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Sodium in PDB 3k08: Crystal Structure of Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex

Protein crystallography data

The structure of Crystal Structure of Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex, PDB code: 3k08 was solved by Y.Jiang, M.G.Derebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 1.62
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 67.780, 67.780, 89.511, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 22.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex (pdb code 3k08). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex, PDB code: 3k08:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 3k08

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Sodium binding site 1 out of 10 in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex


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 Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2

b:13.8
occ:0.25
 NA A:NA5 2.1 32.4 0.2
O A:THR63 2.3 14.6 1.0
C A:THR63 3.5 15.9 1.0
O A:VAL64 3.7 14.2 1.0
NA A:NA8 3.9 55.4 0.2
NA A:NA4 4.0 17.0 0.2
C A:VAL64 4.1 14.5 1.0
CA A:VAL64 4.2 16.1 1.0
OG1 A:THR63 4.3 14.9 1.0
N A:VAL64 4.3 12.8 1.0
CB A:THR63 4.3 15.5 1.0
CA A:THR63 4.5 15.9 1.0
N A:GLY65 4.9 13.8 1.0

Sodium binding site 2 out of 10 in 3k08

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Sodium binding site 2 out of 10 in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex


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 Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na4

b:17.0
occ:0.25
 OG1 A:THR63 2.4 14.9 1.0
O A:HOH1 2.5 33.7 0.2
CB A:THR63 3.4 15.5 1.0
NA A:NA2 4.0 13.8 0.2
O A:THR63 4.2 14.6 1.0
CG2 A:THR63 4.2 17.2 1.0
C A:THR63 4.6 15.9 1.0
CA A:THR63 4.6 15.9 1.0
O A:THR62 4.7 17.6 1.0

Sodium binding site 3 out of 10 in 3k08

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Sodium binding site 3 out of 10 in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex


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 Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na5

b:32.4
occ:0.25
 NA A:NA8 1.9 55.4 0.2
NA A:NA2 2.1 13.8 0.2
O A:VAL64 2.9 14.2 1.0
O A:THR63 3.4 14.6 1.0
C A:VAL64 3.7 14.5 1.0
NA A:NA7 3.8 33.0 0.2
O A:GLY65 4.3 15.7 1.0
N A:GLY65 4.4 13.8 1.0
CA A:GLY65 4.4 15.9 1.0
C A:THR63 4.5 15.9 1.0
C A:GLY65 4.5 16.2 1.0
CA A:VAL64 4.5 16.1 1.0

Sodium binding site 4 out of 10 in 3k08

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Sodium binding site 4 out of 10 in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex


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 Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na6

b:41.4
occ:0.25
 O A:HOH114 2.3 38.8 1.0
NA A:NA7 2.5 33.0 0.2
O A:GLY65 4.3 15.7 1.0
O A:HOH119 4.4 33.2 1.0
NA A:NA8 4.5 55.4 0.2
O A:THR67 4.7 16.3 1.0
CA A:ASN66 4.9 14.9 1.0

Sodium binding site 5 out of 10 in 3k08

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Sodium binding site 5 out of 10 in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex


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 Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na7

b:33.0
occ:0.25
 NA A:NA8 2.0 55.4 0.2
NA A:NA6 2.5 41.4 0.2
O A:GLY65 2.9 15.7 1.0
O A:HOH114 3.4 38.8 1.0
NA A:NA5 3.8 32.4 0.2
C A:GLY65 4.0 16.2 1.0
CA A:ASN66 4.4 14.9 1.0
O A:VAL64 4.5 14.2 1.0
N A:ASN66 4.6 14.3 1.0
CA A:GLY65 5.0 15.9 1.0

Sodium binding site 6 out of 10 in 3k08

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Sodium binding site 6 out of 10 in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex


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 Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na8

b:55.4
occ:0.25
 NA A:NA5 1.9 32.4 0.2
NA A:NA7 2.0 33.0 0.2
O A:GLY65 3.2 15.7 1.0
O A:VAL64 3.2 14.2 1.0
C A:GLY65 3.8 16.2 1.0
NA A:NA2 3.9 13.8 0.2
C A:VAL64 4.3 14.5 1.0
CA A:GLY65 4.3 15.9 1.0
NA A:NA6 4.5 41.4 0.2
N A:ASN66 4.6 14.3 1.0
N A:GLY65 4.8 13.8 1.0
CA A:ASN66 4.9 14.9 1.0
O A:THR63 4.9 14.6 1.0

Sodium binding site 7 out of 10 in 3k08

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Sodium binding site 7 out of 10 in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1

b:21.2
occ:0.25
 NA B:NA10 2.0 70.7 0.2
O B:THR63 2.4 24.3 1.0
C B:THR63 3.6 24.2 1.0
O B:VAL64 3.6 24.5 1.0
C B:VAL64 4.0 25.9 1.0
NA B:NA3 4.1 22.2 0.2
CA B:VAL64 4.2 24.8 1.0
N B:VAL64 4.4 21.4 1.0
OG1 B:THR63 4.4 21.3 1.0
CB B:THR63 4.5 23.8 1.0
CA B:THR63 4.6 22.1 1.0
N B:GLY65 4.9 24.4 1.0

Sodium binding site 8 out of 10 in 3k08

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Sodium binding site 8 out of 10 in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3

b:22.2
occ:0.25
 OG1 B:THR63 2.5 21.3 1.0
O B:HOH115 2.7 42.6 0.2
CB B:THR63 3.5 23.8 1.0
NA B:NA1 4.1 21.2 0.2
O B:THR63 4.1 24.3 1.0
CG2 B:THR63 4.3 19.8 1.0
C B:THR63 4.6 24.2 1.0
CA B:THR63 4.7 22.1 1.0
O B:THR62 4.8 19.9 1.0

Sodium binding site 9 out of 10 in 3k08

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Sodium binding site 9 out of 10 in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na9

b:68.3
occ:0.25
 O B:GLY65 3.0 28.9 1.0
NA B:NA10 3.4 70.7 0.2
C B:GLY65 3.9 29.2 1.0
O B:VAL64 4.3 24.5 1.0
CA B:ASN66 4.4 29.1 1.0
N B:ASN66 4.6 27.2 1.0
CA B:GLY65 4.9 27.9 1.0

Sodium binding site 10 out of 10 in 3k08

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Sodium binding site 10 out of 10 in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Cng Mimicking Nak Mutant, Nak-Ntpp, Na+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na10

b:70.7
occ:0.25
 NA B:NA1 2.0 21.2 0.2
O B:VAL64 2.8 24.5 1.0
NA B:NA9 3.4 68.3 0.2
O B:THR63 3.5 24.3 1.0
C B:VAL64 3.7 25.9 1.0
O B:GLY65 4.2 28.9 1.0
N B:GLY65 4.5 24.4 1.0
C B:GLY65 4.5 29.2 1.0
CA B:GLY65 4.5 27.9 1.0
CA B:VAL64 4.6 24.8 1.0
C B:THR63 4.6 24.2 1.0

Reference:

M.G.Derebe, W.Zeng, Y.Li, A.Alam, Y.Jiang. Structural Studies of Ion Permeation and CA2+ Blockage of A Bacterial Channel Mimicking the Cyclic Nucleotide-Gated Channel Pore. Proc.Natl.Acad.Sci.Usa V. 108 592 2011.
ISSN: ISSN 0027-8424
PubMed: 21187429
DOI: 10.1073/PNAS.1013643108
Page generated: Mon Oct 7 11:07:13 2024

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