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Sodium in PDB 2eb4: Crystal Structure of Apo-Hpcg

Protein crystallography data

The structure of Crystal Structure of Apo-Hpcg, PDB code: 2eb4 was solved by A.Izumi, D.Rea, T.Adachi, S.Unzai, S.Y.Park, D.I.Roper, J.R.H.Tame, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 136.740, 136.740, 192.882, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 22.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Apo-Hpcg (pdb code 2eb4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Apo-Hpcg, PDB code: 2eb4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 2eb4

Go back to Sodium Binding Sites List in 2eb4
Sodium binding site 1 out of 5 in the Crystal Structure of Apo-Hpcg


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 Apo-Hpcg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3001

b:22.8
occ:1.00
 O A:GLN70 2.5 36.5 1.0
O A:ILE75 2.6 38.3 1.0
O A:LYS67 2.7 31.6 1.0
O A:SER73 2.9 40.9 1.0
O A:ALA68 3.0 31.9 1.0
C A:ALA68 3.5 32.1 1.0
C A:GLN70 3.7 36.4 1.0
C A:SER73 3.8 41.0 1.0
C A:ILE75 3.8 38.4 1.0
C A:LYS67 3.9 31.4 1.0
CA A:ALA68 4.0 31.8 1.0
CB A:SER73 4.1 41.0 1.0
N A:GLN70 4.1 34.7 1.0
C A:MET69 4.2 33.8 1.0
N A:MET69 4.3 32.5 1.0
CA A:SER73 4.3 41.0 1.0
N A:ALA68 4.4 31.6 1.0
CA A:GLN70 4.4 35.9 1.0
N A:ILE75 4.4 40.0 1.0
O A:MET69 4.4 33.7 1.0
N A:SER73 4.5 40.8 1.0
OG A:SER73 4.6 41.7 1.0
O A:HOH3194 4.6 45.5 1.0
CA A:ILE75 4.6 39.2 1.0
C A:GLN74 4.7 40.6 1.0
N A:ALA71 4.7 37.1 1.0
CA A:MET69 4.7 33.0 1.0
N A:GLN74 4.7 41.0 1.0
N A:SER76 4.8 37.2 1.0
CA A:SER76 4.9 36.2 1.0
CA A:ALA71 4.9 37.9 1.0
CB A:GLN70 4.9 36.0 1.0

Sodium binding site 2 out of 5 in 2eb4

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Sodium binding site 2 out of 5 in the Crystal Structure of Apo-Hpcg


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 Apo-Hpcg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3002

b:24.4
occ:1.00
 O B:GLN70 2.5 37.4 1.0
O B:ILE75 2.7 37.3 1.0
O B:LYS67 2.7 32.5 1.0
O B:SER73 2.9 41.4 1.0
O B:ALA68 3.0 33.1 1.0
C B:ALA68 3.5 33.1 1.0
C B:GLN70 3.6 37.2 1.0
C B:SER73 3.8 41.2 1.0
C B:LYS67 3.9 32.5 1.0
C B:ILE75 3.9 37.4 1.0
CA B:ALA68 4.0 32.8 1.0
O B:HOH3162 4.0 42.4 1.0
N B:GLN70 4.1 35.7 1.0
CB B:SER73 4.1 41.3 1.0
C B:MET69 4.2 34.9 1.0
N B:MET69 4.3 33.5 1.0
CA B:SER73 4.3 41.2 1.0
CA B:GLN70 4.4 36.7 1.0
N B:ILE75 4.4 39.3 1.0
N B:ALA68 4.4 32.5 1.0
O B:MET69 4.4 34.7 1.0
N B:SER73 4.5 41.0 1.0
OG B:SER73 4.5 41.6 1.0
CA B:ILE75 4.6 38.3 1.0
CA B:MET69 4.7 34.0 1.0
N B:ALA71 4.7 37.9 1.0
C B:GLN74 4.7 40.2 1.0
N B:GLN74 4.8 41.0 1.0
O B:HOH3190 4.8 45.7 1.0
CB B:GLN70 4.8 36.8 1.0
CA B:ALA71 4.9 38.6 1.0
CB B:ILE75 4.9 38.5 1.0
N B:SER76 4.9 36.1 1.0
C B:ALA71 4.9 39.2 1.0
O B:ALA71 5.0 39.4 1.0

Sodium binding site 3 out of 5 in 2eb4

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Sodium binding site 3 out of 5 in the Crystal Structure of Apo-Hpcg


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 Apo-Hpcg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3003

b:25.5
occ:1.00
 O C:GLN70 2.6 36.1 1.0
O C:ILE75 2.7 37.9 1.0
O C:SER73 2.7 40.1 1.0
O C:LYS67 2.7 31.2 1.0
O C:ALA68 3.0 31.6 1.0
C C:ALA68 3.4 31.6 1.0
C C:GLN70 3.7 35.9 1.0
C C:SER73 3.7 40.2 1.0
C C:LYS67 3.8 30.9 1.0
C C:ILE75 3.9 37.9 1.0
CA C:ALA68 3.9 31.2 1.0
C C:MET69 4.0 33.1 1.0
N C:GLN70 4.0 34.1 1.0
N C:MET69 4.2 31.9 1.0
CB C:SER73 4.2 40.4 1.0
O C:MET69 4.2 32.9 1.0
N C:ILE75 4.3 39.2 1.0
N C:ALA68 4.4 31.0 1.0
CA C:SER73 4.4 40.2 1.0
CA C:GLN70 4.4 35.2 1.0
CA C:ILE75 4.6 38.6 1.0
N C:SER73 4.6 40.1 1.0
CA C:MET69 4.6 32.2 1.0
OG C:SER73 4.6 41.0 1.0
C C:GLN74 4.6 39.8 1.0
N C:ALA71 4.7 36.6 1.0
N C:GLN74 4.7 40.2 1.0
O C:HOH3195 4.7 42.8 1.0
CA C:ALA71 4.9 37.5 1.0
N C:SER76 4.9 36.7 1.0
CA C:GLN74 5.0 40.2 1.0

Sodium binding site 4 out of 5 in 2eb4

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Sodium binding site 4 out of 5 in the Crystal Structure of Apo-Hpcg


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 Apo-Hpcg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na3004

b:25.3
occ:1.00
 O D:GLN70 2.6 38.1 1.0
O D:ILE75 2.7 40.3 1.0
O D:LYS67 2.7 33.8 1.0
O D:SER73 2.9 42.3 1.0
O D:ALA68 3.0 34.2 1.0
C D:ALA68 3.5 34.1 1.0
C D:GLN70 3.7 38.0 1.0
C D:SER73 3.8 42.3 1.0
C D:ILE75 3.9 40.3 1.0
C D:LYS67 3.9 33.5 1.0
CA D:ALA68 4.0 34.0 1.0
CB D:SER73 4.1 42.2 1.0
N D:GLN70 4.2 36.3 1.0
C D:MET69 4.2 35.3 1.0
N D:MET69 4.3 34.4 1.0
CA D:SER73 4.3 42.1 1.0
N D:ALA68 4.4 33.8 1.0
O D:MET69 4.4 35.3 1.0
N D:SER73 4.4 41.8 1.0
N D:ILE75 4.4 41.6 1.0
CA D:GLN70 4.5 37.4 1.0
O D:HOH3132 4.5 44.6 1.0
OG D:SER73 4.5 42.5 1.0
CA D:ILE75 4.6 41.0 1.0
N D:ALA71 4.7 38.7 1.0
C D:GLN74 4.7 42.1 1.0
CA D:MET69 4.7 34.7 1.0
N D:SER76 4.8 39.4 1.0
CA D:ALA71 4.8 39.5 1.0
N D:GLN74 4.8 42.4 1.0
C D:ALA71 4.9 40.0 1.0
O D:ALA71 4.9 40.3 1.0
CA D:SER76 4.9 38.5 1.0

Sodium binding site 5 out of 5 in 2eb4

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Sodium binding site 5 out of 5 in the Crystal Structure of Apo-Hpcg


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 Apo-Hpcg within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na3005

b:29.4
occ:1.00
 O E:GLN70 2.6 42.9 1.0
O E:ILE75 2.6 42.8 1.0
O E:LYS67 2.7 38.2 1.0
O E:SER73 2.9 46.2 1.0
O E:ALA68 3.2 39.2 1.0
C E:ALA68 3.6 39.1 1.0
C E:GLN70 3.7 42.7 1.0
C E:ILE75 3.9 42.8 1.0
C E:SER73 3.9 46.2 1.0
C E:LYS67 3.9 38.0 1.0
CA E:ALA68 4.0 38.8 1.0
C E:MET69 4.2 40.5 1.0
N E:GLN70 4.2 41.2 1.0
CB E:SER73 4.2 46.4 1.0
N E:MET69 4.2 39.5 1.0
O E:MET69 4.3 40.4 1.0
N E:ALA68 4.4 38.5 1.0
CA E:SER73 4.4 46.3 1.0
CG2 E:ILE75 4.5 44.2 1.0
N E:ILE75 4.5 44.5 1.0
CA E:GLN70 4.5 42.1 1.0
N E:SER73 4.5 46.2 1.0
N E:ALA71 4.7 43.3 1.0
CA E:MET69 4.7 39.9 1.0
CA E:ILE75 4.7 43.6 1.0
C E:GLN74 4.7 45.4 1.0
CA E:ALA71 4.8 44.2 1.0
N E:SER76 4.8 41.5 1.0
C E:ALA71 4.9 44.7 1.0
O E:ALA71 4.9 44.9 1.0
CG E:GLN70 4.9 42.5 1.0
N E:GLN74 4.9 46.0 1.0
OG E:SER73 4.9 46.8 1.0
CA E:SER76 5.0 40.2 1.0

Reference:

A.Izumi, D.Rea, T.Adachi, S.Unzai, S.Y.Park, D.I.Roper, J.R.H.Tame. Structure and Mechanism of Hpcg, A Hydratase in the Homoprotocatechuate Degradation Pathway of Escherichia Coli J.Mol.Biol. V. 370 899 2007.
ISSN: ISSN 0022-2836
PubMed: 17559873
DOI: 10.1016/J.JMB.2007.05.006
Page generated: Sun Aug 17 10:23:58 2025

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