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Sodium in PDB 1w7z: Crystal Structure of the Free (Uncomplexed) Ecballium Elaterium Trypsin Inhibitor (Eeti-II)

Protein crystallography data

The structure of Crystal Structure of the Free (Uncomplexed) Ecballium Elaterium Trypsin Inhibitor (Eeti-II), PDB code: 1w7z was solved by R.Kraetzner, J.E.Debreczeni, T.Pape, H.Kolmar, T.R.Schneider, I.Uson, G.M.Scheldrick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.13 / 1.67
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 71.160, 82.340, 62.930, 90.00, 118.80, 90.00
R / Rfree (%) 19.4 / 23.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Free (Uncomplexed) Ecballium Elaterium Trypsin Inhibitor (Eeti-II) (pdb code 1w7z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Free (Uncomplexed) Ecballium Elaterium Trypsin Inhibitor (Eeti-II), PDB code: 1w7z:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 1w7z

Go back to Sodium Binding Sites List in 1w7z
Sodium binding site 1 out of 3 in the Crystal Structure of the Free (Uncomplexed) Ecballium Elaterium Trypsin Inhibitor (Eeti-II)


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 the Free (Uncomplexed) Ecballium Elaterium Trypsin Inhibitor (Eeti-II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1032

b:29.2
occ:1.00
 O B:CYS15 2.1 25.3 1.0
O A:CYS15 2.1 24.6 1.0
O B:SER13 2.2 28.7 1.0
O A:SER13 2.3 23.6 1.0
C A:SER13 3.1 23.2 1.0
C B:SER13 3.2 28.4 1.0
C B:CYS15 3.2 22.6 1.0
C A:CYS15 3.3 22.6 1.0
N B:CYS15 3.4 21.5 1.0
N A:CYS15 3.5 20.4 1.0
C B:ASP14 3.7 24.9 1.0
CA A:SER13 3.8 23.2 1.0
C A:ASP14 3.9 21.9 1.0
CA B:SER13 3.9 29.4 1.0
CA B:CYS15 3.9 22.7 1.0
CA A:CYS15 4.0 21.4 1.0
N B:ASP14 4.1 27.1 1.0
N A:ASP14 4.1 22.4 1.0
O B:HOH2013 4.1 37.1 1.0
O B:ASP14 4.1 24.4 1.0
CA B:ASP14 4.2 25.7 1.0
O A:ASP12 4.3 22.3 1.0
N B:LEU16 4.3 21.6 1.0
N A:LEU16 4.3 23.1 1.0
CA A:ASP14 4.4 21.1 1.0
O A:ASP14 4.4 21.8 1.0
O B:ASP12 4.4 30.0 1.0
CA A:LEU16 4.6 23.9 1.0
CA B:LEU16 4.6 22.4 1.0
CB A:SER13 4.6 22.6 1.0
CB B:SER13 4.7 31.4 1.0
C A:LEU16 4.8 24.3 1.0
N A:SER13 4.9 22.2 1.0
O A:LEU16 4.9 22.7 1.0
C B:LEU16 5.0 23.1 1.0
CB A:CYS15 5.0 21.3 1.0

Sodium binding site 2 out of 3 in 1w7z

Go back to Sodium Binding Sites List in 1w7z
Sodium binding site 2 out of 3 in the Crystal Structure of the Free (Uncomplexed) Ecballium Elaterium Trypsin Inhibitor (Eeti-II)


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 the Free (Uncomplexed) Ecballium Elaterium Trypsin Inhibitor (Eeti-II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1032

b:25.6
occ:1.00
 O C:SER13 2.1 27.3 1.0
O C:CYS15 2.2 26.1 1.0
O D:CYS15 2.2 25.1 1.0
O D:SER13 2.2 22.4 1.0
C C:SER13 3.1 28.0 1.0
C D:SER13 3.2 21.9 1.0
C C:CYS15 3.3 23.8 1.0
C D:CYS15 3.3 20.3 1.0
N C:CYS15 3.4 24.0 1.0
N D:CYS15 3.5 19.5 1.0
C C:ASP14 3.6 24.7 1.0
CA D:SER13 3.8 22.1 1.0
C D:ASP14 3.8 19.9 1.0
CA C:SER13 3.9 28.3 1.0
N C:ASP14 3.9 26.9 1.0
CA C:CYS15 3.9 23.7 1.0
O C:ASP14 4.0 25.1 1.0
CA D:CYS15 4.0 19.0 1.0
CA C:ASP14 4.1 26.8 1.0
O D:HOH2012 4.1 31.1 1.0
N D:ASP14 4.1 20.4 1.0
O D:ASP12 4.3 21.0 1.0
N C:LEU16 4.3 22.3 1.0
CA D:ASP14 4.4 19.4 1.0
O D:ASP14 4.4 19.4 1.0
N D:LEU16 4.4 19.5 1.0
O C:ASP12 4.5 27.2 1.0
CA D:LEU16 4.6 20.6 1.0
CB C:SER13 4.6 30.0 1.0
CB D:SER13 4.6 22.6 1.0
CA C:LEU16 4.6 22.3 1.0
C D:LEU16 4.8 21.8 1.0
N D:SER13 5.0 20.8 1.0

Sodium binding site 3 out of 3 in 1w7z

Go back to Sodium Binding Sites List in 1w7z
Sodium binding site 3 out of 3 in the Crystal Structure of the Free (Uncomplexed) Ecballium Elaterium Trypsin Inhibitor (Eeti-II)


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 the Free (Uncomplexed) Ecballium Elaterium Trypsin Inhibitor (Eeti-II) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1031

b:32.4
occ:1.00
 O F:CYS15 2.0 28.6 1.0
O E:CYS15 2.3 27.3 1.0
O E:SER13 2.3 31.3 1.0
O F:SER13 2.4 26.2 1.0
C F:CYS15 3.2 26.3 1.0
C E:SER13 3.2 31.4 1.0
C F:SER13 3.2 25.7 1.0
C E:CYS15 3.3 26.4 1.0
N F:CYS15 3.5 23.0 1.0
N E:CYS15 3.5 25.6 1.0
C E:ASP14 3.7 27.5 1.0
C F:ASP14 3.9 24.0 1.0
CA F:CYS15 3.9 24.2 1.0
CA F:SER13 3.9 25.6 1.0
CA E:CYS15 4.0 25.5 1.0
CA E:SER13 4.0 31.7 1.0
O E:HOH2011 4.1 45.3 1.0
N E:ASP14 4.1 30.2 1.0
N F:ASP14 4.1 24.0 1.0
N F:LEU16 4.2 26.0 1.0
O E:ASP14 4.2 27.0 1.0
CA E:ASP14 4.2 29.9 1.0
O F:ASP12 4.3 25.1 1.0
N E:LEU16 4.4 25.2 1.0
O F:ASP14 4.4 24.6 1.0
CA F:ASP14 4.4 25.2 1.0
CA F:LEU16 4.4 27.1 1.0
O E:ASP12 4.5 29.8 1.0
C F:LEU16 4.7 27.9 1.0
CA E:LEU16 4.7 26.9 1.0
CB F:SER13 4.7 26.6 1.0
CB E:SER13 4.8 32.3 1.0
O F:LEU16 4.8 28.4 1.0
CB F:CYS15 5.0 24.0 1.0

Reference:

R.Kraetzner, J.E.Debreczeni, T.Pape, T.R.Schneider, A.Wentzel, H.Kolmar, G.M.Scheldrick, I.Uson. Structure of Ecballium Elaterium Trypsin Inhibitor II (Eeti-II): A Rigid Molecular Scaffold Acta Crystallogr.,Sect.D V. 61 1255 2005.
ISSN: ISSN 0907-4449
PubMed: 16131759
DOI: 10.1107/S0907444905021207
Page generated: Mon Oct 7 00:24:20 2024

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