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Sodium in PDB 3wgu: Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without Oligomycin

Enzymatic activity of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without Oligomycin

All present enzymatic activity of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without Oligomycin:
3.6.3.9;

Protein crystallography data

The structure of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without Oligomycin, PDB code: 3wgu 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 (°) 106.383, 211.600, 257.124, 90.00, 90.00, 90.00
R / Rfree (%) 26.5 / 29.9

Other elements in 3wgu:

The structure of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin (pdb code 3wgu). 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 Without Oligomycin, PDB code: 3wgu:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3wgu

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Sodium binding site 1 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2005

b:0.6
occ:1.00
 O A:VAL325 2.3 70.5 1.0
O A:HOH2101 2.4 44.6 1.0
OD1 A:ASP804 2.5 87.8 1.0
O A:ALA323 2.5 79.4 1.0
O A:VAL322 2.7 58.0 1.0
C A:ALA323 2.9 75.0 1.0
C A:VAL325 3.0 73.7 1.0
N A:VAL325 3.1 73.1 1.0
OE2 A:GLU327 3.3 0.2 1.0
CA A:ALA323 3.4 73.3 1.0
CG A:ASP804 3.5 80.5 1.0
N A:ASN324 3.7 72.3 1.0
C A:VAL322 3.7 65.6 1.0
CA A:VAL325 3.7 71.5 1.0
NA A:NA2006 3.7 86.5 1.0
OD2 A:ASP804 3.7 85.4 1.0
N A:PRO326 3.9 75.9 1.0
C A:ASN324 3.9 72.5 1.0
N A:ALA323 4.0 71.1 1.0
CA A:ASN324 4.1 71.5 1.0
CD A:GLU327 4.1 0.7 1.0
CA A:PRO326 4.1 78.8 1.0
OE1 A:GLU327 4.3 0.7 1.0
CB A:VAL325 4.7 66.4 1.0
CB A:ALA323 4.8 75.7 1.0
OD1 A:ASP808 4.8 97.7 1.0
OD1 A:ASN776 4.8 95.0 1.0
CB A:ASP804 4.8 66.4 1.0
N A:GLU327 4.9 80.7 1.0
O A:ASN324 4.9 76.8 1.0

Sodium binding site 2 out of 8 in 3wgu

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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 Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2006

b:86.5
occ:1.00
 OE1 A:GLU779 2.5 90.1 1.0
O A:ALA323 2.6 79.4 1.0
OD1 A:ASP808 2.8 97.7 1.0
OD1 A:ASN776 3.1 95.0 1.0
OG A:SER775 3.2 95.6 1.0
CB A:SER775 3.4 90.0 1.0
O A:HOH2101 3.4 44.6 1.0
CD A:GLU779 3.5 89.3 1.0
O A:THR772 3.5 89.7 1.0
CG A:ASN776 3.5 88.5 1.0
N A:ASN776 3.5 65.0 1.0
NA A:NA2005 3.7 0.6 1.0
OE2 A:GLU779 3.7 98.0 1.0
OD1 A:ASP804 3.7 87.8 1.0
CG A:ASP808 3.8 94.5 1.0
ND2 A:ASN776 3.8 94.9 1.0
C A:ALA323 3.9 75.0 1.0
C A:SER775 3.9 77.9 1.0
CA A:ASN776 4.0 68.6 1.0
CA A:SER775 4.2 85.3 1.0
CB A:ASN776 4.4 76.7 1.0
OD2 A:ASP808 4.5 96.7 1.0
O A:SER775 4.5 87.8 1.0
C A:THR772 4.7 82.3 1.0
CA A:ALA323 4.7 73.3 1.0
CB A:ASP808 4.7 86.7 1.0
N A:SER775 4.8 88.2 1.0
CG A:GLU779 4.8 77.0 1.0
N A:ASN324 4.8 72.3 1.0
CA A:ASN324 4.8 71.5 1.0
ND2 A:ASN324 4.9 69.1 1.0
CG A:ASP804 4.9 80.5 1.0

Sodium binding site 3 out of 8 in 3wgu

Go back to Sodium Binding Sites List in 3wgu
Sodium binding site 3 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2007

b:0.9
occ:1.00
 O A:TYR771 2.4 93.0 1.0
OG1 A:THR774 2.5 80.9 1.0
NE2 A:GLN923 2.5 79.3 1.0
OE1 A:GLN923 2.6 83.8 1.0
CD A:GLN923 2.9 79.9 1.0
OD2 A:ASP808 3.1 96.7 1.0
OG A:SER775 3.1 95.6 1.0
C A:TYR771 3.4 89.9 1.0
OD2 A:ASP926 3.6 76.2 1.0
CE1 A:TYR771 3.6 84.8 1.0
CZ A:TYR771 3.6 90.7 1.0
CD1 A:TYR771 3.7 81.1 1.0
CE2 A:TYR771 3.7 84.0 1.0
CG A:TYR771 3.8 84.5 1.0
CD2 A:TYR771 3.8 81.1 1.0
N A:SER775 3.9 88.2 1.0
CB A:THR774 3.9 73.8 1.0
CB A:SER775 4.1 90.0 1.0
CA A:THR772 4.1 81.4 1.0
N A:THR772 4.2 82.0 1.0
OH A:TYR771 4.2 0.7 1.0
CG A:ASP808 4.3 94.5 1.0
CA A:TYR771 4.3 92.3 1.0
C A:THR772 4.3 82.3 1.0
CG A:GLN923 4.4 77.1 1.0
N A:THR774 4.5 70.3 1.0
O A:THR772 4.5 89.7 1.0
OE1 A:GLN854 4.6 66.3 1.0
CA A:SER775 4.6 85.3 1.0
CA A:THR774 4.6 78.2 1.0
CB A:TYR771 4.7 91.7 1.0
CG2 A:THR774 4.8 69.9 1.0
CG A:ASP926 4.8 77.1 1.0
C A:THR774 4.8 83.4 1.0
N A:LEU773 4.8 76.2 1.0
OD1 A:ASP808 4.9 97.7 1.0

Sodium binding site 4 out of 8 in 3wgu

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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 Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2008

b:0.9
occ:1.00
 O A:ALA721 2.6 55.7 1.0
O A:HOH2113 2.6 65.8 1.0
O A:HOH2112 3.1 72.0 1.0
O A:HOH2111 3.2 56.8 1.0
O A:LYS719 3.3 81.2 1.0
C A:ALA721 3.8 53.0 1.0
O A:LYS720 4.2 46.9 1.0
CA A:ASP722 4.3 56.8 1.0
NZ A:LYS719 4.3 96.0 1.0
O A:ASP722 4.3 61.2 1.0
C A:ASP722 4.3 55.9 1.0
C A:LYS719 4.4 71.9 1.0
N A:ASP722 4.5 54.0 1.0
C A:LYS720 4.5 44.0 1.0
N A:ALA721 4.8 32.7 1.0
CA A:ALA721 4.9 42.0 1.0

Sodium binding site 5 out of 8 in 3wgu

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Sodium binding site 5 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na2005

b:84.1
occ:1.00
 O C:VAL325 2.2 92.2 1.0
OD1 C:ASP804 2.2 75.3 1.0
O C:ALA323 2.5 0.7 1.0
O C:VAL322 2.7 85.0 1.0
C C:VAL325 3.0 87.2 1.0
C C:ALA323 3.1 95.9 1.0
CG C:ASP804 3.1 75.3 1.0
N C:VAL325 3.1 86.9 1.0
OE2 C:GLU327 3.2 0.2 1.0
O C:HOH2101 3.2 0.6 1.0
NA C:NA2006 3.3 0.2 1.0
OD2 C:ASP804 3.4 78.3 1.0
CA C:VAL325 3.6 83.7 1.0
N C:ASN324 3.7 92.7 1.0
CA C:ALA323 3.8 94.0 1.0
C C:VAL322 3.8 82.6 1.0
C C:ASN324 3.8 90.2 1.0
N C:PRO326 3.9 82.5 1.0
CA C:ASN324 4.1 92.7 1.0
CD C:GLU327 4.1 0.2 1.0
N C:ALA323 4.3 89.5 1.0
CA C:PRO326 4.3 80.2 1.0
CB C:ASP804 4.4 71.5 1.0
OE1 C:GLU327 4.4 0.1 1.0
CB C:VAL325 4.5 81.4 1.0
OD1 C:ASP808 4.5 95.7 1.0
N C:GLU327 4.7 87.9 1.0
OD1 C:ASN776 4.7 0.6 1.0
O C:ASN324 4.7 91.1 1.0

Sodium binding site 6 out of 8 in 3wgu

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Sodium binding site 6 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na2006

b:0.2
occ:1.00
 O C:ALA323 2.4 0.7 1.0
OE1 C:GLU779 2.5 75.4 1.0
O C:HOH2101 2.6 0.6 1.0
OD1 C:ASP808 2.7 95.7 1.0
OG C:SER775 2.9 55.8 1.0
OD1 C:ASN776 3.1 0.6 1.0
OD1 C:ASP804 3.2 75.3 1.0
NA C:NA2005 3.3 84.1 1.0
CD C:GLU779 3.4 82.0 1.0
OE2 C:GLU779 3.5 92.3 1.0
C C:ALA323 3.6 95.9 1.0
CG C:ASP808 3.7 92.3 1.0
CB C:SER775 3.8 60.0 1.0
O C:THR772 3.9 74.8 1.0
CG C:ASN776 4.0 0.3 1.0
N C:ASN776 4.0 70.9 1.0
CG C:ASP804 4.2 75.3 1.0
CA C:ALA323 4.4 94.0 1.0
OD2 C:ASP808 4.4 93.5 1.0
C C:SER775 4.4 72.5 1.0
CA C:ASN776 4.5 79.8 1.0
CB C:ASP804 4.5 71.5 1.0
ND2 C:ASN776 4.6 0.5 1.0
CA C:ASP804 4.6 72.0 1.0
N C:ASN324 4.6 92.7 1.0
CA C:SER775 4.7 69.0 1.0
CB C:ASP808 4.7 84.7 1.0
CA C:ASN324 4.7 92.7 1.0
CG C:GLU779 4.8 78.4 1.0
CB C:ASN776 4.8 93.7 1.0

Sodium binding site 7 out of 8 in 3wgu

Go back to Sodium Binding Sites List in 3wgu
Sodium binding site 7 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na2007

b:0.2
occ:1.00
 OG1 C:THR774 2.5 67.4 1.0
O C:TYR771 2.5 61.3 1.0
OG C:SER775 2.5 55.8 1.0
OD2 C:ASP808 2.8 93.5 1.0
N C:SER775 2.9 74.1 1.0
OE1 C:GLN923 3.1 83.1 1.0
CB C:SER775 3.1 60.0 1.0
NE2 C:GLN923 3.5 90.5 1.0
C C:THR772 3.6 69.3 1.0
CA C:SER775 3.6 69.0 1.0
C C:TYR771 3.7 62.6 1.0
O C:THR772 3.7 74.8 1.0
N C:THR774 3.7 73.0 1.0
CD C:GLN923 3.7 84.1 1.0
CB C:THR774 3.7 62.7 1.0
CG C:ASP808 3.8 92.3 1.0
CA C:THR772 3.9 66.7 1.0
C C:THR774 3.9 74.9 1.0
CA C:THR774 3.9 74.7 1.0
N C:LEU773 4.0 65.5 1.0
OD1 C:ASP808 4.1 95.7 1.0
OD2 C:ASP926 4.2 87.8 1.0
N C:THR772 4.2 63.8 1.0
C C:LEU773 4.2 71.0 1.0
CA C:LEU773 4.7 63.8 1.0
CG2 C:THR774 4.8 58.5 1.0
O C:LEU773 4.9 75.0 1.0
CA C:TYR771 4.9 63.5 1.0
C C:SER775 4.9 72.5 1.0
CE2 C:TYR771 4.9 82.0 1.0
CD2 C:TYR771 4.9 80.2 1.0
CZ C:TYR771 5.0 77.7 1.0
CG C:TYR771 5.0 72.6 1.0

Sodium binding site 8 out of 8 in 3wgu

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Sodium binding site 8 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na2008

b:62.8
occ:1.00
 O C:HOH2111 2.3 59.1 1.0
O C:LYS719 3.3 70.3 1.0
NZ C:LYS719 3.3 84.0 1.0
O C:ALA721 3.5 65.5 1.0
O C:HOH2112 3.6 50.3 1.0
OD2 C:ASP740 3.7 85.3 1.0
OD1 C:ASP740 3.7 91.7 1.0
O C:HOH2110 4.1 39.1 1.0
CG C:ASP740 4.1 83.6 1.0
O C:LEU718 4.3 58.1 1.0
CE C:LYS719 4.3 85.5 1.0
C C:LYS719 4.3 66.7 1.0
O C:ASP722 4.4 72.5 1.0
C C:ALA721 4.7 62.6 1.0
CA C:LYS719 4.8 59.1 1.0
C C:ASP722 4.9 69.4 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 13:56:43 2024

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