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Sodium in PDB 7cjs: Structure of Aquaporin

Protein crystallography data

The structure of Structure of Aquaporin, PDB code: 7cjs was solved by Y.Saitoh, J.F.Ma, M.Suga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.84 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.568, 92.453, 166.126, 90, 102.14, 90
R / Rfree (%) 24.5 / 27.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Aquaporin (pdb code 7cjs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Structure of Aquaporin, PDB code: 7cjs:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 7cjs

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Sodium binding site 1 out of 8 in the Structure of Aquaporin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Aquaporin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:48.7
occ:1.00
O A:ALA190 2.3 23.9 1.0
O A:THR188 2.4 31.4 1.0
O A:HOH420 2.6 50.1 1.0
O A:HOH498 2.6 50.0 1.0
O A:HOH470 2.6 35.5 1.0
HO3 A:BOG302 3.3 112.2 1.0
C A:THR188 3.4 31.1 1.0
C A:ALA190 3.5 25.8 1.0
H A:GLY192 3.5 30.0 1.0
O3 A:BOG302 3.7 93.5 1.0
HA A:VAL191 3.7 30.6 1.0
HA A:THR188 3.8 38.2 1.0
C A:ARG189 4.1 29.8 1.0
N A:ALA190 4.1 28.8 1.0
CA A:THR188 4.1 31.9 1.0
HA A:ARG189 4.2 36.8 1.0
HO2 A:BOG302 4.2 111.0 1.0
N A:ARG189 4.3 29.4 1.0
H A:ALA190 4.3 34.6 1.0
O2 A:BOG302 4.3 92.5 1.0
N A:GLY192 4.4 25.0 1.0
O A:ARG189 4.4 29.6 1.0
CA A:ARG189 4.4 30.7 1.0
N A:VAL191 4.4 25.8 1.0
CA A:ALA190 4.4 27.3 1.0
CA A:VAL191 4.5 25.5 1.0
HB A:THR188 4.5 39.9 1.0
O A:ASP187 4.6 27.2 1.0
O A:HOH426 4.7 37.3 1.0
H2 A:BOG302 4.8 111.5 1.0
O A:HOH424 4.8 50.5 1.0
C3 A:BOG302 4.9 93.3 1.0
CB A:THR188 4.9 33.2 1.0
C2 A:BOG302 5.0 92.9 1.0
C A:VAL191 5.0 25.6 1.0

Sodium binding site 2 out of 8 in 7cjs

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Sodium binding site 2 out of 8 in the Structure of Aquaporin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Aquaporin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:41.3
occ:1.00
O B:HOH478 2.2 47.6 1.0
O B:ALA190 2.2 22.4 1.0
O B:HOH493 2.5 47.0 1.0
O B:HOH482 2.5 31.9 1.0
O B:HOH414 2.6 47.3 1.0
O B:THR188 2.6 28.6 1.0
H B:GLY192 3.4 28.6 1.0
C B:ALA190 3.5 23.6 1.0
C B:THR188 3.5 28.0 1.0
HA B:VAL191 3.7 28.8 1.0
HA B:THR188 3.8 33.3 1.0
C B:ARG189 4.1 24.4 1.0
N B:ALA190 4.1 23.8 1.0
N B:GLY192 4.2 23.9 1.0
CA B:THR188 4.2 27.8 1.0
H B:ALA190 4.3 28.6 1.0
O B:HOH426 4.3 28.4 1.0
HA B:ARG189 4.3 30.6 1.0
N B:VAL191 4.4 24.1 1.0
O B:ARG189 4.4 24.3 1.0
CA B:VAL191 4.4 23.9 1.0
N B:ARG189 4.4 26.2 1.0
CA B:ALA190 4.4 23.8 1.0
O B:ASP187 4.5 24.6 1.0
CA B:ARG189 4.5 25.5 1.0
HB B:THR188 4.7 34.1 1.0
C B:VAL191 4.9 23.9 1.0
HA3 B:GLY192 4.9 29.6 1.0
OE2 B:GLU193 5.0 34.8 1.0

Sodium binding site 3 out of 8 in 7cjs

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Sodium binding site 3 out of 8 in the Structure of Aquaporin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Aquaporin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:45.9
occ:1.00
O C:HOH487 2.0 49.1 1.0
O C:ALA190 2.3 24.0 1.0
O C:THR188 2.4 32.9 1.0
O C:HOH444 2.5 45.0 1.0
O C:HOH528 2.6 60.0 1.0
O C:HOH499 2.6 38.3 1.0
C C:THR188 3.4 32.3 1.0
H C:GLY192 3.5 26.9 1.0
C C:ALA190 3.5 24.9 1.0
HA C:THR188 3.7 37.6 1.0
HA C:VAL191 3.7 29.1 1.0
N C:ALA190 4.0 29.1 1.0
CA C:THR188 4.1 31.3 1.0
H C:ALA190 4.1 34.9 1.0
C C:ARG189 4.1 34.3 1.0
HA C:ARG189 4.2 43.2 1.0
N C:GLY192 4.3 22.4 1.0
N C:ARG189 4.3 34.3 1.0
CA C:ALA190 4.4 26.9 1.0
N C:VAL191 4.4 25.0 1.0
CA C:ARG189 4.5 36.0 1.0
CA C:VAL191 4.5 24.3 1.0
O C:HOH427 4.5 45.2 1.0
HB C:THR188 4.5 39.3 1.0
O C:ARG189 4.5 35.5 1.0
O C:ASP187 4.6 29.2 1.0
O C:HOH421 4.7 32.2 1.0
CB C:THR188 4.9 32.8 1.0
C C:VAL191 5.0 24.4 1.0
HA C:ALA190 5.0 32.3 1.0

Sodium binding site 4 out of 8 in 7cjs

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Sodium binding site 4 out of 8 in the Structure of Aquaporin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Aquaporin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:43.7
occ:1.00
O D:HOH484 2.3 46.4 1.0
O D:HOH482 2.4 48.5 1.0
O D:ALA190 2.4 24.6 1.0
O D:HOH490 2.6 36.6 1.0
O D:HOH483 2.6 37.2 1.0
O D:THR188 2.7 25.5 1.0
H D:GLY192 3.3 31.0 1.0
C D:ALA190 3.6 25.0 1.0
C D:THR188 3.6 24.6 1.0
HA D:VAL191 3.7 27.8 1.0
HA D:THR188 3.9 30.1 1.0
N D:GLY192 4.1 25.8 1.0
N D:ALA190 4.2 25.9 1.0
C D:ARG189 4.3 24.4 1.0
HA D:ARG189 4.3 28.1 1.0
O D:HOH425 4.4 30.1 1.0
CA D:THR188 4.4 25.1 1.0
H D:ALA190 4.4 31.0 1.0
CA D:VAL191 4.4 23.1 1.0
N D:VAL191 4.5 23.5 1.0
N D:ARG189 4.5 23.1 1.0
O D:ASP187 4.5 24.1 1.0
CA D:ALA190 4.5 26.1 1.0
CA D:ARG189 4.6 23.4 1.0
O D:ARG189 4.7 24.3 1.0
HA3 D:GLY192 4.7 32.9 1.0
HB D:THR188 4.8 32.0 1.0
C D:VAL191 4.8 23.9 1.0
OE2 D:GLU193 4.8 30.8 1.0

Sodium binding site 5 out of 8 in 7cjs

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Sodium binding site 5 out of 8 in the Structure of Aquaporin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Aquaporin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na301

b:42.8
occ:1.00
O E:ALA190 2.2 26.5 1.0
O E:HOH435 2.4 50.8 1.0
O E:THR188 2.5 29.2 1.0
O E:HOH490 2.5 56.2 1.0
O E:HOH447 2.6 66.9 1.0
O E:HOH476 2.6 36.2 1.0
C E:THR188 3.4 28.7 1.0
C E:ALA190 3.4 23.0 1.0
H E:GLY192 3.4 29.7 1.0
HA E:VAL191 3.6 29.0 1.0
HA E:THR188 3.7 34.8 1.0
C E:ARG189 4.0 28.2 1.0
N E:ALA190 4.0 24.1 1.0
CA E:THR188 4.1 29.0 1.0
HA E:ARG189 4.2 35.3 1.0
N E:GLY192 4.2 24.7 1.0
N E:ARG189 4.3 27.8 1.0
H E:ALA190 4.3 28.9 1.0
O E:ARG189 4.3 28.8 1.0
N E:VAL191 4.3 23.7 1.0
CA E:ALA190 4.3 22.4 1.0
CA E:VAL191 4.4 24.2 1.0
O E:HOH471 4.4 54.2 1.0
CA E:ARG189 4.4 29.4 1.0
O E:ASP187 4.4 23.1 1.0
HB E:THR188 4.6 36.4 1.0
O E:HOH409 4.8 36.1 1.0
C E:VAL191 4.9 24.4 1.0
HA E:ALA190 4.9 26.9 1.0
CB E:THR188 5.0 30.4 1.0
HA3 E:GLY192 5.0 30.7 1.0
OE2 E:GLU193 5.0 31.5 1.0

Sodium binding site 6 out of 8 in 7cjs

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Sodium binding site 6 out of 8 in the Structure of Aquaporin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Aquaporin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na301

b:46.0
occ:1.00
O F:HOH466 2.2 43.0 1.0
O F:ALA190 2.3 21.8 1.0
O F:THR188 2.5 25.2 1.0
O F:HOH481 2.5 32.2 1.0
O F:HOH489 2.5 49.1 1.0
O F:HOH408 2.6 39.0 1.0
H F:GLY192 3.4 28.7 1.0
C F:THR188 3.5 24.6 1.0
C F:ALA190 3.5 22.3 1.0
HA F:VAL191 3.7 28.8 1.0
HA F:THR188 3.8 29.6 1.0
O F:HOH446 4.1 57.4 1.0
N F:ALA190 4.1 21.8 1.0
C F:ARG189 4.1 22.9 1.0
N F:GLY192 4.2 23.9 1.0
CA F:THR188 4.2 24.7 1.0
HA F:ARG189 4.3 28.3 1.0
H F:ALA190 4.3 26.2 1.0
N F:ARG189 4.3 23.7 1.0
O F:HOH429 4.4 27.5 1.0
CA F:VAL191 4.4 24.0 1.0
N F:VAL191 4.4 23.2 1.0
CA F:ALA190 4.4 22.1 1.0
O F:ARG189 4.5 22.9 1.0
CA F:ARG189 4.5 23.6 1.0
O F:ASP187 4.5 22.2 1.0
HB F:THR188 4.6 31.8 1.0
C F:VAL191 4.9 24.0 1.0
HA3 F:GLY192 4.9 29.1 1.0

Sodium binding site 7 out of 8 in 7cjs

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Sodium binding site 7 out of 8 in the Structure of Aquaporin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Aquaporin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na301

b:38.9
occ:1.00
O G:HOH486 2.2 41.4 1.0
O G:ALA190 2.3 23.9 1.0
O G:HOH429 2.4 41.1 1.0
O G:THR188 2.4 29.7 1.0
O G:HOH500 2.5 35.1 1.0
O G:HOH533 2.6 43.7 1.0
H G:GLY192 3.4 23.1 1.0
C G:THR188 3.4 29.6 1.0
C G:ALA190 3.5 24.8 1.0
HA G:THR188 3.7 34.6 1.0
HA G:VAL191 3.7 26.8 1.0
N G:ALA190 4.1 29.0 1.0
CA G:THR188 4.1 28.9 1.0
H G:ALA190 4.2 34.8 1.0
N G:GLY192 4.2 19.3 1.0
C G:ARG189 4.3 31.2 1.0
HA G:ARG189 4.4 38.1 1.0
N G:ARG189 4.4 30.4 1.0
N G:VAL191 4.4 23.4 1.0
CA G:VAL191 4.4 22.3 1.0
CA G:ALA190 4.5 27.2 1.0
O G:HOH432 4.5 28.5 1.0
HB G:THR188 4.5 37.2 1.0
O G:HOH406 4.6 44.0 1.0
O G:ASP187 4.6 27.4 1.0
CA G:ARG189 4.6 31.8 1.0
O G:ARG189 4.7 31.7 1.0
C G:VAL191 4.9 21.8 1.0
OE2 G:GLU193 4.9 29.5 1.0
HA3 G:GLY192 4.9 22.9 1.0
CB G:THR188 5.0 31.0 1.0

Sodium binding site 8 out of 8 in 7cjs

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Sodium binding site 8 out of 8 in the Structure of Aquaporin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of Aquaporin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na301

b:44.3
occ:1.00
O H:ALA190 2.2 23.4 1.0
O H:HOH489 2.3 43.3 1.0
O H:HOH499 2.4 44.4 1.0
O H:HOH483 2.4 30.1 1.0
O H:THR188 2.6 28.1 1.0
O H:HOH462 2.7 44.7 1.0
H H:GLY192 3.3 31.9 1.0
C H:ALA190 3.4 23.9 1.0
C H:THR188 3.5 26.5 1.0
HA H:VAL191 3.7 26.2 1.0
HA H:THR188 3.8 31.9 1.0
N H:ALA190 4.0 23.8 1.0
C H:ARG189 4.1 23.4 1.0
N H:GLY192 4.1 26.6 1.0
H H:ALA190 4.2 28.5 1.0
CA H:THR188 4.2 26.6 1.0
HA H:ARG189 4.2 28.3 1.0
N H:VAL191 4.4 22.3 1.0
CA H:ALA190 4.4 24.7 1.0
N H:ARG189 4.4 24.6 1.0
O H:ASP187 4.4 22.4 1.0
CA H:VAL191 4.4 21.8 1.0
O H:HOH424 4.4 32.0 1.0
CA H:ARG189 4.5 23.6 1.0
O H:ARG189 4.5 22.8 1.0
HB H:THR188 4.7 33.5 1.0
HA3 H:GLY192 4.8 34.3 1.0
C H:VAL191 4.9 22.9 1.0
OE2 H:GLU193 4.9 30.7 1.0
HA H:ALA190 5.0 29.6 1.0

Reference:

Y.Saitoh, J.F.Ma, M.Suga. Structure of Aquaporin Nat Commun 2021.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-021-26535-X
Page generated: Tue Oct 8 16:22:57 2024

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