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Sodium in PDB 8dqm: Crystal Structure of Isoaspartyl Aminopeptidase From Roseivivax Halodurans Dsm 15395

Protein crystallography data

The structure of Crystal Structure of Isoaspartyl Aminopeptidase From Roseivivax Halodurans Dsm 15395, PDB code: 8dqm was solved by I.Sharon, T.M.Schmeing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 98.96 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.222, 154.593, 197.911, 90, 90, 90
R / Rfree (%) 24.3 / 26.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Isoaspartyl Aminopeptidase From Roseivivax Halodurans Dsm 15395 (pdb code 8dqm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Isoaspartyl Aminopeptidase From Roseivivax Halodurans Dsm 15395, PDB code: 8dqm:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8dqm

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Sodium binding site 1 out of 4 in the Crystal Structure of Isoaspartyl Aminopeptidase From Roseivivax Halodurans Dsm 15395


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 Isoaspartyl Aminopeptidase From Roseivivax Halodurans Dsm 15395 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:71.7
occ:1.00
 O A:GLU66 2.4 39.9 1.0
O A:ALA71 2.4 42.2 1.0
O A:ARG73 2.4 34.0 1.0
O A:LEU63 2.5 29.1 1.0
O A:GLU64 2.5 28.2 1.0
O A:PHE69 2.6 35.5 1.0
C A:GLU64 3.1 30.9 1.0
C A:GLU66 3.4 29.4 1.0
CA A:GLU64 3.4 35.8 1.0
C A:LEU63 3.5 31.5 1.0
C A:ALA71 3.5 36.0 1.0
C A:ARG73 3.6 34.4 1.0
C A:PHE69 3.6 35.2 1.0
N A:GLU66 3.8 31.6 1.0
N A:GLU64 3.9 35.8 1.0
N A:ARG73 3.9 34.4 1.0
N A:ALA71 4.0 37.0 1.0
N A:ASP65 4.0 27.8 1.0
CA A:GLU66 4.1 23.3 1.0
CB A:PHE69 4.1 26.0 1.0
CA A:PHE69 4.2 27.6 1.0
N A:PHE69 4.2 31.1 1.0
CA A:ALA71 4.3 30.7 1.0
CA A:ARG73 4.3 33.3 1.0
C A:ASP65 4.3 32.2 1.0
N A:PRO67 4.3 30.8 1.0
CA A:PRO67 4.4 33.0 1.0
C A:GLY72 4.5 33.1 1.0
CB A:ALA71 4.5 28.1 1.0
N A:GLY72 4.6 38.1 1.0
CB A:GLU66 4.6 25.1 1.0
N A:GLY74 4.6 34.9 1.0
CB A:ARG73 4.6 36.6 1.0
N A:ASN70 4.7 38.6 1.0
CA A:ASP65 4.7 30.8 1.0
CA A:GLY72 4.8 31.2 1.0
C A:PRO67 4.8 29.7 1.0
CB A:GLU64 4.8 34.8 1.0
O A:ASP65 4.8 33.0 1.0
CA A:LEU63 4.9 30.3 1.0
CA A:GLY74 4.9 39.9 1.0

Sodium binding site 2 out of 4 in 8dqm

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Sodium binding site 2 out of 4 in the Crystal Structure of Isoaspartyl Aminopeptidase From Roseivivax Halodurans Dsm 15395


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 Isoaspartyl Aminopeptidase From Roseivivax Halodurans Dsm 15395 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:38.6
occ:1.00
 O C:ARG73 2.3 36.2 1.0
O C:PHE69 2.3 40.6 1.0
O C:ALA71 2.3 40.9 1.0
O C:GLU66 2.4 37.6 1.0
O C:LEU63 2.7 38.2 1.0
O C:GLU64 2.8 37.7 1.0
C C:PHE69 3.4 44.0 1.0
C C:GLU64 3.4 38.6 1.0
C C:ARG73 3.4 34.9 1.0
C C:GLU66 3.5 40.2 1.0
C C:ALA71 3.5 36.9 1.0
CA C:GLU64 3.7 39.0 1.0
C C:LEU63 3.7 38.5 1.0
N C:ALA71 3.8 30.7 1.0
CA C:PHE69 4.0 40.4 1.0
N C:ARG73 4.0 42.9 1.0
N C:PHE69 4.0 42.9 1.0
CB C:PHE69 4.0 34.4 1.0
N C:GLU66 4.1 39.9 1.0
N C:GLU64 4.2 40.7 1.0
CA C:ALA71 4.2 31.3 1.0
CA C:ARG73 4.3 34.5 1.0
CA C:GLU66 4.3 40.1 1.0
N C:PRO67 4.3 40.2 1.0
CA C:PRO67 4.4 39.6 1.0
N C:ASP65 4.4 39.1 1.0
N C:GLY74 4.4 35.9 1.0
N C:ASN70 4.4 39.8 1.0
C C:GLY72 4.5 36.0 1.0
CB C:ALA71 4.5 37.0 1.0
C C:ASP65 4.6 40.2 1.0
N C:GLY72 4.6 38.5 1.0
CA C:GLY74 4.6 37.1 1.0
C C:PRO67 4.7 35.9 1.0
CB C:GLU66 4.7 37.7 1.0
CB C:ARG73 4.7 40.0 1.0
C C:GLY74 4.8 42.1 1.0
C C:ASN70 4.8 35.6 1.0
CA C:GLY72 4.9 33.8 1.0
CA C:ASN70 4.9 37.9 1.0

Sodium binding site 3 out of 4 in 8dqm

Go back to Sodium Binding Sites List in 8dqm
Sodium binding site 3 out of 4 in the Crystal Structure of Isoaspartyl Aminopeptidase From Roseivivax Halodurans Dsm 15395


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 Isoaspartyl Aminopeptidase From Roseivivax Halodurans Dsm 15395 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na201

b:42.0
occ:1.00
 O E:ARG73 2.2 40.0 1.0
O E:ALA71 2.3 44.8 1.0
O E:PHE69 2.4 43.0 1.0
O E:GLU66 2.4 42.3 1.0
O E:LEU63 2.7 41.2 1.0
O E:GLU64 2.7 38.0 1.0
C E:GLU64 3.4 38.8 1.0
C E:ARG73 3.4 38.4 1.0
C E:PHE69 3.4 44.9 1.0
C E:GLU66 3.4 39.6 1.0
C E:ALA71 3.5 39.8 1.0
CA E:GLU64 3.7 40.4 1.0
C E:LEU63 3.8 38.2 1.0
N E:ALA71 3.8 39.7 1.0
N E:ARG73 3.9 36.2 1.0
CA E:PHE69 4.0 44.2 1.0
N E:PHE69 4.1 42.1 1.0
N E:GLU66 4.1 39.4 1.0
CB E:PHE69 4.1 37.6 1.0
CA E:ARG73 4.2 37.3 1.0
CA E:ALA71 4.2 36.0 1.0
N E:GLU64 4.2 38.4 1.0
N E:PRO67 4.3 43.9 1.0
CA E:GLU66 4.3 41.8 1.0
CA E:PRO67 4.3 42.7 1.0
N E:ASP65 4.3 40.3 1.0
N E:GLY74 4.4 34.6 1.0
C E:GLY72 4.4 36.6 1.0
N E:ASN70 4.5 40.4 1.0
C E:ASP65 4.5 43.3 1.0
CA E:GLY74 4.6 38.8 1.0
N E:GLY72 4.6 39.4 1.0
CB E:ALA71 4.6 35.0 1.0
C E:PRO67 4.6 40.3 1.0
CB E:ARG73 4.7 41.3 1.0
C E:GLY74 4.8 39.7 1.0
CB E:GLU66 4.8 46.4 1.0
CA E:GLY72 4.8 36.0 1.0
C E:ASN70 4.8 41.0 1.0
CA E:ASN70 5.0 40.5 1.0
O E:GLY72 5.0 39.4 1.0
CA E:ASP65 5.0 42.1 1.0

Sodium binding site 4 out of 4 in 8dqm

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Sodium binding site 4 out of 4 in the Crystal Structure of Isoaspartyl Aminopeptidase From Roseivivax Halodurans Dsm 15395


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 Isoaspartyl Aminopeptidase From Roseivivax Halodurans Dsm 15395 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na201

b:29.2
occ:1.00
 O G:ARG73 2.2 26.8 1.0
O G:ALA71 2.3 33.4 1.0
O G:GLU66 2.4 27.8 1.0
O G:GLU64 2.6 32.8 1.0
O G:PHE69 2.6 35.5 1.0
O G:LEU63 2.7 30.9 1.0
C G:GLU64 3.2 35.6 1.0
C G:GLU66 3.4 29.8 1.0
C G:ARG73 3.4 32.6 1.0
C G:ALA71 3.5 34.6 1.0
CA G:GLU64 3.6 34.5 1.0
C G:PHE69 3.6 34.4 1.0
C G:LEU63 3.7 27.8 1.0
N G:ARG73 3.8 32.8 1.0
N G:GLU66 3.9 27.1 1.0
N G:ALA71 3.9 37.1 1.0
N G:GLU64 4.1 27.9 1.0
CA G:ARG73 4.1 32.4 1.0
N G:ASP65 4.2 35.3 1.0
CA G:GLU66 4.2 29.3 1.0
CA G:PHE69 4.2 28.2 1.0
CA G:ALA71 4.2 36.7 1.0
CB G:PHE69 4.2 24.3 1.0
N G:PHE69 4.2 31.9 1.0
N G:PRO67 4.2 30.2 1.0
CA G:PRO67 4.3 28.7 1.0
C G:ASP65 4.3 31.1 1.0
C G:GLY72 4.4 27.0 1.0
N G:GLY74 4.4 31.3 1.0
N G:GLY72 4.5 39.7 1.0
CB G:ARG73 4.5 29.4 1.0
CB G:ALA71 4.6 33.4 1.0
N G:ASN70 4.6 38.6 1.0
CA G:GLY74 4.7 34.5 1.0
CB G:GLU66 4.7 29.4 1.0
C G:PRO67 4.7 30.7 1.0
CA G:GLY72 4.7 28.8 1.0
CA G:ASP65 4.8 30.6 1.0
O G:ASP65 4.9 33.5 1.0
C G:GLY74 4.9 41.0 1.0
CB G:GLU64 4.9 33.3 1.0
C G:ASN70 5.0 35.6 1.0
O G:GLY72 5.0 30.8 1.0

Reference:

I.Sharon, T.M.Schmeing. Crystal Structure of Isoaspartyl Dipeptidase From Leucothrix Mucor DSM2157 To Be Published.
Page generated: Mon Aug 18 13:54:04 2025

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