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Sodium in PDB 5mdr: Crystal Structure of in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose

Protein crystallography data

The structure of Crystal Structure of in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose, PDB code: 5mdr was solved by M.Zahn, B.Van Den Berg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 130.02 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 146.552, 121.941, 147.155, 90.00, 117.92, 90.00
R / Rfree (%) 17.2 / 18.4

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 in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose (pdb code 5mdr). 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 in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose, PDB code: 5mdr:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 18 in 5mdr

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Sodium binding site 1 out of 18 in the Crystal Structure of in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


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 in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na413

b:26.8
occ:1.00
 OE1 A:GLN146 2.3 23.2 1.0
O A:HOH770 2.3 33.9 1.0
O A:HOH558 2.4 23.4 1.0
O A:HOH762 2.4 22.8 1.0
OD1 A:ASP174 2.5 22.7 1.0
OD2 A:ASP174 2.8 25.1 1.0
OE1 A:GLN149 2.9 22.8 1.0
CG A:ASP174 3.0 23.2 1.0
O A:HOH507 3.1 24.5 1.0
CD A:GLN146 3.5 23.4 1.0
CD A:GLN149 3.8 23.2 1.0
NE2 A:GLN149 4.0 23.9 1.0
O A:HOH718 4.2 37.3 1.0
CB A:GLN146 4.3 22.1 1.0
O A:HOH678 4.3 24.9 1.0
NE2 A:GLN146 4.4 23.7 1.0
CG A:GLN146 4.4 22.6 1.0
O A:HOH724 4.4 49.8 1.0
O A:HOH653 4.4 26.7 1.0
CA A:GLN146 4.5 22.4 1.0
CB A:ASP174 4.5 22.8 1.0
OD1 A:ASP147 4.8 25.6 1.0
N A:ASP147 4.8 22.0 1.0
O A:HOH773 4.8 32.3 1.0

Sodium binding site 2 out of 18 in 5mdr

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Sodium binding site 2 out of 18 in the Crystal Structure of in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


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 in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na414

b:28.9
occ:1.00
 O A:GLY46 2.3 30.4 1.0
O C:HOH608 2.3 25.8 1.0
O A:HOH758 2.5 26.3 1.0
O A:ASN44 2.5 29.3 1.0
O C:GLY181 2.5 30.4 1.0
O A:ASP43 2.5 32.3 1.0
C A:ASN44 3.2 30.9 1.0
C A:GLY46 3.5 31.2 1.0
C A:ASP43 3.6 33.1 1.0
CA A:ASN44 3.6 31.0 1.0
C C:GLY181 3.7 31.0 1.0
O A:HOH650 3.9 43.4 1.0
O A:HOH639 3.9 28.9 1.0
N A:GLY46 4.0 31.1 1.0
O A:HOH523 4.0 36.4 1.0
N A:ASN44 4.1 32.2 1.0
N A:LEU45 4.2 30.7 1.0
CA C:ASP182 4.2 32.5 1.0
C A:LEU45 4.2 30.4 1.0
N C:ASP182 4.3 31.7 1.0
CA A:GLY46 4.4 31.3 1.0
CB C:ASP182 4.4 34.0 1.0
CB C:ALA176 4.5 29.0 1.0
CA C:ALA176 4.5 28.4 1.0
N A:GLY47 4.5 31.3 1.0
CA A:LEU45 4.6 30.6 1.0
N C:GLY181 4.7 30.4 1.0
CA A:GLY47 4.7 32.0 1.0
O C:ALA176 4.7 26.5 1.0
O A:LEU45 4.7 30.1 1.0
CA C:GLY181 4.8 31.1 1.0
CA A:ASP43 4.9 34.9 1.0

Sodium binding site 3 out of 18 in 5mdr

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Sodium binding site 3 out of 18 in the Crystal Structure of in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


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 in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na415

b:30.5
occ:1.00
 O A:PRO82 2.3 26.3 1.0
O C:HOH569 2.3 26.3 1.0
OD1 A:ASP81 2.3 27.4 1.0
O A:HOH638 2.5 26.7 1.0
O A:GLY85 2.5 26.7 1.0
O A:HOH515 2.7 42.9 1.0
C A:PRO82 3.4 26.0 1.0
CG A:ASP81 3.4 28.1 1.0
O A:ASP81 3.5 26.0 1.0
C A:GLY85 3.6 27.2 1.0
C A:ASP81 3.7 26.1 1.0
O A:HOH628 3.9 39.5 1.0
N A:PRO82 4.0 25.7 1.0
N A:GLY85 4.1 27.1 1.0
N A:SER83 4.1 26.1 1.0
CA A:SER83 4.2 26.3 1.0
ND2 C:ASN151 4.2 24.4 1.0
CA A:ASP81 4.2 26.0 1.0
OD2 A:ASP81 4.3 28.4 1.0
CB A:ASP81 4.3 26.7 1.0
CA A:PRO82 4.3 26.3 1.0
CA A:GLY85 4.4 27.7 1.0
O C:GLY177 4.4 27.5 1.0
O A:LEU50 4.5 31.2 1.0
OD1 C:ASN151 4.5 24.8 1.0
C A:SER83 4.5 25.6 1.0
N A:GLY86 4.6 27.5 1.0
O A:GLY86 4.6 26.0 1.0
N A:PHE84 4.6 26.0 1.0
C A:GLY86 4.7 26.6 1.0
CD A:PRO82 4.7 26.1 1.0
CB C:SER150 4.7 23.5 1.0
CA A:GLY86 4.7 27.1 1.0
CG C:ASN151 4.8 25.0 1.0
OE1 A:GLN49 5.0 27.1 1.0

Sodium binding site 4 out of 18 in 5mdr

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Sodium binding site 4 out of 18 in the Crystal Structure of in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


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 in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na416

b:24.2
occ:1.00
 O B:GLY46 2.3 26.6 1.0
O A:HOH647 2.4 23.7 1.0
O B:HOH736 2.4 22.1 1.0
O A:GLY181 2.4 24.1 1.0
O B:ASN44 2.5 25.2 1.0
O B:ASP43 2.6 28.6 1.0
C B:ASN44 3.2 27.0 1.0
C B:GLY46 3.6 27.3 1.0
C A:GLY181 3.6 24.7 1.0
C B:ASP43 3.7 29.4 1.0
CA B:ASN44 3.7 27.6 1.0
O B:HOH670 3.9 37.9 1.0
O B:HOH585 4.0 25.3 1.0
N B:GLY46 4.1 26.8 1.0
CA A:ASP182 4.1 25.4 1.0
N B:ASN44 4.1 28.6 1.0
N B:LEU45 4.2 26.9 1.0
O B:HOH540 4.2 34.3 1.0
C B:LEU45 4.3 26.1 1.0
N A:ASP182 4.3 24.7 1.0
CB A:ASP182 4.3 27.4 1.0
CA B:GLY46 4.4 27.3 1.0
CB A:ALA176 4.4 22.6 1.0
CA A:ALA176 4.4 23.0 1.0
N B:GLY47 4.5 27.4 1.0
N A:GLY181 4.6 24.3 1.0
CA B:LEU45 4.7 27.0 1.0
O A:ALA176 4.7 23.5 1.0
CA B:GLY47 4.7 27.5 1.0
CA A:GLY181 4.7 24.3 1.0
O B:LEU45 4.7 26.3 1.0
CA B:ASP43 4.9 31.4 1.0

Sodium binding site 5 out of 18 in 5mdr

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Sodium binding site 5 out of 18 in the Crystal Structure of in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


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 in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na409

b:29.8
occ:1.00
 O B:PRO82 2.3 23.8 1.0
OD1 B:ASP81 2.3 28.2 1.0
O A:HOH562 2.3 25.1 1.0
O B:HOH648 2.4 23.4 1.0
O B:GLY85 2.5 25.1 1.0
O B:HOH507 2.7 45.2 1.0
C B:PRO82 3.3 24.2 1.0
CG B:ASP81 3.4 27.2 1.0
O B:ASP81 3.5 25.5 1.0
C B:ASP81 3.6 25.6 1.0
C B:GLY85 3.6 25.1 1.0
O B:HOH679 3.8 42.6 1.0
N B:PRO82 4.0 25.1 1.0
N B:SER83 4.1 24.7 1.0
N B:GLY85 4.1 26.2 1.0
CA B:SER83 4.2 25.5 1.0
CA B:ASP81 4.2 25.5 1.0
OD2 B:ASP81 4.2 28.4 1.0
ND2 A:ASN151 4.3 20.4 1.0
CA B:PRO82 4.3 24.9 1.0
CB B:ASP81 4.3 26.3 1.0
CA B:GLY85 4.4 25.8 1.0
O A:GLY177 4.4 23.5 1.0
O B:LEU50 4.5 30.1 1.0
OD1 A:ASN151 4.5 21.4 1.0
C B:SER83 4.5 25.2 1.0
N B:GLY86 4.6 25.7 1.0
CD B:PRO82 4.6 25.3 1.0
O B:GLY86 4.6 23.1 1.0
N B:PHE84 4.7 24.8 1.0
C B:GLY86 4.7 24.4 1.0
CB A:SER150 4.7 20.5 1.0
CA B:GLY86 4.8 25.4 1.0
CG A:ASN151 4.8 21.1 1.0

Sodium binding site 6 out of 18 in 5mdr

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Sodium binding site 6 out of 18 in the Crystal Structure of in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


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 in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na410

b:31.1
occ:1.00
 OE1 B:GLN146 2.3 25.3 1.0
O B:HOH746 2.3 36.7 1.0
O B:HOH739 2.4 25.7 1.0
O B:HOH579 2.4 26.2 1.0
OD1 B:ASP174 2.5 27.5 1.0
OD2 B:ASP174 2.8 29.5 1.0
OE1 B:GLN149 2.9 25.7 1.0
CG B:ASP174 3.1 28.0 1.0
O B:HOH506 3.1 28.3 1.0
CD B:GLN146 3.5 25.4 1.0
CD B:GLN149 3.7 25.6 1.0
NE2 B:GLN149 4.0 26.1 1.0
O B:HOH646 4.2 45.6 1.0
CB B:GLN146 4.3 24.4 1.0
O B:HOH660 4.4 31.4 1.0
CG B:GLN146 4.4 25.1 1.0
NE2 B:GLN146 4.4 25.5 1.0
O B:HOH607 4.5 28.5 1.0
CA B:GLN146 4.5 24.7 1.0
CB B:ASP174 4.6 27.0 1.0
OD1 B:ASP147 4.7 25.1 1.0
N B:ASP147 4.8 23.6 1.0
O B:HOH742 4.8 33.1 1.0
O B:ARG148 5.0 21.9 1.0

Sodium binding site 7 out of 18 in 5mdr

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Sodium binding site 7 out of 18 in the Crystal Structure of in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


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 in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na411

b:27.8
occ:1.00
 O C:GLY46 2.3 31.4 1.0
O B:HOH603 2.4 23.9 1.0
O C:HOH739 2.4 24.7 1.0
O B:GLY181 2.4 28.6 1.0
O C:ASN44 2.5 30.4 1.0
O C:ASP43 2.6 33.4 1.0
C C:ASN44 3.2 31.5 1.0
C C:GLY46 3.6 31.9 1.0
C B:GLY181 3.6 29.9 1.0
CA C:ASN44 3.6 32.2 1.0
C C:ASP43 3.7 34.3 1.0
O C:HOH659 3.8 45.8 1.0
O C:HOH590 4.0 31.3 1.0
N C:GLY46 4.0 31.6 1.0
CA B:ASP182 4.1 30.3 1.0
N C:ASN44 4.1 33.5 1.0
O C:HOH527 4.1 39.9 1.0
N C:LEU45 4.2 31.8 1.0
C C:LEU45 4.2 30.9 1.0
N B:ASP182 4.3 30.0 1.0
CB B:ASP182 4.3 32.3 1.0
CA C:GLY46 4.4 32.2 1.0
CB B:ALA176 4.4 28.0 1.0
CA B:ALA176 4.4 27.4 1.0
N C:GLY47 4.5 31.7 1.0
N B:GLY181 4.6 30.0 1.0
CA C:LEU45 4.7 31.4 1.0
O B:ALA176 4.7 26.8 1.0
O C:LEU45 4.7 30.3 1.0
CA B:GLY181 4.7 30.4 1.0
CA C:GLY47 4.7 31.9 1.0
CA C:ASP43 4.9 36.5 1.0

Sodium binding site 8 out of 18 in 5mdr

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Sodium binding site 8 out of 18 in the Crystal Structure of in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


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 in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na408

b:31.6
occ:1.00
 OE1 C:GLN146 2.2 27.8 1.0
O C:HOH566 2.4 27.9 1.0
O C:HOH743 2.4 28.9 1.0
O C:HOH753 2.4 38.3 1.0
OD1 C:ASP174 2.5 27.9 1.0
OD2 C:ASP174 2.8 29.9 1.0
OE1 C:GLN149 2.8 26.0 1.0
CG C:ASP174 3.0 28.7 1.0
O C:HOH504 3.0 29.2 1.0
CD C:GLN146 3.5 27.6 1.0
CD C:GLN149 3.7 26.7 1.0
NE2 C:GLN149 3.9 27.6 1.0
O C:HOH680 4.1 47.3 1.0
O C:HOH725 4.2 61.2 1.0
CB C:GLN146 4.3 26.2 1.0
NE2 C:GLN146 4.3 28.1 1.0
CG C:GLN146 4.4 26.7 1.0
O C:HOH690 4.4 32.5 1.0
O C:HOH585 4.5 28.8 1.0
CA C:GLN146 4.5 26.5 1.0
CB C:ASP174 4.5 27.9 1.0
OD1 C:ASP147 4.7 28.4 1.0
O C:HOH749 4.8 34.5 1.0
N C:ASP147 4.8 25.7 1.0
O C:ARG148 5.0 23.5 1.0

Sodium binding site 9 out of 18 in 5mdr

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Sodium binding site 9 out of 18 in the Crystal Structure of in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


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 in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na409

b:31.9
occ:1.00
 O C:PRO82 2.3 25.1 1.0
OD1 C:ASP81 2.3 28.9 1.0
O B:HOH552 2.4 25.4 1.0
O C:HOH642 2.5 25.7 1.0
O C:GLY85 2.5 27.6 1.0
O C:HOH506 2.7 42.0 1.0
C C:PRO82 3.3 26.1 1.0
CG C:ASP81 3.5 29.1 1.0
O C:ASP81 3.5 27.6 1.0
C C:GLY85 3.6 28.4 1.0
C C:ASP81 3.7 26.1 1.0
O C:HOH681 4.0 43.2 1.0
N C:PRO82 4.0 25.9 1.0
N C:GLY85 4.1 27.4 1.0
N C:SER83 4.1 26.2 1.0
CA C:SER83 4.2 26.5 1.0
CA C:ASP81 4.3 26.3 1.0
ND2 B:ASN151 4.3 22.9 1.0
OD2 C:ASP81 4.3 29.8 1.0
CA C:PRO82 4.3 26.2 1.0
CB C:ASP81 4.3 27.5 1.0
CA C:GLY85 4.4 27.8 1.0
O B:GLY177 4.4 26.1 1.0
O C:LEU50 4.5 31.4 1.0
C C:SER83 4.5 26.8 1.0
OD1 B:ASN151 4.5 24.5 1.0
N C:GLY86 4.5 27.6 1.0
O C:GLY86 4.6 25.5 1.0
N C:PHE84 4.6 26.2 1.0
C C:GLY86 4.6 27.2 1.0
CD C:PRO82 4.6 26.3 1.0
CA C:GLY86 4.7 28.5 1.0
CB B:SER150 4.7 22.3 1.0
CG B:ASN151 4.8 23.6 1.0
OE1 C:GLN49 5.0 25.8 1.0

Sodium binding site 10 out of 18 in 5mdr

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Sodium binding site 10 out of 18 in the Crystal Structure of in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


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 in Vitro Folded Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na410

b:25.1
occ:1.00
 O D:GLY46 2.3 25.2 1.0
O F:HOH640 2.4 22.5 1.0
O D:HOH724 2.4 21.9 1.0
O F:GLY181 2.5 23.6 1.0
O D:ASN44 2.5 25.6 1.0
O D:ASP43 2.5 28.1 1.0
C D:ASN44 3.2 26.3 1.0
C D:GLY46 3.6 26.1 1.0
C F:GLY181 3.6 25.4 1.0
C D:ASP43 3.7 28.6 1.0
CA D:ASN44 3.7 27.2 1.0
O D:HOH625 3.8 38.7 1.0
O D:HOH574 4.0 24.8 1.0
N D:GLY46 4.0 25.7 1.0
CA F:ASP182 4.1 24.9 1.0
N D:ASN44 4.1 27.9 1.0
O D:HOH519 4.2 34.8 1.0
N D:LEU45 4.2 26.0 1.0
C D:LEU45 4.3 25.6 1.0
N F:ASP182 4.3 24.1 1.0
CB F:ASP182 4.3 26.3 1.0
CA D:GLY46 4.4 26.2 1.0
CB F:ALA176 4.4 23.2 1.0
CA F:ALA176 4.5 22.9 1.0
N D:GLY47 4.5 26.1 1.0
N F:GLY181 4.6 24.7 1.0
CA D:GLY47 4.7 26.6 1.0
CA D:LEU45 4.7 26.0 1.0
O F:ALA176 4.7 22.7 1.0
O D:LEU45 4.7 24.6 1.0
CA F:GLY181 4.7 25.5 1.0
CA D:ASP43 4.9 30.3 1.0

Reference:

A.Aunkham, M.Zahn, A.Kesireddy, K.R.Pothula, A.Schulte, A.Basle, U.Kleinekathofer, W.Suginta, B.Van Den Berg. Structural Basis For Chitin Acquisition By Marine Vibrio Species. Nat Commun V. 9 220 2018.
ISSN: ESSN 2041-1723
PubMed: 29335469
DOI: 10.1038/S41467-017-02523-Y
Page generated: Mon Aug 18 01:02:18 2025

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