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Sodium in PDB 8juq: Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A

Protein crystallography data

The structure of Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A, PDB code: 8juq was solved by S.Sanram, W.Suginta, R.Robinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.38 / 2.21
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 99.327, 102.919, 172.58, 90, 95.29, 90
R / Rfree (%) 18.9 / 22.2

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (pdb code 8juq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 18 binding sites of Sodium where determined in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A, PDB code: 8juq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 18 in 8juq

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Sodium binding site 1 out of 18 in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A


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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:30.4
occ:1.00
 O A:PRO82 2.2 21.7 1.0
O C:HOH556 2.4 22.2 1.0
OD1 A:ASP81 2.4 30.3 1.0
O A:GLY85 2.5 26.5 1.0
O A:HOH528 2.6 18.6 1.0
O A:HOH577 3.1 37.9 1.0
C A:PRO82 3.2 21.5 1.0
O A:ASP81 3.4 16.9 1.0
CG A:ASP81 3.5 30.1 1.0
C A:GLY85 3.6 28.1 1.0
C A:ASP81 3.6 21.0 1.0
N A:PRO82 3.9 22.0 1.0
N A:GLY85 4.0 27.1 1.0
N A:SER83 4.0 19.4 1.0
CA A:SER83 4.1 20.2 1.0
OD2 A:ASP81 4.2 26.1 1.0
CA A:PRO82 4.2 19.1 1.0
CA A:ASP81 4.3 23.6 1.0
CB A:ASP81 4.3 20.8 1.0
CA A:GLY85 4.3 20.4 1.0
ND2 C:ASN151 4.4 20.2 1.0
C A:SER83 4.4 18.7 1.0
O C:GLY177 4.5 25.9 1.0
N A:PHE84 4.5 22.8 1.0
O A:LEU50 4.6 28.2 1.0
O A:GLY86 4.6 25.9 1.0
C A:GLY86 4.6 28.3 1.0
N A:GLY86 4.6 29.8 1.0
OD1 C:ASN151 4.6 20.0 1.0
CD A:PRO82 4.7 16.9 1.0
CA A:GLY86 4.8 21.5 1.0
O A:HOH516 4.9 30.4 1.0
O A:HOH615 4.9 23.5 1.0
CG C:ASN151 4.9 18.9 1.0
OE1 A:GLN49 5.0 24.3 1.0
CB C:SER150 5.0 16.1 1.0

Sodium binding site 2 out of 18 in 8juq

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Sodium binding site 2 out of 18 in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A


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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:12.8
occ:1.00
 O A:HOH563 2.2 30.0 1.0
OE1 A:GLN146 2.3 25.6 1.0
O A:HOH604 2.4 33.1 1.0
OE1 A:GLN149 2.4 19.9 1.0
O A:HOH505 2.4 19.5 1.0
OD1 A:ASP174 2.5 25.2 1.0
OD2 A:ASP174 2.6 26.5 1.0
CG A:ASP174 2.9 29.4 1.0
CD A:GLN149 3.5 21.8 1.0
CD A:GLN146 3.5 21.7 1.0
NE2 A:GLN149 3.9 22.0 1.0
CB A:GLN146 4.3 19.8 1.0
CG A:GLN146 4.4 20.5 1.0
CB A:ASP174 4.4 20.3 1.0
NE2 A:GLN146 4.5 20.4 1.0
O A:HOH624 4.5 33.8 1.0
O A:HOH588 4.5 27.7 1.0
O A:HOH610 4.5 34.5 1.0
O A:HOH593 4.6 27.5 1.0
O A:ARG148 4.6 21.9 1.0
CA A:GLN146 4.6 22.1 1.0
OD1 A:ASP147 4.7 27.7 1.0
CG A:GLN149 4.8 16.7 1.0
N A:ASP147 4.9 25.0 1.0

Sodium binding site 3 out of 18 in 8juq

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Sodium binding site 3 out of 18 in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A


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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:25.1
occ:1.00
 O A:GLY46 2.3 24.6 1.0
O A:HOH612 2.3 23.9 1.0
O A:ASN44 2.4 25.2 1.0
O A:ASP43 2.4 27.5 1.0
O C:HOH575 2.5 21.5 1.0
O C:GLY181 2.5 26.4 1.0
C A:ASN44 3.1 28.0 1.0
C A:GLY46 3.5 27.5 1.0
C A:ASP43 3.5 30.4 1.0
CA A:ASN44 3.6 29.2 1.0
C C:GLY181 3.6 26.3 1.0
N A:GLY46 3.9 23.4 1.0
N A:ASN44 4.0 27.8 1.0
O A:HOH576 4.0 24.1 1.0
N A:LEU45 4.0 25.3 1.0
CA C:ASP182 4.1 29.3 1.0
C A:LEU45 4.1 23.2 1.0
CA A:GLY46 4.3 24.4 1.0
N C:ASP182 4.3 27.3 1.0
O A:HOH620 4.3 38.7 1.0
CB C:ASP182 4.3 27.3 1.0
CB C:ALA176 4.4 22.0 1.0
CA C:ALA176 4.4 28.2 1.0
N A:GLY47 4.5 22.5 1.0
O A:LEU45 4.5 22.8 1.0
CA A:LEU45 4.6 26.0 1.0
CA A:GLY47 4.6 22.0 1.0
N C:GLY181 4.7 25.2 1.0
O C:ALA176 4.7 22.6 1.0
CA C:GLY181 4.8 24.0 1.0
CA A:ASP43 4.8 31.8 1.0
O C:HOH614 5.0 25.6 1.0
CB A:ASN44 5.0 24.9 1.0

Sodium binding site 4 out of 18 in 8juq

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Sodium binding site 4 out of 18 in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A


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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:12.3
occ:1.00
 O B:HOH550 2.0 30.7 1.0
O B:HOH607 2.1 33.8 1.0
OE1 B:GLN146 2.3 20.7 1.0
OD1 B:ASP174 2.4 26.6 1.0
OE1 B:GLN149 2.4 17.6 1.0
O B:HOH506 2.4 20.3 1.0
OD2 B:ASP174 2.7 28.9 1.0
CG B:ASP174 2.9 26.4 1.0
CD B:GLN149 3.3 16.2 1.0
CD B:GLN146 3.5 24.8 1.0
NE2 B:GLN149 3.6 18.0 1.0
CB B:GLN146 4.2 21.1 1.0
CG B:GLN146 4.3 19.0 1.0
O B:HOH620 4.3 38.1 1.0
O B:HOH605 4.4 28.4 1.0
CB B:ASP174 4.4 24.2 1.0
NE2 B:GLN146 4.5 20.6 1.0
O B:ARG148 4.5 19.1 1.0
O B:HOH596 4.5 27.4 1.0
CA B:GLN146 4.6 24.4 1.0
OD1 B:ASP147 4.6 25.0 1.0
CG B:GLN149 4.7 16.5 1.0
N B:ASP147 4.9 20.8 1.0

Sodium binding site 5 out of 18 in 8juq

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Sodium binding site 5 out of 18 in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A


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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:24.8
occ:1.00
 O B:GLY46 2.3 25.4 1.0
O B:ASN44 2.4 23.5 1.0
O B:ASP43 2.4 28.7 1.0
O A:HOH561 2.5 21.9 1.0
O B:HOH622 2.5 26.9 1.0
O A:GLY181 2.5 26.1 1.0
C B:ASN44 3.1 26.3 1.0
C B:GLY46 3.5 22.6 1.0
C B:ASP43 3.5 29.1 1.0
CA B:ASN44 3.6 24.0 1.0
C A:GLY181 3.6 27.5 1.0
N B:GLY46 3.9 25.1 1.0
O B:HOH586 4.0 26.8 1.0
CA A:ASP182 4.0 25.9 1.0
N B:LEU45 4.0 22.3 1.0
N B:ASN44 4.0 26.6 1.0
C B:LEU45 4.1 25.1 1.0
CB A:ASP182 4.1 26.9 1.0
O B:HOH625 4.1 35.0 1.0
O B:HOH535 4.1 24.9 1.0
CB A:ALA176 4.3 22.2 1.0
N A:ASP182 4.3 22.6 1.0
CA B:GLY46 4.4 23.2 1.0
CA A:ALA176 4.4 24.4 1.0
N B:GLY47 4.5 20.8 1.0
CA B:LEU45 4.5 26.4 1.0
O B:LEU45 4.6 23.4 1.0
O A:ALA176 4.7 18.7 1.0
CA B:GLY47 4.7 23.4 1.0
N A:GLY181 4.7 24.9 1.0
CA A:GLY181 4.8 21.1 1.0
CA B:ASP43 4.8 30.3 1.0
O A:HOH582 5.0 29.1 1.0
CB B:ASN44 5.0 23.2 1.0

Sodium binding site 6 out of 18 in 8juq

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Sodium binding site 6 out of 18 in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A


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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:30.0
occ:1.00
 O B:PRO82 2.2 18.6 1.0
OD1 B:ASP81 2.3 34.8 1.0
O A:HOH526 2.4 22.9 1.0
O B:GLY85 2.5 22.2 1.0
O B:HOH560 2.5 20.9 1.0
C B:PRO82 3.3 22.2 1.0
CG B:ASP81 3.4 31.6 1.0
O B:ASP81 3.5 17.5 1.0
O B:HOH595 3.5 32.8 1.0
C B:GLY85 3.6 27.4 1.0
C B:ASP81 3.6 17.6 1.0
N B:PRO82 4.0 18.6 1.0
N B:GLY85 4.0 24.6 1.0
N B:SER83 4.1 20.2 1.0
CA B:SER83 4.1 24.1 1.0
CA B:ASP81 4.2 20.1 1.0
CA B:PRO82 4.3 19.7 1.0
OD2 B:ASP81 4.3 29.1 1.0
CB B:ASP81 4.3 23.1 1.0
CA B:GLY85 4.3 20.0 1.0
ND2 A:ASN151 4.4 20.1 1.0
O B:GLY86 4.4 28.3 1.0
C B:SER83 4.5 20.8 1.0
O A:GLY177 4.5 24.1 1.0
N B:PHE84 4.5 21.5 1.0
C B:GLY86 4.5 32.6 1.0
N B:GLY86 4.6 27.3 1.0
CD B:PRO82 4.6 17.6 1.0
O B:LEU50 4.7 26.4 1.0
OD1 A:ASN151 4.7 21.5 1.0
CA B:GLY86 4.7 26.2 1.0
OE1 B:GLN49 4.9 24.9 1.0
CB A:SER150 5.0 21.6 1.0
CG A:ASN151 5.0 22.4 1.0

Sodium binding site 7 out of 18 in 8juq

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Sodium binding site 7 out of 18 in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A


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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:25.1
occ:1.00
 O C:ASP43 2.4 23.9 1.0
O C:ASN44 2.4 22.3 1.0
O B:GLY181 2.4 22.0 1.0
O C:GLY46 2.5 23.5 1.0
O C:HOH627 2.5 25.1 1.0
O B:HOH538 2.7 22.2 1.0
C C:ASN44 3.0 23.7 1.0
CA C:ASN44 3.4 25.6 1.0
C C:ASP43 3.5 27.8 1.0
C B:GLY181 3.5 23.1 1.0
C C:GLY46 3.7 20.3 1.0
N C:ASN44 3.9 23.0 1.0
O C:HOH598 3.9 36.6 1.0
CA B:ASP182 3.9 22.8 1.0
N C:LEU45 3.9 21.5 1.0
N C:GLY46 4.0 23.9 1.0
CB B:ASP182 4.1 24.2 1.0
O C:HOH585 4.1 24.1 1.0
C C:LEU45 4.1 23.8 1.0
N B:ASP182 4.2 21.5 1.0
CB B:ALA176 4.3 18.8 1.0
CA B:ALA176 4.4 18.8 1.0
CA C:GLY46 4.4 22.9 1.0
O C:HOH510 4.5 27.7 1.0
CA C:LEU45 4.5 25.0 1.0
N B:GLY181 4.6 21.0 1.0
O C:LEU45 4.6 24.8 1.0
O B:ALA176 4.7 20.8 1.0
N C:GLY47 4.7 22.4 1.0
CA B:GLY181 4.7 21.8 1.0
CA C:GLY47 4.8 26.1 1.0
CA C:ASP43 4.8 31.5 1.0
CB C:ASN44 4.9 26.0 1.0

Sodium binding site 8 out of 18 in 8juq

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Sodium binding site 8 out of 18 in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A


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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:12.9
occ:1.00
 O C:HOH607 2.3 27.8 1.0
O C:HOH616 2.3 32.6 1.0
OE1 C:GLN146 2.4 21.8 1.0
OD1 C:ASP174 2.4 28.0 1.0
OE1 C:GLN149 2.4 21.7 1.0
OD2 C:ASP174 2.5 25.8 1.0
CG C:ASP174 2.8 23.8 1.0
CD C:GLN149 3.4 23.1 1.0
CD C:GLN146 3.5 21.7 1.0
NE2 C:GLN149 3.7 22.9 1.0
CB C:GLN146 4.2 16.6 1.0
CG C:GLN146 4.3 16.1 1.0
CB C:ASP174 4.4 24.5 1.0
O C:HOH592 4.5 27.6 1.0
NE2 C:GLN146 4.5 22.1 1.0
O C:HOH595 4.5 27.0 1.0
O C:HOH594 4.6 35.3 1.0
O C:ARG148 4.6 20.0 1.0
CA C:GLN146 4.7 18.2 1.0
CG C:GLN149 4.8 17.1 1.0
O C:HOH519 5.0 37.1 1.0
N C:ASP147 5.0 19.5 1.0

Sodium binding site 9 out of 18 in 8juq

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Sodium binding site 9 out of 18 in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A


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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na404

b:22.3
occ:0.75
 O C:PRO82 2.2 18.4 1.0
OD1 C:ASP81 2.3 31.4 1.0
O C:GLY85 2.5 22.3 1.0
O C:HOH551 2.5 19.0 1.0
O C:HOH571 2.6 23.4 1.0
C C:PRO82 3.3 20.7 1.0
CG C:ASP81 3.4 32.7 1.0
O C:ASP81 3.4 19.7 1.0
C C:ASP81 3.6 18.3 1.0
C C:GLY85 3.6 25.2 1.0
N C:PRO82 3.9 16.1 1.0
N C:GLY85 4.0 27.1 1.0
O C:HOH524 4.0 35.2 1.0
N C:SER83 4.1 19.1 1.0
CA C:SER83 4.2 22.5 1.0
OD2 C:ASP81 4.2 31.4 1.0
CA C:ASP81 4.2 21.4 1.0
CA C:PRO82 4.2 21.3 1.0
CB C:ASP81 4.3 21.2 1.0
CA C:GLY85 4.4 19.2 1.0
ND2 B:ASN151 4.4 16.2 1.0
O C:GLY86 4.4 34.0 1.0
C C:SER83 4.5 22.0 1.0
C C:GLY86 4.5 33.8 1.0
O B:GLY177 4.6 23.7 1.0
N C:PHE84 4.6 20.1 1.0
O C:LEU50 4.6 28.5 1.0
OD1 B:ASN151 4.6 19.6 1.0
N C:GLY86 4.6 30.8 1.0
CD C:PRO82 4.6 17.4 1.0
CA C:GLY86 4.7 29.6 1.0
CB B:SER150 4.9 18.6 1.0
CG B:ASN151 4.9 20.0 1.0
OE1 C:GLN49 5.0 23.2 1.0

Sodium binding site 10 out of 18 in 8juq

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Sodium binding site 10 out of 18 in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A


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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na401

b:21.8
occ:1.00
 O G:HOH560 2.1 37.1 1.0
OE1 G:GLN146 2.3 27.1 1.0
O G:HOH580 2.4 31.2 1.0
OD1 G:ASP174 2.4 35.3 1.0
OE1 G:GLN149 2.5 27.3 1.0
OD2 G:ASP174 2.5 36.1 1.0
CG G:ASP174 2.8 30.1 1.0
CD G:GLN149 3.5 22.9 1.0
CD G:GLN146 3.5 28.4 1.0
NE2 G:GLN149 3.9 30.0 1.0
O G:HOH578 4.3 34.9 1.0
CG G:GLN146 4.3 23.1 1.0
CB G:ASP174 4.3 28.2 1.0
CB G:GLN146 4.3 28.0 1.0
NE2 G:GLN146 4.4 26.3 1.0
O G:ARG148 4.6 23.8 1.0
O G:HOH585 4.6 37.4 1.0
CA G:GLN146 4.7 28.0 1.0
CG G:GLN149 4.8 24.0 1.0
OD1 G:ASP147 5.0 39.0 1.0
N G:ASP147 5.0 29.3 1.0

Reference:

S.Sanram, W.Suginta. Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A To Be Published.
Page generated: Wed Oct 9 12:39:16 2024

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