Manganese in PDB 8jbm: Crystal Structure of Na+,K+-Atpase in the E1.MN2+ State

The structure of Crystal Structure of Na+,K+-Atpase in the E1.MN2+ State, PDB code: 8jbm 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)	12.00 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	196.984, 74.426, 162.976, 90, 116.33, 90
R / Rfree (%)	22.4 / 27.8

The binding sites of Manganese atom in the Crystal Structure of Na+,K+-Atpase in the E1.MN2+ State (pdb code 8jbm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of Na+,K+-Atpase in the E1.MN2+ State, PDB code: 8jbm:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Crystal Structure of Na+,K+-Atpase in the E1.MN2+ State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Na+,K+-Atpase in the E1.MN2+ State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1101 b:77.2 occ:1.00 OD1 A:ASP710 2.1 77.1 1.0 O A:HOH1207 2.4 64.7 1.0 CG A:ASP710 3.1 73.5 1.0 OD2 A:ASP710 3.4 79.5 1.0 OD1 A:ASP714 3.6 84.2 1.0 N A:GLY711 3.8 62.7 1.0 OD2 A:ASP714 4.1 62.0 1.0 CG A:ASP714 4.2 66.1 1.0 CA A:GLY711 4.4 72.4 1.0 CB A:ASP710 4.5 57.6 1.0 N A:ASP710 4.5 56.1 1.0 C A:ASP710 4.6 57.5 1.0 OD2 A:ASP369 4.7 64.5 1.0 CA A:ASP710 4.7 52.0 1.0 O A:HOH1204 4.8 70.7 1.0 NZ A:LYS691 4.9 71.3 1.0 CG A:PRO688 5.0 90.2 1.0

Manganese binding site 2 out of 6 in the Crystal Structure of Na+,K+-Atpase in the E1.MN2+ State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Na+,K+-Atpase in the E1.MN2+ State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1102 b:69.3 occ:1.00 OD1 A:ASP804 2.1 70.6 1.0 OG A:SER775 2.2 49.8 1.0 OE2 A:GLU779 2.2 60.0 1.0 O A:HOH1203 2.2 46.3 1.0 CB A:SER775 2.5 45.2 1.0 CD A:GLU779 3.2 56.1 1.0 CG A:ASP804 3.3 62.4 1.0 OE1 A:GLU779 3.5 46.2 1.0 OD2 A:ASP804 3.8 76.9 1.0 CA A:SER775 3.8 60.1 1.0 O A:HOH1208 3.9 51.1 1.0 C A:SER775 4.1 68.6 1.0 O A:SER775 4.1 71.2 1.0 O A:THR772 4.3 65.2 1.0 CB A:ASP804 4.5 46.4 1.0 CA A:ASP804 4.5 45.9 1.0 CG A:GLU779 4.6 60.1 1.0 OD1 A:ASP808 4.6 83.6 1.0 N A:SER775 4.6 67.4 1.0 CG2 A:ILE803 4.7 24.2 1.0 NE2 A:GLN923 4.8 64.4 1.0 N A:ASN776 4.8 64.1 1.0 ND2 A:ASN776 4.9 82.1 1.0 CB A:ASP808 4.9 50.4 1.0 CG A:ASP808 5.0 72.4 1.0 N A:ASP804 5.0 65.8 1.0

Manganese binding site 3 out of 6 in the Crystal Structure of Na+,K+-Atpase in the E1.MN2+ State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Na+,K+-Atpase in the E1.MN2+ State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1103 b:55.0 occ:1.00 OD2 A:ASP740 2.1 65.0 1.0 O A:HOH1209 2.4 58.3 1.0 CG A:ASP740 3.1 60.3 1.0 OD1 A:ASP740 3.5 66.5 1.0 O A:ALA721 3.6 45.6 1.0 O A:LYS719 3.7 50.5 1.0 O A:LEU718 3.9 42.7 1.0 C A:LYS719 4.4 46.7 1.0 CB A:ASP740 4.4 50.5 1.0 O A:ASP722 4.4 52.1 1.0 CA A:LYS719 4.4 48.0 1.0 C A:ALA721 4.9 39.6 1.0 N A:GLY724 4.9 48.0 1.0 C A:ASP722 4.9 42.9 1.0 C A:LEU718 5.0 49.0 1.0

Manganese binding site 4 out of 6 in the Crystal Structure of Na+,K+-Atpase in the E1.MN2+ State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Na+,K+-Atpase in the E1.MN2+ State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1101 b:80.2 occ:1.00 O C:HOH1209 2.0 37.4 1.0 OD1 C:ASP710 2.1 74.6 1.0 O C:HOH1202 2.4 63.7 1.0 CG C:ASP710 3.1 67.8 1.0 OD2 C:ASP710 3.5 79.3 1.0 OD2 C:ASP369 3.8 75.4 1.0 OD2 C:ASP714 4.2 79.4 1.0 N C:GLY711 4.4 67.0 1.0 CB C:ASP710 4.5 50.9 1.0 N C:ASP710 4.6 60.4 1.0 NZ C:LYS691 4.9 64.4 1.0 CA C:ASP710 4.9 55.1 1.0 CG C:ASP369 4.9 68.0 1.0 C C:ASP710 5.0 59.2 1.0

Manganese binding site 5 out of 6 in the Crystal Structure of Na+,K+-Atpase in the E1.MN2+ State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Na+,K+-Atpase in the E1.MN2+ State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1102 b:68.5 occ:1.00 OD1 C:ASP804 2.1 72.6 1.0 OE2 C:GLU779 2.1 72.9 1.0 O C:HOH1206 2.2 81.5 1.0 OG C:SER775 2.2 48.5 1.0 CB C:SER775 2.7 52.9 1.0 CD C:GLU779 2.9 68.6 1.0 OE1 C:GLU779 3.0 62.4 1.0 CG C:ASP804 3.0 76.7 1.0 OD2 C:ASP804 3.2 86.9 1.0 CA C:SER775 4.0 67.4 1.0 C C:SER775 4.1 68.1 1.0 O C:SER775 4.2 61.4 1.0 CG C:GLU779 4.4 68.8 1.0 CB C:ASP804 4.5 67.0 1.0 O C:THR772 4.5 48.9 1.0 CG2 C:ILE803 4.6 64.1 1.0 ND2 C:ASN776 4.6 75.2 1.0 N C:ASN776 4.6 69.6 1.0 N C:SER775 4.8 71.7 1.0 CA C:ASP804 4.8 57.2 1.0 OD2 C:ASP808 4.9 100.1 1.0

Manganese binding site 6 out of 6 in the Crystal Structure of Na+,K+-Atpase in the E1.MN2+ State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Na+,K+-Atpase in the E1.MN2+ State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1103 b:72.9 occ:1.00 OD1 C:ASP740 2.2 78.7 1.0 O C:HOH1210 2.2 48.6 1.0 O C:HOH1205 2.3 39.9 1.0 O C:LYS719 3.2 58.4 1.0 CG C:ASP740 3.3 73.3 1.0 OD2 C:ASP740 3.7 77.8 1.0 O C:ALA721 4.0 53.2 1.0 C C:LYS719 4.2 62.6 1.0 O C:LEU718 4.2 52.1 1.0 CA C:LYS719 4.3 69.6 1.0 CB C:ASP740 4.6 58.1 1.0 CD C:LYS719 4.6 120.3 1.0 O C:ASP722 4.7 76.2 1.0 O C:ALA738 4.9 73.0 1.0 CE C:LYS719 5.0 133.1 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