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Sodium in PDB 8zxi: Peptide Channel Interactions in the Truncated Vhchip Nanopore

Protein crystallography data

The structure of Peptide Channel Interactions in the Truncated Vhchip Nanopore, PDB code: 8zxi was solved by S.Sanram, W.Suginta, R.C.Robinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.87 / 3.12
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.085, 182.602, 196.808, 90, 90, 90
R / Rfree (%) 19.5 / 25.2

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Sodium atom in the Peptide Channel Interactions in the Truncated Vhchip Nanopore (pdb code 8zxi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 16 binding sites of Sodium where determined in the Peptide Channel Interactions in the Truncated Vhchip Nanopore, PDB code: 8zxi:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in 8zxi

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Sodium binding site 1 out of 16 in the Peptide Channel Interactions in the Truncated Vhchip Nanopore


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Peptide Channel Interactions in the Truncated Vhchip Nanopore within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:13.3
occ:1.00
 OE1 A:GLN149 2.3 19.6 1.0
OE1 A:GLN146 2.3 23.1 1.0
OD1 A:ASP174 2.5 24.8 1.0
OD2 A:ASP174 3.1 27.0 1.0
CG A:ASP174 3.2 25.4 1.0
CD A:GLN149 3.3 23.5 1.0
CD A:GLN146 3.5 21.8 1.0
OD1 A:ASP147 3.6 24.7 1.0
NE2 A:GLN149 3.7 24.5 1.0
O A:ARG148 3.9 17.9 1.0
CB A:GLN146 4.2 26.8 1.0
NE2 A:GLN146 4.3 26.4 1.0
CG A:GLN146 4.4 20.2 1.0
CA A:GLN146 4.5 21.3 1.0
N A:ASP147 4.5 20.4 1.0
O A:HOH518 4.6 16.3 1.0
CG A:GLN149 4.6 18.6 1.0
CG A:ASP147 4.7 27.0 1.0
CB A:ASP174 4.7 20.7 1.0
CB A:GLN149 4.9 15.8 1.0
C A:ARG148 4.9 17.2 1.0

Sodium binding site 2 out of 16 in 8zxi

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Sodium binding site 2 out of 16 in the Peptide Channel Interactions in the Truncated Vhchip Nanopore


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Peptide Channel Interactions in the Truncated Vhchip Nanopore within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:14.3
occ:1.00
 OD2 A:ASP156 2.6 54.4 1.0
CG A:ASP156 3.4 39.0 1.0
OD1 A:ASP156 3.9 31.1 1.0
OG A:SER165 4.0 37.6 1.0
CB A:ASP167 4.1 19.4 1.0
CB A:ASP156 4.4 33.9 1.0
CE1 A:HIS191 4.6 38.0 1.0
O A:ILE166 4.7 37.2 1.0
ND1 A:HIS191 4.8 39.0 1.0
CB A:SER165 4.9 37.9 1.0
CA A:ASP167 5.0 29.7 1.0

Sodium binding site 3 out of 16 in 8zxi

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Sodium binding site 3 out of 16 in the Peptide Channel Interactions in the Truncated Vhchip Nanopore


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Peptide Channel Interactions in the Truncated Vhchip Nanopore within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:30.4
occ:1.00
 O A:PRO82 2.1 27.1 1.0
O A:HOH508 2.5 21.6 1.0
O A:GLY85 2.8 30.1 1.0
OD1 A:ASP81 2.9 29.8 1.0
C A:PRO82 3.1 21.8 1.0
CA A:SER83 3.5 23.2 1.0
O A:ASP81 3.7 16.1 1.0
N A:SER83 3.7 19.6 1.0
N A:GLY85 3.9 23.2 1.0
C A:GLY85 3.9 27.4 1.0
C A:SER83 4.0 25.6 1.0
N A:PHE84 4.0 24.6 1.0
CG A:ASP81 4.0 33.1 1.0
C A:ASP81 4.0 19.8 1.0
O A:LEU50 4.1 24.4 1.0
N A:PRO82 4.3 23.6 1.0
CA A:PRO82 4.3 23.9 1.0
CA A:GLY85 4.5 22.8 1.0
OE1 A:GLN49 4.5 26.1 1.0
CA A:ASP81 4.8 22.4 1.0
O A:SER83 4.8 22.9 1.0
CB A:SER83 4.8 22.4 1.0
OD2 A:ASP81 4.8 30.6 1.0
CB A:ASP81 4.9 27.9 1.0
C A:PHE84 4.9 23.5 1.0
O A:GLY86 4.9 31.5 1.0
CA A:PHE84 4.9 23.4 1.0
N A:GLY86 5.0 30.0 1.0

Sodium binding site 4 out of 16 in 8zxi

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Sodium binding site 4 out of 16 in the Peptide Channel Interactions in the Truncated Vhchip Nanopore


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Peptide Channel Interactions in the Truncated Vhchip Nanopore within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:18.9
occ:1.00
 OD1 B:ASP167 2.2 33.7 1.0
OD2 B:ASP167 2.9 29.3 1.0
CG B:ASP167 2.9 33.3 1.0
OD2 B:ASP156 2.9 39.8 1.0
CG B:ASP156 3.6 30.3 1.0
CB B:ASP156 4.0 30.1 1.0
O B:HOH545 4.0 22.0 1.0
O B:ILE166 4.3 28.3 1.0
O B:SER157 4.4 38.0 1.0
OD1 B:ASP156 4.4 28.6 1.0
CB B:ASP167 4.5 22.7 1.0
NH2 B:ARG154 4.6 28.4 1.0
CA B:ASP156 4.7 31.5 1.0
CB B:SER165 4.7 38.9 1.0
O B:HOH542 4.8 20.7 1.0
NE2 B:HIS191 4.9 42.3 1.0
C B:ILE166 4.9 29.5 1.0

Sodium binding site 5 out of 16 in 8zxi

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Sodium binding site 5 out of 16 in the Peptide Channel Interactions in the Truncated Vhchip Nanopore


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Peptide Channel Interactions in the Truncated Vhchip Nanopore within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:36.7
occ:1.00
 O B:GLY85 2.3 38.5 1.0
O B:PRO82 2.7 33.9 1.0
OD1 B:ASP81 2.9 38.2 1.0
C B:GLY85 3.5 35.9 1.0
O F:GLY177 3.6 39.3 1.0
C B:PRO82 3.8 32.4 1.0
CG B:ASP81 3.9 42.2 1.0
N B:GLY85 3.9 39.0 1.0
OD1 F:ASN151 3.9 29.0 1.0
CA B:SER83 4.2 32.1 1.0
ND2 F:ASN151 4.3 27.1 1.0
CA B:GLY85 4.3 35.9 1.0
O B:ASP81 4.3 34.0 1.0
OE1 B:GLN49 4.3 37.5 1.0
OD2 B:ASP81 4.3 45.9 1.0
N B:PHE84 4.4 28.7 1.0
N B:SER83 4.5 31.8 1.0
CB F:SER150 4.5 27.9 1.0
O B:LEU50 4.5 31.1 1.0
N B:GLY86 4.5 34.1 1.0
C B:ASP81 4.5 35.5 1.0
CG F:ASN151 4.5 31.0 1.0
C B:SER83 4.6 28.4 1.0
OG F:SER150 4.6 31.4 1.0
CA B:GLY86 4.7 36.6 1.0
C F:GLY177 4.7 37.6 1.0
C B:GLY86 4.8 34.1 1.0
N B:PRO82 4.8 32.6 1.0
CA B:PRO82 4.9 29.9 1.0
O B:GLY86 5.0 34.6 1.0
CB B:ASP81 5.0 33.7 1.0

Sodium binding site 6 out of 16 in 8zxi

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Sodium binding site 6 out of 16 in the Peptide Channel Interactions in the Truncated Vhchip Nanopore


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Peptide Channel Interactions in the Truncated Vhchip Nanopore within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:34.2
occ:1.00
 O F:GLY181 2.3 32.1 1.0
O B:GLY46 2.5 37.4 1.0
O B:ASN44 2.8 37.0 1.0
O B:ASP43 3.2 40.9 1.0
C F:GLY181 3.5 35.2 1.0
CB F:ALA176 3.7 33.6 1.0
C B:GLY46 3.7 30.7 1.0
C B:ASN44 3.8 39.2 1.0
CA F:ASP182 3.9 40.0 1.0
CA F:ALA176 4.0 36.0 1.0
N F:ASP182 4.1 41.8 1.0
O F:ALA176 4.2 31.3 1.0
CA B:ASN44 4.3 40.7 1.0
CA B:GLY47 4.3 25.2 1.0
C B:ASP43 4.3 39.6 1.0
N B:GLY47 4.5 28.1 1.0
CB F:ASP182 4.6 46.5 1.0
C F:ALA176 4.6 32.7 1.0
N B:GLY46 4.6 28.3 1.0
C B:LEU45 4.6 28.8 1.0
O B:LEU45 4.7 33.3 1.0
CA F:GLY181 4.7 34.8 1.0
N F:GLY181 4.7 39.1 1.0
N B:ASN44 4.8 44.2 1.0
CA B:GLY46 4.8 27.7 1.0
N B:LEU45 4.8 36.4 1.0

Sodium binding site 7 out of 16 in 8zxi

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Sodium binding site 7 out of 16 in the Peptide Channel Interactions in the Truncated Vhchip Nanopore


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Peptide Channel Interactions in the Truncated Vhchip Nanopore within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na407

b:15.0
occ:1.00
 OE1 B:GLN146 2.2 27.1 1.0
OD2 B:ASP174 2.4 20.8 1.0
OE1 B:GLN149 2.4 26.2 1.0
CG B:ASP174 3.1 25.9 1.0
OD1 B:ASP174 3.1 29.1 1.0
CD B:GLN149 3.3 26.0 1.0
O B:ASP147 3.4 43.2 1.0
CD B:GLN146 3.4 22.4 1.0
CG B:GLN149 3.7 25.7 1.0
OD1 B:ASP147 4.0 47.5 1.0
O B:ARG148 4.1 26.2 1.0
NE2 B:GLN146 4.3 23.9 1.0
NE2 B:GLN149 4.3 22.8 1.0
OD2 B:ASP147 4.3 41.9 1.0
N B:ASP147 4.3 29.9 1.0
CG B:ASP147 4.4 41.1 1.0
CG B:GLN146 4.5 22.0 1.0
CB B:GLN146 4.5 22.1 1.0
C B:ASP147 4.5 44.4 1.0
CB B:ASP174 4.6 16.5 1.0
CA B:GLN146 4.8 26.4 1.0
C B:ARG148 4.8 25.3 1.0
CB B:GLN149 4.9 18.4 1.0
CA B:GLN149 4.9 24.1 1.0

Sodium binding site 8 out of 16 in 8zxi

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Sodium binding site 8 out of 16 in the Peptide Channel Interactions in the Truncated Vhchip Nanopore


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Peptide Channel Interactions in the Truncated Vhchip Nanopore within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:14.9
occ:1.00
 O C:HOH502 2.1 34.4 1.0
O C:HOH522 2.2 25.1 1.0
O C:HOH536 2.3 33.4 1.0
OD1 C:ASP167 2.5 38.5 1.0
OD1 C:ASP156 2.6 27.8 1.0
O C:HOH518 2.6 31.6 1.0
CG C:ASP167 3.3 35.3 1.0
OD2 C:ASP167 3.5 36.8 1.0
CG C:ASP156 3.6 30.3 1.0
O C:HOH537 4.0 24.7 1.0
CB C:ASP156 4.1 35.2 1.0
NH2 C:ARG154 4.4 32.6 1.0
O C:SER157 4.5 38.8 1.0
O C:ILE166 4.6 33.1 1.0
CB C:SER165 4.6 36.6 1.0
OD2 C:ASP156 4.7 31.9 1.0
CB C:ASP167 4.7 26.4 1.0
CA C:ASP156 4.7 35.5 1.0
OG C:SER165 4.8 39.1 1.0
NE2 C:HIS191 4.9 39.8 1.0
N C:SER157 5.0 37.1 1.0

Sodium binding site 9 out of 16 in 8zxi

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Sodium binding site 9 out of 16 in the Peptide Channel Interactions in the Truncated Vhchip Nanopore


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Peptide Channel Interactions in the Truncated Vhchip Nanopore within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na404

b:22.6
occ:1.00
 OE1 D:GLN146 2.3 29.8 1.0
OD1 D:ASP174 2.4 32.6 1.0
OD2 D:ASP174 2.5 21.6 1.0
CG D:ASP174 2.8 24.8 1.0
CD D:GLN146 3.5 22.6 1.0
OD1 D:ASP147 3.6 28.2 1.0
O D:ARG148 3.7 32.6 1.0
CB D:GLN149 3.7 18.5 1.0
CA D:GLN149 4.1 28.2 1.0
NE2 D:GLN146 4.3 24.4 1.0
CB D:ASP174 4.3 15.8 1.0
C D:ARG148 4.5 25.1 1.0
CB D:GLN146 4.5 24.6 1.0
CG D:GLN146 4.6 18.2 1.0
N D:ASP147 4.6 23.6 1.0
N D:GLN149 4.7 25.9 1.0
CG D:ASP147 4.8 28.9 1.0
CA D:GLN146 4.9 24.6 1.0

Sodium binding site 10 out of 16 in 8zxi

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Sodium binding site 10 out of 16 in the Peptide Channel Interactions in the Truncated Vhchip Nanopore


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Peptide Channel Interactions in the Truncated Vhchip Nanopore within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na405

b:25.0
occ:1.00
 OD1 D:ASP167 2.2 40.5 1.0
OD1 D:ASP156 2.5 36.2 1.0
CG D:ASP167 3.1 38.6 1.0
OD2 D:ASP167 3.4 40.6 1.0
CG D:ASP156 3.6 31.4 1.0
OG D:SER165 4.0 43.1 1.0
O D:ILE166 4.1 34.1 1.0
CE1 D:HIS191 4.2 44.6 1.0
CB D:ASP156 4.3 28.7 1.0
NH2 D:ARG154 4.3 28.0 1.0
CB D:ASP167 4.5 25.3 1.0
ND1 D:HIS191 4.6 44.1 1.0
OD2 D:ASP156 4.6 29.8 1.0
C D:ILE166 4.7 34.0 1.0
O D:SER157 4.7 34.4 1.0
CB D:SER165 4.8 41.5 1.0
CA D:ASP156 4.8 32.3 1.0
CA D:ASP167 4.9 24.8 1.0
N D:ASP167 5.0 30.8 1.0

Reference:

S.Sanram, W.Suginta, R.C.Robinson. Structure and Function of Truncated Vhchip To Be Published.
Page generated: Mon Aug 18 16:32:46 2025

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