure of Dimethylated Rslex in Complex with Cucurbit[7]Uril


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Dimethylated Rslex in Complex with Cucurbit[7]Uril within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:52.4
occ:1.00
O N:HOH309 2.9 46.8 1.0
O02 N:QQ7201 3.0 44.1 1.0
O03 N:QQ7201 3.0 42.8 1.0
O N:HOH304 3.4 46.5 1.0
C11 N:QQ7201 4.0 43.3 1.0
C08 N:QQ7201 4.1 41.2 1.0
C06 N:QQ7201 4.1 41.6 1.0
N06 N:QQ7201 4.5 41.3 1.0
N04 N:QQ7201 4.6 43.8 1.0

Sodium binding site 6 out of 6 in 6su0

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Sodium binding site 6 out of 6 in the Crystal Structure of Dimethylated Rslex in Complex with Cucurbit[7]Uril


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Dimethylated Rslex in Complex with Cucurbit[7]Uril within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na201

b:75.1
occ:1.00
O O:QQ7202 2.2 44.4 1.0
O12 O:QQ7202 3.2 46.7 1.0
C35 O:QQ7202 3.4 49.0 1.0
C33 O:QQ7202 4.0 55.0 1.0
O O:HOH308 4.1 47.8 1.0
N25 O:QQ7202 4.1 52.1 1.0
C29 O:QQ7202 4.2 51.7 1.0
O06 O:QQ7202 4.4 43.3 1.0
N O:QQ7202 4.5 43.9 1.0
N24 O:QQ7202 4.6 55.1 1.0
C41 O:QQ7202 4.8 47.8 1.0

Reference:

F.Guagnini, S.Engilberge, K.O.Ramberg, J.Perez, P.B.Crowley. Engineered Assembly of A Protein-Cucurbituril Biohybrid. Chem.Commun.(Camb.) V. 56 360 2020.
ISSN: ESSN 1364-548X
PubMed: 31825399
DOI: 10.1039/C9CC07198A
Page generated: Tue Oct 8 13:31:41 2024

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