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Sodium in PDB 3io1: Crystal Structure of Aminobenzoyl-Glutamate Utilization Protein From Klebsiella Pneumoniae

Protein crystallography data

The structure of Crystal Structure of Aminobenzoyl-Glutamate Utilization Protein From Klebsiella Pneumoniae, PDB code: 3io1 was solved by D.Kumaran, K.Baumann, S.K.Burley, S.Swaminathan, New York Sgxresearch Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.02 / 2.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 183.390, 48.519, 107.998, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 26

Other elements in 3io1:

The structure of Crystal Structure of Aminobenzoyl-Glutamate Utilization Protein From Klebsiella Pneumoniae also contains other interesting chemical elements:

Yttrium (Y) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Aminobenzoyl-Glutamate Utilization Protein From Klebsiella Pneumoniae (pdb code 3io1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Aminobenzoyl-Glutamate Utilization Protein From Klebsiella Pneumoniae, PDB code: 3io1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3io1

Go back to Sodium Binding Sites List in 3io1
Sodium binding site 1 out of 2 in the Crystal Structure of Aminobenzoyl-Glutamate Utilization Protein From Klebsiella Pneumoniae


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 Aminobenzoyl-Glutamate Utilization Protein From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:49.3
occ:1.00
OD2 A:ASP151 2.3 63.8 1.0
OD2 A:ASP116 2.4 60.5 1.0
OD1 A:ASP151 2.4 62.2 1.0
OE1 A:GLU183 2.4 40.5 1.0
CG A:ASP151 2.7 63.5 1.0
CG A:ASP116 3.4 57.1 1.0
CD A:GLU183 3.4 41.3 1.0
OE2 A:GLU184 3.6 58.8 1.0
CG A:GLU183 3.9 38.4 1.0
OD1 A:ASP116 3.9 59.2 1.0
CB A:GLU183 4.0 38.6 1.0
OE1 A:GLU184 4.1 58.4 1.0
CB A:ASP151 4.2 63.6 1.0
CD A:GLU184 4.2 56.3 1.0
OE2 A:GLU183 4.3 43.3 1.0
CB A:ASP116 4.4 54.6 1.0
OD2 A:ASP118 4.5 55.9 1.0
O A:ASP118 4.6 54.2 1.0
O A:HIS150 4.6 64.7 1.0
CE1 A:HIS153 4.7 58.1 1.0
ND1 A:HIS153 4.8 58.9 1.0
CD2 A:HIS150 4.8 62.9 1.0
N A:GLU184 4.9 39.3 1.0
CA A:ASP151 5.0 63.7 1.0

Sodium binding site 2 out of 2 in 3io1

Go back to Sodium Binding Sites List in 3io1
Sodium binding site 2 out of 2 in the Crystal Structure of Aminobenzoyl-Glutamate Utilization Protein From Klebsiella Pneumoniae


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 Aminobenzoyl-Glutamate Utilization Protein From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:49.7
occ:1.00
OD1 B:ASP151 2.0 38.6 1.0
OD2 B:ASP151 2.3 42.4 1.0
CG B:ASP151 2.4 39.0 1.0
OE1 B:GLU183 2.5 30.7 1.0
OE2 B:GLU184 2.8 49.3 1.0
OD2 B:ASP116 3.3 36.2 1.0
CG B:ASP116 3.4 32.5 1.0
OD1 B:ASP116 3.5 35.9 1.0
CD B:GLU183 3.6 32.0 1.0
CD B:GLU184 3.8 46.5 1.0
O B:ASP118 3.9 38.2 1.0
CB B:GLU183 3.9 25.8 1.0
CB B:ASP151 4.0 43.3 1.0
OD2 B:ASP118 4.0 37.3 1.0
CG B:GLU184 4.1 41.8 1.0
CG B:GLU183 4.2 30.5 1.0
CB B:ASP116 4.3 31.4 1.0
CG B:ASP118 4.5 33.9 1.0
N B:GLU184 4.6 29.1 1.0
OD1 B:ASP118 4.6 32.8 1.0
OE2 B:GLU183 4.7 37.1 1.0
C B:ASP118 4.7 37.8 1.0
CE1 B:HIS153 4.8 35.5 1.0
ND1 B:HIS153 4.8 35.6 1.0
OE1 B:GLU184 4.8 48.0 1.0
C B:GLU183 4.9 26.2 1.0
CA B:ASP151 4.9 44.4 1.0
CA B:GLU183 4.9 24.8 1.0

Reference:

D.Kumaran, K.Baumann, S.K.Burley, S.Swaminathan. Crystal Structure of Aminobenzoyl-Glutamate Utilization Protein From Klebsiella Pneumoniae To Be Published.
Page generated: Mon Oct 7 10:59:59 2024

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