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Sodium in PDB 3wgv: Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin

Enzymatic activity of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin

All present enzymatic activity of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin:
3.6.3.9;

Protein crystallography data

The structure of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin, PDB code: 3wgv was solved by R.Kanai, H.Ogawa, 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) 15.99 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.285, 210.183, 256.086, 90.00, 90.00, 90.00
R / Rfree (%) 27 / 29.8

Other elements in 3wgv:

The structure of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Magnesium (Mg) 4 atoms
Aluminium (Al) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin (pdb code 3wgv). 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 A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin, PDB code: 3wgv:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3wgv

Go back to Sodium Binding Sites List in 3wgv
Sodium binding site 1 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


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 A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2005

b:95.2
occ:1.00
 OD1 A:ASP804 2.3 73.4 1.0
O A:VAL325 2.3 68.4 1.0
O A:VAL322 2.3 58.3 1.0
O A:HOH2101 2.4 40.1 1.0
OE2 A:GLU327 2.8 72.8 1.0
O A:ALA323 3.1 69.4 1.0
CG A:ASP804 3.1 72.5 1.0
C A:VAL325 3.2 65.5 1.0
C A:ALA323 3.2 66.6 1.0
OD2 A:ASP804 3.3 78.9 1.0
C A:VAL322 3.4 61.7 1.0
CA A:ALA323 3.5 67.4 1.0
N A:VAL325 3.5 64.8 1.0
CD A:GLU327 3.6 72.3 1.0
N A:ALA323 3.9 62.9 1.0
OE1 A:GLU327 3.9 71.6 1.0
N A:ASN324 4.0 61.0 1.0
CA A:VAL325 4.0 63.0 1.0
NA A:NA2006 4.0 66.0 1.0
N A:PRO326 4.1 62.3 1.0
CA A:PRO326 4.3 64.2 1.0
C A:ASN324 4.4 60.4 1.0
CB A:ASP804 4.5 65.1 1.0
CA A:ASN324 4.5 59.1 1.0
N A:GLU327 4.7 70.0 1.0
CA A:VAL322 4.7 61.2 1.0
CB A:VAL325 4.8 57.1 1.0
OD1 A:ASP808 4.8 93.0 1.0
CB A:ALA323 4.8 74.3 1.0
CG A:GLU327 4.8 70.1 1.0

Sodium binding site 2 out of 8 in 3wgv

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Sodium binding site 2 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


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 A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2006

b:66.0
occ:1.00
 OE1 A:GLU779 2.5 68.8 1.0
O A:ALA323 2.7 69.4 1.0
OD1 A:ASP808 2.7 93.0 1.0
OD1 A:ASN776 3.1 65.8 1.0
O A:HOH2101 3.1 40.1 1.0
OG A:SER775 3.1 66.3 1.0
CB A:SER775 3.3 64.6 1.0
CD A:GLU779 3.4 69.8 1.0
OE2 A:GLU779 3.6 74.0 1.0
CG A:ASN776 3.6 69.9 1.0
O A:THR772 3.6 63.4 1.0
N A:ASN776 3.6 49.6 1.0
OD1 A:ASP804 3.7 73.4 1.0
CG A:ASP808 3.8 89.4 1.0
C A:SER775 3.8 57.0 1.0
C A:ALA323 3.9 66.6 1.0
ND2 A:ASN776 4.0 78.6 1.0
NA A:NA2005 4.0 95.2 1.0
CA A:ASN776 4.1 54.4 1.0
CA A:SER775 4.1 62.4 1.0
O A:SER775 4.4 62.1 1.0
CB A:ASN776 4.5 61.5 1.0
OD2 A:ASP808 4.5 90.2 1.0
CA A:ALA323 4.6 67.4 1.0
CB A:ASP808 4.6 81.4 1.0
N A:SER775 4.7 65.6 1.0
CG A:GLU779 4.8 68.9 1.0
C A:THR772 4.8 60.3 1.0
CG A:ASP804 4.9 72.5 1.0
N A:ASN324 4.9 61.0 1.0
CA A:ASN324 4.9 59.1 1.0

Sodium binding site 3 out of 8 in 3wgv

Go back to Sodium Binding Sites List in 3wgv
Sodium binding site 3 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


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 A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2007

b:98.9
occ:1.00
 O A:TYR771 2.3 68.8 1.0
OG1 A:THR774 2.6 55.4 1.0
OE1 A:GLN923 2.7 76.1 1.0
NE2 A:GLN923 2.8 75.6 1.0
CD A:GLN923 3.1 74.2 1.0
C A:TYR771 3.2 70.5 1.0
OD2 A:ASP808 3.2 90.2 1.0
CE1 A:TYR771 3.3 64.9 1.0
CZ A:TYR771 3.3 65.9 1.0
CD1 A:TYR771 3.3 64.1 1.0
OD2 A:ASP926 3.3 69.3 1.0
CG A:TYR771 3.4 65.1 1.0
CE2 A:TYR771 3.4 62.5 1.0
CD2 A:TYR771 3.4 61.9 1.0
OG A:SER775 3.5 66.3 1.0
N A:THR772 4.0 70.0 1.0
CA A:TYR771 4.0 70.0 1.0
OH A:TYR771 4.0 69.7 1.0
CB A:THR774 4.1 58.8 1.0
CA A:THR772 4.1 67.0 1.0
N A:SER775 4.2 65.6 1.0
CB A:TYR771 4.3 69.8 1.0
C A:THR772 4.4 60.3 1.0
CG A:ASP808 4.4 89.4 1.0
CB A:SER775 4.5 64.6 1.0
CG A:ASP926 4.6 67.1 1.0
N A:THR774 4.6 59.3 1.0
CG A:GLN923 4.6 69.5 1.0
O A:THR772 4.7 63.4 1.0
CG2 A:THR774 4.7 59.7 1.0
CA A:THR774 4.8 62.2 1.0
OE1 A:GLN854 4.8 42.9 1.0
N A:LEU773 4.9 53.3 1.0
CA A:SER775 5.0 62.4 1.0

Sodium binding site 4 out of 8 in 3wgv

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Sodium binding site 4 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


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 A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2008

b:59.6
occ:1.00
 O A:ALA721 2.9 34.0 1.0
O A:LYS719 3.1 57.5 1.0
O A:HOH2105 3.1 28.9 1.0
O A:HOH2106 3.3 47.0 1.0
O A:HOH2107 3.4 45.2 1.0
O A:LYS720 4.0 35.0 1.0
C A:ALA721 4.1 34.5 1.0
C A:LYS719 4.3 53.8 1.0
NZ A:LYS719 4.4 91.3 1.0
C A:LYS720 4.4 37.4 1.0
O A:ASP722 4.6 36.9 1.0
CA A:ASP722 4.7 42.0 1.0
C A:ASP722 4.7 39.5 1.0
N A:ASP722 4.9 39.6 1.0
N A:ALA721 5.0 30.5 1.0

Sodium binding site 5 out of 8 in 3wgv

Go back to Sodium Binding Sites List in 3wgv
Sodium binding site 5 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


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 A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na2005

b:0.2
occ:1.00
 O C:VAL325 2.3 84.5 1.0
O C:ALA323 2.4 89.2 1.0
O C:VAL322 2.4 64.7 1.0
OD1 C:ASP804 2.5 83.4 1.0
OD2 C:ASP804 2.8 78.9 1.0
C C:ALA323 2.8 83.5 1.0
CG C:ASP804 2.9 81.3 1.0
C C:VAL325 3.1 76.1 1.0
N C:VAL325 3.1 76.6 1.0
OE2 C:GLU327 3.3 70.9 1.0
CA C:ALA323 3.4 84.6 1.0
C C:VAL322 3.5 70.7 1.0
O C:HOH2101 3.5 62.8 1.0
N C:ASN324 3.5 79.0 1.0
NA C:NA2006 3.6 83.9 1.0
CA C:VAL325 3.7 73.5 1.0
C C:ASN324 3.9 79.7 1.0
N C:ALA323 3.9 77.8 1.0
CA C:ASN324 4.0 78.6 1.0
CD C:GLU327 4.1 71.5 1.0
N C:PRO326 4.1 70.7 1.0
OE1 C:GLU327 4.2 67.1 1.0
CB C:ASP804 4.2 79.5 1.0
CA C:PRO326 4.5 69.1 1.0
CB C:VAL325 4.5 74.6 1.0
OD1 C:ASN776 4.6 75.0 1.0
OD1 C:ASP808 4.6 97.2 1.0
CA C:VAL322 4.8 51.7 1.0
CB C:ALA323 4.8 91.0 1.0
O C:ASN324 4.9 81.7 1.0
N C:GLU327 4.9 76.8 1.0

Sodium binding site 6 out of 8 in 3wgv

Go back to Sodium Binding Sites List in 3wgv
Sodium binding site 6 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


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 A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na2006

b:83.9
occ:1.00
 OD1 C:ASP808 2.4 97.2 1.0
OG C:SER775 2.4 59.4 1.0
OE1 C:GLU779 2.8 78.8 1.0
O C:ALA323 2.8 89.2 1.0
OD1 C:ASN776 2.9 75.0 1.0
O C:HOH2101 3.0 62.8 1.0
OD1 C:ASP804 3.4 83.4 1.0
O C:THR772 3.5 68.5 1.0
NA C:NA2005 3.6 0.2 1.0
CG C:ASP808 3.7 95.7 1.0
CG C:ASN776 3.7 78.2 1.0
CD C:GLU779 3.7 80.1 1.0
CB C:SER775 3.8 62.5 1.0
OE2 C:GLU779 3.8 84.1 1.0
N C:ASN776 3.9 68.5 1.0
C C:ALA323 4.1 83.5 1.0
C C:SER775 4.2 65.2 1.0
CG C:ASP804 4.3 81.3 1.0
CA C:ASN776 4.3 75.2 1.0
ND2 C:ASN776 4.3 81.5 1.0
OD2 C:ASP808 4.4 96.1 1.0
CA C:SER775 4.5 62.5 1.0
CB C:ASN776 4.6 78.0 1.0
CB C:ASP808 4.6 90.7 1.0
O C:SER775 4.7 64.3 1.0
C C:THR772 4.8 65.5 1.0
CB C:ASP804 4.8 79.5 1.0
N C:SER775 4.8 59.0 1.0
NA C:NA2007 4.8 78.0 1.0
CA C:ALA323 4.9 84.6 1.0
CA C:ASP804 4.9 81.0 1.0

Sodium binding site 7 out of 8 in 3wgv

Go back to Sodium Binding Sites List in 3wgv
Sodium binding site 7 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


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 A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na2007

b:78.0
occ:1.00
 O C:TYR771 2.3 62.8 1.0
OG1 C:THR774 2.7 53.4 1.0
N C:SER775 2.8 59.0 1.0
OD2 C:ASP808 2.9 96.1 1.0
OG C:SER775 2.9 59.4 1.0
CB C:SER775 3.0 62.5 1.0
OE1 C:GLN923 3.0 56.4 1.0
CA C:SER775 3.4 62.5 1.0
O C:THR772 3.5 68.5 1.0
C C:TYR771 3.5 64.8 1.0
C C:THR772 3.5 65.5 1.0
NE2 C:GLN923 3.5 56.0 1.0
N C:THR774 3.6 62.5 1.0
CD C:GLN923 3.7 57.5 1.0
CA C:THR772 3.7 63.9 1.0
CG C:ASP808 3.7 95.7 1.0
C C:THR774 3.8 57.2 1.0
OD1 C:ASP808 3.9 97.2 1.0
CB C:THR774 3.9 58.5 1.0
CA C:THR774 3.9 61.8 1.0
N C:THR772 4.1 63.4 1.0
N C:LEU773 4.1 65.0 1.0
OD2 C:ASP926 4.2 68.8 1.0
C C:LEU773 4.3 61.4 1.0
C C:SER775 4.7 65.2 1.0
CA C:TYR771 4.7 65.5 1.0
CA C:LEU773 4.7 62.6 1.0
CD2 C:TYR771 4.7 61.0 1.0
CE2 C:TYR771 4.7 62.7 1.0
CZ C:TYR771 4.8 62.4 1.0
CG C:TYR771 4.8 59.0 1.0
NA C:NA2006 4.8 83.9 1.0
CG2 C:THR774 4.9 55.8 1.0
CD1 C:TYR771 4.9 58.6 1.0
CE1 C:TYR771 4.9 60.7 1.0
O C:THR774 4.9 51.5 1.0
N C:ASN776 4.9 68.5 1.0

Sodium binding site 8 out of 8 in 3wgv

Go back to Sodium Binding Sites List in 3wgv
Sodium binding site 8 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


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 A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na2008

b:46.5
occ:1.00
 O C:HOH2107 2.3 64.7 1.0
O C:HOH2106 3.1 33.6 1.0
O C:LYS719 3.4 32.1 1.0
O C:HOH2108 3.5 57.6 1.0
NZ C:LYS719 3.6 53.3 1.0
OD1 C:ASP740 3.6 83.1 1.0
OD2 C:ASP740 3.9 81.6 1.0
O C:ALA721 4.0 51.5 1.0
CG C:ASP740 4.2 77.1 1.0
CE C:LYS719 4.3 58.4 1.0
C C:LYS719 4.5 44.8 1.0
O C:LEU718 4.7 31.5 1.0
O C:ASP722 4.8 53.9 1.0
CA C:LYS719 4.9 31.4 1.0

Reference:

R.Kanai, H.Ogawa, B.Vilsen, F.Cornelius, C.Toyoshima. Crystal Structure of A NA1-Bound NA1,K1-Atpase Preceding the E1P State Nature V. 502 201 2013.
ISSN: ISSN 0028-0836
Page generated: Mon Oct 7 13:56:41 2024

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