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Sodium in PDB 7eqm: Apo Truncated Vhchip (Delta 1-19)

Protein crystallography data

The structure of Apo Truncated Vhchip (Delta 1-19), PDB code: 7eqm was solved by A.Aunkham, S.Sanram, W.Suginta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.244, 151.388, 95.827, 90, 111.12, 90
R / Rfree (%) 17.8 / 22.5

Other elements in 7eqm:

The structure of Apo Truncated Vhchip (Delta 1-19) also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Apo Truncated Vhchip (Delta 1-19) (pdb code 7eqm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Apo Truncated Vhchip (Delta 1-19), PDB code: 7eqm:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 7eqm

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Sodium binding site 1 out of 12 in the Apo Truncated Vhchip (Delta 1-19)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apo Truncated Vhchip (Delta 1-19) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:31.1
occ:1.00
 O A:PRO82 2.3 27.1 1.0
O A:HOH550 2.3 29.3 1.0
O A:HOH527 2.5 24.7 1.0
O A:GLY85 2.5 34.5 1.0
OD1 A:ASP81 2.6 31.9 1.0
O A:HOH557 2.9 34.5 1.0
C A:PRO82 3.3 27.9 1.0
CG A:ASP81 3.5 30.0 1.0
C A:GLY85 3.6 29.8 1.0
O A:ASP81 3.6 22.8 1.0
C A:ASP81 3.7 28.8 1.0
N A:GLY85 3.8 33.1 1.0
N A:SER83 4.0 22.9 1.0
N A:PRO82 4.0 30.1 1.0
CA A:SER83 4.0 27.9 1.0
CA A:GLY85 4.2 27.2 1.0
CA A:PRO82 4.2 26.2 1.0
OD2 A:ASP81 4.3 28.6 1.0
O A:LEU50 4.3 29.3 1.0
O B:GLY177 4.3 26.8 1.0
CA A:ASP81 4.3 29.7 1.0
C A:SER83 4.3 25.8 1.0
ND2 B:ASN151 4.4 24.1 1.0
CB A:ASP81 4.4 27.4 1.0
OD1 B:ASN151 4.4 30.6 1.0
N A:PHE84 4.5 24.3 1.0
N A:GLY86 4.7 30.3 1.0
CD A:PRO82 4.8 24.4 1.0
C A:GLY86 4.8 33.0 1.0
O A:GLY86 4.8 32.6 1.0
OE1 A:GLN49 4.8 30.0 1.0
CG B:ASN151 4.8 27.8 1.0
CA A:GLY86 4.9 28.3 1.0
O A:SER83 4.9 30.0 1.0
C A:PHE84 5.0 30.5 1.0
CB B:SER150 5.0 24.4 1.0

Sodium binding site 2 out of 12 in 7eqm

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Sodium binding site 2 out of 12 in the Apo Truncated Vhchip (Delta 1-19)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Apo Truncated Vhchip (Delta 1-19) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:34.4
occ:1.00
 O A:HOH584 2.1 26.3 1.0
O A:HOH526 2.2 25.6 1.0
OD2 A:ASP156 2.2 29.2 1.0
OD1 A:ASP167 2.3 28.3 1.0
O A:HOH568 2.4 32.1 1.0
CG A:ASP156 3.3 29.8 1.0
CG A:ASP167 3.4 30.4 1.0
CB A:ASP156 3.8 24.4 1.0
OD2 A:ASP167 3.9 29.8 1.0
NH2 A:ARG154 4.0 27.4 1.0
OD1 A:ASP156 4.4 29.2 1.0
O A:ILE166 4.4 28.1 1.0
CA A:ASP156 4.5 28.2 1.0
CB A:ASP167 4.6 27.6 1.0
O A:SER157 4.8 33.8 1.0
OG A:SER165 4.9 36.0 1.0
CB A:SER165 5.0 30.2 1.0
C A:ILE166 5.0 28.2 1.0

Sodium binding site 3 out of 12 in 7eqm

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Sodium binding site 3 out of 12 in the Apo Truncated Vhchip (Delta 1-19)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Apo Truncated Vhchip (Delta 1-19) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:57.0
occ:1.00
 OD1 A:ASP33 2.9 40.6 1.0
O A:TYR34 3.1 43.9 1.0
CG A:ASP33 3.9 40.3 1.0
OD2 A:ASP33 4.1 48.0 1.0
C A:TYR34 4.2 40.4 1.0
OD2 A:ASP42 4.3 46.9 1.0
CG A:ASP42 4.9 44.2 1.0
CB A:ASP42 4.9 36.6 1.0
O A:HOH532 4.9 27.6 1.0
CA A:ASP35 4.9 40.3 1.0
N A:TYR34 5.0 30.7 1.0

Sodium binding site 4 out of 12 in 7eqm

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Sodium binding site 4 out of 12 in the Apo Truncated Vhchip (Delta 1-19)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Apo Truncated Vhchip (Delta 1-19) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:47.7
occ:1.00
 O A:HOH594 2.4 38.4 1.0
O A:HOH503 2.4 36.0 1.0
OD1 A:ASN289 3.5 43.1 1.0
OD2 A:ASP279 4.0 39.9 1.0
N A:ASN289 4.1 36.4 1.0
CA A:ASN289 4.3 36.8 1.0
OD1 A:ASP279 4.3 40.5 1.0
CG A:ASN289 4.5 44.6 1.0
CG A:ASP279 4.6 38.8 1.0
OG A:SER291 4.6 34.6 1.0
CB A:ASN289 5.0 39.8 1.0

Sodium binding site 5 out of 12 in 7eqm

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Sodium binding site 5 out of 12 in the Apo Truncated Vhchip (Delta 1-19)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Apo Truncated Vhchip (Delta 1-19) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:42.4
occ:1.00
 O A:HOH596 2.2 41.9 1.0
O A:PHE318 2.4 34.5 1.0
OD2 A:ASP338 2.6 34.1 1.0
OD1 A:ASP338 2.6 33.0 1.0
OD1 A:ASP317 2.7 35.5 1.0
CG A:ASP338 3.0 29.3 1.0
N A:PHE318 3.4 30.4 1.0
C A:PHE318 3.5 31.0 1.0
CG A:ASP317 3.9 37.5 1.0
CA A:PHE318 4.0 28.7 1.0
C A:ASP317 4.1 32.0 1.0
O A:ASN319 4.4 38.0 1.0
O A:HOH578 4.4 35.6 1.0
CA A:ASP317 4.4 31.7 1.0
CG A:GLU320 4.5 37.1 1.0
CB A:ASP338 4.5 30.9 1.0
O A:HOH593 4.6 34.3 1.0
N A:ASN319 4.6 34.0 1.0
CB A:PHE318 4.7 30.6 1.0
C A:ASN319 4.7 35.3 1.0
OD2 A:ASP317 4.7 34.4 1.0
CB A:ASP317 4.8 32.3 1.0
OE2 A:GLU320 4.8 67.1 1.0
O A:ASP317 4.8 37.7 1.0

Sodium binding site 6 out of 12 in 7eqm

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Sodium binding site 6 out of 12 in the Apo Truncated Vhchip (Delta 1-19)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Apo Truncated Vhchip (Delta 1-19) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:33.8
occ:1.00
 O A:HOH558 2.3 27.5 1.0
O A:GLY46 2.4 30.3 1.0
O B:GLY181 2.4 31.9 1.0
O A:ASN44 2.6 34.2 1.0
O A:ASP43 2.6 38.3 1.0
C A:ASN44 3.2 38.3 1.0
C B:GLY181 3.5 33.7 1.0
C A:GLY46 3.6 30.6 1.0
CA A:ASN44 3.7 34.6 1.0
C A:ASP43 3.7 38.9 1.0
N A:GLY46 4.0 33.3 1.0
N A:ASN44 4.1 35.0 1.0
CA B:ASP182 4.1 34.8 1.0
C A:LEU45 4.2 30.3 1.0
N A:LEU45 4.2 38.9 1.0
O A:HOH589 4.2 37.7 1.0
N B:ASP182 4.2 38.7 1.0
CB B:ALA176 4.3 24.4 1.0
CA B:ALA176 4.3 27.2 1.0
O A:HOH554 4.3 35.4 1.0
CA A:GLY46 4.4 29.9 1.0
CB B:ASP182 4.4 31.5 1.0
N B:GLY181 4.4 31.6 1.0
O B:ALA176 4.5 27.4 1.0
O A:LEU45 4.5 33.4 1.0
CA B:GLY181 4.6 31.6 1.0
N A:GLY47 4.6 32.0 1.0
CA A:LEU45 4.6 32.4 1.0
CA A:GLY47 4.7 32.3 1.0
CA B:GLY179 4.8 30.4 1.0
C B:ALA176 4.9 30.2 1.0
C B:GLY179 5.0 34.6 1.0

Sodium binding site 7 out of 12 in 7eqm

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Sodium binding site 7 out of 12 in the Apo Truncated Vhchip (Delta 1-19)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Apo Truncated Vhchip (Delta 1-19) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:31.1
occ:1.00
 O B:HOH548 2.2 24.9 1.0
O B:HOH506 2.3 22.3 1.0
OD1 B:ASP167 2.3 30.3 1.0
OD2 B:ASP156 2.3 30.2 1.0
O B:HOH598 2.4 28.9 1.0
CG B:ASP167 3.1 28.7 1.0
OD2 B:ASP167 3.3 29.0 1.0
CG B:ASP156 3.4 32.5 1.0
CB B:ASP156 3.8 29.1 1.0
NH2 B:ARG154 4.0 32.6 1.0
O B:HOH604 4.1 37.1 1.0
CB B:ASP167 4.4 28.7 1.0
OD1 B:ASP156 4.5 28.7 1.0
CA B:ASP156 4.5 27.5 1.0
O B:ILE166 4.6 29.9 1.0
OG B:SER165 4.8 32.4 1.0
O B:SER157 4.8 23.9 1.0
NE2 B:HIS191 4.9 29.0 1.0

Sodium binding site 8 out of 12 in 7eqm

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Sodium binding site 8 out of 12 in the Apo Truncated Vhchip (Delta 1-19)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Apo Truncated Vhchip (Delta 1-19) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:34.2
occ:1.00
 O B:GLY85 2.2 27.6 1.0
O B:HOH566 2.4 25.8 1.0
OD1 B:ASP81 2.5 26.9 1.0
O B:PRO82 2.5 28.2 1.0
O C:HOH508 2.6 30.3 1.0
O B:HOH519 3.1 28.5 1.0
C B:GLY85 3.3 31.6 1.0
C B:PRO82 3.5 31.8 1.0
CG B:ASP81 3.5 31.7 1.0
O B:ASP81 3.6 28.3 1.0
C B:ASP81 3.7 31.4 1.0
N B:GLY85 3.9 31.8 1.0
N B:PRO82 4.1 30.2 1.0
CA B:GLY85 4.1 29.1 1.0
CA B:ASP81 4.1 28.7 1.0
CB B:ASP81 4.2 29.1 1.0
N B:SER83 4.2 28.4 1.0
CA B:SER83 4.2 28.3 1.0
ND2 C:ASN151 4.4 24.0 1.0
O C:GLY177 4.4 28.8 1.0
OD2 B:ASP81 4.4 31.9 1.0
N B:GLY86 4.4 26.5 1.0
CA B:PRO82 4.4 28.2 1.0
O B:GLY86 4.5 28.6 1.0
C B:GLY86 4.5 27.4 1.0
O B:LEU50 4.5 29.5 1.0
C B:SER83 4.6 31.5 1.0
CA B:GLY86 4.6 26.6 1.0
N B:PHE84 4.6 31.2 1.0
CD B:PRO82 4.6 26.1 1.0
OD1 C:ASN151 4.6 25.8 1.0
CB C:SER150 4.8 28.8 1.0
O C:HOH588 4.9 29.3 1.0
CG C:ASN151 4.9 26.5 1.0
N B:GLU87 5.0 25.1 1.0

Sodium binding site 9 out of 12 in 7eqm

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Sodium binding site 9 out of 12 in the Apo Truncated Vhchip (Delta 1-19)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Apo Truncated Vhchip (Delta 1-19) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:34.2
occ:1.00
 O B:HOH597 2.4 32.2 1.0
O B:GLY46 2.4 33.5 1.0
O C:GLY181 2.6 38.7 1.0
O B:ASN44 2.6 33.0 1.0
O B:ASP43 2.6 39.0 1.0
C B:ASN44 3.4 36.5 1.0
C B:GLY46 3.7 36.3 1.0
C C:GLY181 3.7 34.4 1.0
C B:ASP43 3.8 40.1 1.0
CA B:ASN44 3.8 37.1 1.0
O B:HOH530 4.0 25.5 1.0
CA C:ASP182 4.1 34.3 1.0
N B:GLY46 4.3 35.4 1.0
N B:ASN44 4.3 36.5 1.0
CB C:ALA176 4.3 28.9 1.0
C B:LEU45 4.3 36.3 1.0
CA C:ALA176 4.3 31.9 1.0
N B:LEU45 4.3 37.3 1.0
N C:ASP182 4.4 32.4 1.0
CB C:ASP182 4.5 35.1 1.0
N B:GLY47 4.6 37.0 1.0
O B:LEU45 4.6 36.7 1.0
CA B:GLY47 4.6 31.9 1.0
CA B:GLY46 4.6 33.2 1.0
O C:ALA176 4.6 39.8 1.0
O B:HOH533 4.7 35.9 1.0
N C:GLY181 4.7 37.4 1.0
CA B:LEU45 4.8 37.1 1.0
CA C:GLY181 4.9 36.2 1.0
CA C:GLY179 5.0 30.9 1.0
CA B:ASP43 5.0 41.9 1.0

Sodium binding site 10 out of 12 in 7eqm

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Sodium binding site 10 out of 12 in the Apo Truncated Vhchip (Delta 1-19)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Apo Truncated Vhchip (Delta 1-19) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:28.0
occ:1.00
 O C:HOH541 2.2 23.8 1.0
O C:HOH548 2.2 32.8 1.0
OD2 C:ASP156 2.3 35.9 1.0
OD1 C:ASP167 2.3 30.1 1.0
O C:HOH502 2.4 30.9 1.0
CG C:ASP167 3.3 33.7 1.0
CG C:ASP156 3.4 38.0 1.0
OD2 C:ASP167 3.6 32.5 1.0
CB C:ASP156 3.8 33.1 1.0
NH2 C:ARG154 4.2 29.7 1.0
OD1 C:ASP156 4.4 29.7 1.0
CA C:ASP156 4.6 29.1 1.0
CB C:ASP167 4.6 28.9 1.0
OG C:SER165 4.6 29.2 1.0
O C:ILE166 4.8 33.2 1.0
O C:SER157 4.9 29.4 1.0
CB C:SER165 5.0 30.5 1.0

Reference:

A.Aunkham, S.Sanram, W.Suginta. Structure and Functionof Truncated Vhchip To Be Published.
Page generated: Tue Oct 8 16:42:28 2024

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