Sodium in PDB 8jbk: Crystal Structure of Na+,K+-Atpase in the E1.3NA+ State

The structure of Crystal Structure of Na+,K+-Atpase in the E1.3NA+ State, PDB code: 8jbk was solved by R.Kanai, B.Vilsen, F.Cornelius, C.Toyoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	193.74, 74.49, 162.56, 90, 115.72, 90
R / Rfree (%)	22.9 / 27

The structure of Crystal Structure of Na+,K+-Atpase in the E1.3NA+ State also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Na+,K+-Atpase in the E1.3NA+ State (pdb code 8jbk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Na+,K+-Atpase in the E1.3NA+ State, PDB code: 8jbk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Crystal Structure of Na+,K+-Atpase in the E1.3NA+ State


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 Na+,K+-Atpase in the E1.3NA+ State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:61.7 occ:1.00 OE2 A:GLU327 2.4 70.9 1.0 O A:HOH1206 2.4 95.4 1.0 OD1 A:ASP804 2.4 59.6 1.0 O A:VAL325 2.5 70.9 1.0 O A:ALA323 2.6 73.1 1.0 O A:VAL322 3.2 62.4 1.0 C A:ALA323 3.4 64.1 1.0 C A:VAL325 3.4 62.1 1.0 CD A:GLU327 3.5 71.7 1.0 CG A:ASP804 3.6 54.8 1.0 CA A:ALA323 3.8 59.1 1.0 NA A:NA1103 3.8 73.1 1.0 N A:VAL325 3.9 45.7 1.0 N A:PRO326 4.1 48.2 1.0 CA A:PRO326 4.1 36.3 1.0 CG A:GLU327 4.2 72.6 1.0 OD2 A:ASP804 4.2 58.8 1.0 C A:VAL322 4.2 55.4 1.0 N A:GLU327 4.3 49.4 1.0 CA A:VAL325 4.3 53.7 1.0 N A:ASN324 4.4 59.1 1.0 OD1 A:ASP808 4.4 60.3 1.0 N A:ALA323 4.5 58.3 1.0 OE1 A:GLU327 4.5 70.7 1.0 C A:ASN324 4.5 51.5 1.0 C A:PRO326 4.7 41.4 1.0 CB A:ASP804 4.7 45.9 1.0 CA A:ASN324 4.8 53.2 1.0 CG A:ASP808 5.0 56.8 1.0 CB A:ALA323 5.0 54.6 1.0

Sodium binding site 2 out of 8 in the Crystal Structure of Na+,K+-Atpase in the E1.3NA+ State


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 Na+,K+-Atpase in the E1.3NA+ State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1103 b:73.1 occ:1.00 OG A:SER775 2.4 50.6 1.0 OE1 A:GLU779 2.4 57.2 1.0 O A:HOH1206 2.5 95.4 1.0 OD1 A:ASN776 2.5 54.6 1.0 O A:ALA323 2.7 73.1 1.0 OD1 A:ASP808 3.1 60.3 1.0 CD A:GLU779 3.3 58.4 1.0 OE2 A:GLU779 3.4 59.5 1.0 CB A:SER775 3.7 49.2 1.0 CG A:ASN776 3.7 56.8 1.0 C A:ALA323 3.8 64.1 1.0 NA A:NA1102 3.8 61.7 1.0 N A:ASN776 3.9 50.9 1.0 C A:SER775 3.9 51.7 1.0 O A:THR772 4.0 39.0 1.0 CG A:ASP808 4.1 56.8 1.0 O A:SER775 4.2 54.2 1.0 CA A:ASN776 4.2 47.7 1.0 OD1 A:ASP804 4.3 59.6 1.0 CA A:SER775 4.3 52.9 1.0 CA A:ALA323 4.5 59.1 1.0 ND2 A:ASN776 4.6 63.4 1.0 CB A:ASN776 4.6 47.9 1.0 OD2 A:ASP808 4.6 60.0 1.0 N A:ASN324 4.7 59.1 1.0 CA A:ASN324 4.7 53.2 1.0 CB A:ALA323 4.7 54.6 1.0 CG A:GLU779 4.7 57.0 1.0 N A:SER775 4.8 57.6 1.0 O A:HOH1203 4.8 63.3 1.0

Sodium binding site 3 out of 8 in the Crystal Structure of Na+,K+-Atpase in the E1.3NA+ State


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 Na+,K+-Atpase in the E1.3NA+ State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1104 b:49.5 occ:1.00 OG1 A:THR774 2.3 44.6 1.0 O A:TYR771 2.4 46.9 1.0 O A:HOH1203 2.4 63.3 1.0 OE1 A:GLN923 2.5 42.0 1.0 NE2 A:GLN923 2.7 48.9 1.0 OD2 A:ASP926 2.9 54.9 1.0 CD A:GLN923 3.0 42.0 1.0 CE1 A:TYR771 3.0 48.6 1.0 CD1 A:TYR771 3.1 53.9 1.0 CZ A:TYR771 3.5 36.9 1.0 C A:TYR771 3.5 38.7 1.0 CG A:TYR771 3.6 47.8 1.0 CB A:THR774 3.7 55.3 1.0 CG A:ASP926 3.9 52.0 1.0 CE2 A:TYR771 4.0 37.4 1.0 CD2 A:TYR771 4.0 42.6 1.0 OH A:TYR771 4.1 34.1 1.0 CG2 A:THR774 4.2 66.8 1.0 CA A:TYR771 4.2 36.8 1.0 N A:SER775 4.2 57.6 1.0 OD2 A:ASP808 4.3 60.0 1.0 CB A:ASP926 4.4 46.3 1.0 N A:THR774 4.4 53.9 1.0 CG A:GLN923 4.5 41.6 1.0 OE1 A:GLN854 4.5 52.4 1.0 CA A:THR774 4.5 52.4 1.0 CB A:TYR771 4.5 44.7 1.0 N A:THR772 4.5 34.3 1.0 NE2 A:GLN854 4.6 43.4 1.0 CB A:SER775 4.6 49.2 1.0 CA A:THR772 4.7 28.7 1.0 C A:THR774 4.7 53.2 1.0 C A:THR772 4.8 34.4 1.0 O A:THR772 4.9 39.0 1.0 CA A:SER775 4.9 52.9 1.0 OD1 A:ASP926 5.0 52.1 1.0

Sodium binding site 4 out of 8 in the Crystal Structure of Na+,K+-Atpase in the E1.3NA+ State


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 Na+,K+-Atpase in the E1.3NA+ State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1105 b:48.0 occ:1.00 OD2 A:ASP740 2.5 58.1 1.0 O A:HOH1213 2.5 72.9 1.0 O A:LYS719 2.7 53.3 1.0 O A:ALA721 2.9 41.4 1.0 O A:LEU718 3.0 21.2 1.0 C A:LYS719 3.3 45.7 1.0 CA A:LYS719 3.4 45.3 1.0 CG A:ASP740 3.6 59.1 1.0 O A:HOH1210 3.7 49.3 1.0 OD1 A:ASP740 4.0 67.3 1.0 C A:LEU718 4.0 25.5 1.0 C A:ALA721 4.0 38.4 1.0 N A:LYS719 4.2 35.5 1.0 N A:LYS720 4.4 41.1 1.0 CD A:LYS719 4.4 90.3 1.0 N A:ALA721 4.4 40.0 1.0 O A:ASP722 4.5 39.4 1.0 N A:GLY724 4.5 41.9 1.0 CB A:LYS719 4.6 61.4 1.0 C A:ASP722 4.7 39.2 1.0 CG A:LYS719 4.7 77.6 1.0 O A:ALA738 4.7 42.5 1.0 C A:LYS720 4.7 35.6 1.0 CA A:ALA721 4.8 36.1 1.0 CB A:ASP740 4.8 45.6 1.0

Sodium binding site 5 out of 8 in the Crystal Structure of Na+,K+-Atpase in the E1.3NA+ State


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 Na+,K+-Atpase in the E1.3NA+ State within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1102 b:76.3 occ:1.00 OD1 C:ASP804 2.4 59.3 1.0 OE2 C:GLU327 2.4 94.7 1.0 O C:VAL325 2.5 75.3 1.0 O C:HOH1207 2.5 95.7 1.0 O C:ALA323 2.6 80.0 1.0 O C:VAL322 3.3 72.7 1.0 C C:VAL325 3.3 69.7 1.0 C C:ALA323 3.4 69.0 1.0 CG C:ASP804 3.5 58.1 1.0 CD C:GLU327 3.6 96.3 1.0 NA C:NA1103 3.8 88.7 1.0 OD2 C:ASP804 3.8 61.3 1.0 CA C:ALA323 3.9 65.5 1.0 N C:VAL325 3.9 66.3 1.0 CA C:PRO326 4.0 69.5 1.0 N C:PRO326 4.0 66.5 1.0 CG C:GLU327 4.3 95.6 1.0 CA C:VAL325 4.3 66.7 1.0 N C:GLU327 4.3 68.6 1.0 OD1 C:ASP808 4.3 74.2 1.0 C C:VAL322 4.3 66.5 1.0 N C:ASN324 4.4 62.5 1.0 C C:ASN324 4.5 66.9 1.0 OE1 C:GLU327 4.6 93.8 1.0 N C:ALA323 4.6 65.8 1.0 C C:PRO326 4.7 67.5 1.0 CB C:ASP804 4.7 53.8 1.0 CG C:ASP808 4.7 69.3 1.0 CB C:ASP808 4.8 59.8 1.0 CA C:ASN324 4.9 60.6 1.0

Sodium binding site 6 out of 8 in the Crystal Structure of Na+,K+-Atpase in the E1.3NA+ State


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 Na+,K+-Atpase in the E1.3NA+ State within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1103 b:88.7 occ:1.00 OG C:SER775 2.4 44.4 1.0 OE1 C:GLU779 2.5 64.7 1.0 OD1 C:ASN776 2.5 67.9 1.0 O C:HOH1207 2.5 95.7 1.0 O C:ALA323 2.6 80.0 1.0 OD1 C:ASP808 2.9 74.2 1.0 OE2 C:GLU779 3.2 66.4 1.0 CD C:GLU779 3.2 61.7 1.0 CB C:SER775 3.6 41.5 1.0 CG C:ASN776 3.6 71.9 1.0 C C:ALA323 3.6 69.0 1.0 NA C:NA1102 3.8 76.3 1.0 OD1 C:ASP804 3.9 59.3 1.0 N C:ASN776 3.9 61.0 1.0 C C:SER775 3.9 48.3 1.0 CG C:ASP808 3.9 69.3 1.0 O C:THR772 4.1 47.8 1.0 O C:SER775 4.2 50.6 1.0 CA C:ASN776 4.2 66.8 1.0 CA C:SER775 4.3 42.0 1.0 CA C:ALA323 4.4 65.5 1.0 ND2 C:ASN776 4.5 79.2 1.0 OD2 C:ASP808 4.5 72.8 1.0 CB C:ALA323 4.5 64.9 1.0 N C:ASN324 4.5 62.5 1.0 CB C:ASN776 4.6 67.6 1.0 CA C:ASN324 4.7 60.6 1.0 CG C:GLU779 4.7 52.6 1.0 N C:SER775 4.8 50.0 1.0 CG C:ASP804 5.0 58.1 1.0

Sodium binding site 7 out of 8 in the Crystal Structure of Na+,K+-Atpase in the E1.3NA+ State


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 Na+,K+-Atpase in the E1.3NA+ State within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1104 b:67.7 occ:1.00 OD2 C:ASP926 2.4 53.2 1.0 OG1 C:THR774 2.4 44.8 1.0 O C:HOH1203 2.4 50.1 1.0 O C:TYR771 2.4 48.2 1.0 OE1 C:GLN923 2.5 47.2 1.0 NE2 C:GLN923 3.0 44.2 1.0 CE1 C:TYR771 3.0 52.5 1.0 CD1 C:TYR771 3.0 50.6 1.0 CD C:GLN923 3.1 43.5 1.0 CZ C:TYR771 3.4 49.9 1.0 CG C:ASP926 3.5 50.3 1.0 C C:TYR771 3.5 44.2 1.0 CG C:TYR771 3.5 50.4 1.0 CB C:THR774 3.7 49.4 1.0 CE2 C:TYR771 3.8 49.0 1.0 CD2 C:TYR771 3.8 50.7 1.0 CB C:ASP926 4.0 40.4 1.0 CG2 C:THR774 4.0 55.5 1.0 CA C:TYR771 4.0 47.1 1.0 OH C:TYR771 4.1 50.6 1.0 OE1 C:GLN854 4.2 70.1 1.0 CB C:TYR771 4.3 47.5 1.0 N C:SER775 4.4 50.0 1.0 N C:THR774 4.5 68.6 1.0 OD1 C:ASP926 4.5 52.5 1.0 CG C:GLN923 4.5 39.3 1.0 CA C:THR774 4.5 58.4 1.0 N C:THR772 4.6 40.5 1.0 OD2 C:ASP808 4.6 72.8 1.0 NE2 C:GLN854 4.7 52.5 1.0 C C:THR774 4.8 53.9 1.0 CA C:THR772 4.8 41.0 1.0 CD C:GLN854 4.9 57.7 1.0 CB C:SER775 5.0 41.5 1.0

Sodium binding site 8 out of 8 in the Crystal Structure of Na+,K+-Atpase in the E1.3NA+ State


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 Na+,K+-Atpase in the E1.3NA+ State within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1105 b:62.4 occ:1.00 OD2 C:ASP740 2.4 65.8 1.0 O C:HOH1211 2.5 54.7 1.0 O C:LYS719 2.6 61.4 1.0 O C:ALA721 2.8 60.1 1.0 O C:LEU718 2.8 35.2 1.0 C C:LYS719 3.2 62.4 1.0 CA C:LYS719 3.4 58.3 1.0 CG C:ASP740 3.5 62.5 1.0 C C:LEU718 3.8 34.5 1.0 OD1 C:ASP740 3.9 65.5 1.0 C C:ALA721 3.9 54.9 1.0 N C:LYS719 4.1 45.6 1.0 N C:LYS720 4.2 64.7 1.0 N C:ALA721 4.2 47.7 1.0 N C:GLY724 4.4 27.2 1.0 O C:ASP722 4.5 33.8 1.0 C C:LYS720 4.5 50.4 1.0 CD C:LYS719 4.5 88.7 1.0 CB C:LYS719 4.6 61.3 1.0 CA C:ALA721 4.6 47.2 1.0 C C:ASP722 4.6 44.0 1.0 O C:ALA738 4.7 44.4 1.0 CG C:LYS719 4.7 75.3 1.0 CB C:ASP740 4.8 50.8 1.0 CA C:LYS720 4.8 56.3 1.0 N C:ASP722 5.0 53.7 1.0 O C:LYS720 5.0 48.8 1.0

R.Kanai, B.Vilsen, F.Cornelius, C.Toyoshima. Crystal Structures of Na + ,K + -Atpase Reveal the Mechanism That Converts the K + -Bound Form to Na + -Bound Form and Opens and Closes the Cytoplasmic Gate. Febs Lett. 2023.
ISSN: ISSN 0014-5793
PubMed: 37357620
DOI: 10.1002/1873-3468.14689