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Sodium in PDB 3fkr: Structure of L-2-Keto-3-Deoxyarabonate Dehydratase Complex with Pyruvate

Protein crystallography data

The structure of Structure of L-2-Keto-3-Deoxyarabonate Dehydratase Complex with Pyruvate, PDB code: 3fkr was solved by N.Shimada, B.Mikami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 79.259, 79.259, 206.527, 90.00, 90.00, 120.00
R / Rfree (%) 19.6 / 23.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of L-2-Keto-3-Deoxyarabonate Dehydratase Complex with Pyruvate (pdb code 3fkr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of L-2-Keto-3-Deoxyarabonate Dehydratase Complex with Pyruvate, PDB code: 3fkr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3fkr

Go back to Sodium Binding Sites List in 3fkr
Sodium binding site 1 out of 2 in the Structure of L-2-Keto-3-Deoxyarabonate Dehydratase Complex with Pyruvate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of L-2-Keto-3-Deoxyarabonate Dehydratase Complex with Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:14.6
occ:1.00
OE2 A:GLU184 2.0 22.7 1.0
NZ A:KPI182 2.2 21.8 1.0
O A:HOH1087 2.4 31.1 1.0
O1 A:KPI182 2.4 55.0 1.0
CD A:GLU184 2.7 24.5 1.0
OE1 A:GLU184 2.7 25.5 1.0
CX1 A:KPI182 2.9 24.6 1.0
CX2 A:KPI182 3.0 26.7 1.0
CE A:KPI182 3.1 17.6 1.0
O A:HOH1088 3.8 38.2 1.0
N A:GLU210 4.0 20.1 1.0
CG A:GLU184 4.1 31.5 1.0
OE2 A:GLU211 4.1 33.6 1.0
O2 A:KPI182 4.1 29.6 1.0
CD A:KPI182 4.2 17.4 1.0
C1 A:KPI182 4.4 31.3 1.0
OE1 A:GLN154 4.4 31.2 1.0
CA A:GLU210 4.7 19.4 1.0
CA A:GLY209 4.7 17.4 1.0
C A:GLY209 4.8 21.4 1.0
CB A:GLU184 5.0 30.6 1.0

Sodium binding site 2 out of 2 in 3fkr

Go back to Sodium Binding Sites List in 3fkr
Sodium binding site 2 out of 2 in the Structure of L-2-Keto-3-Deoxyarabonate Dehydratase Complex with Pyruvate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of L-2-Keto-3-Deoxyarabonate Dehydratase Complex with Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na408

b:14.4
occ:1.00
OE2 B:GLU184 2.1 20.9 1.0
NZ B:KPI182 2.3 19.5 1.0
O B:HOH1046 2.3 32.1 1.0
O2 B:KPI182 2.4 59.5 1.0
O B:HOH895 2.7 50.7 1.0
CD B:GLU184 2.8 30.0 1.0
OE1 B:GLU184 2.8 23.5 1.0
CX1 B:KPI182 3.0 29.6 1.0
CX2 B:KPI182 3.0 19.6 1.0
CE B:KPI182 3.1 17.7 1.0
O B:HOH1041 3.4 40.0 1.0
O B:HOH997 4.0 31.2 1.0
N B:GLU210 4.0 15.7 1.0
OE2 B:GLU211 4.0 32.5 1.0
CG B:GLU184 4.2 28.9 1.0
O1 B:KPI182 4.2 38.2 1.0
CD B:KPI182 4.2 21.8 1.0
OE1 B:GLN154 4.4 29.6 1.0
C1 B:KPI182 4.4 37.9 1.0
CA B:GLY209 4.7 16.9 1.0
CA B:GLU210 4.8 21.6 1.0
C B:GLY209 4.8 17.2 1.0

Reference:

N.Shimada, B.Mikami, S.Watanabe, T.Kodaki, K.Makino. Structural Analysis of L -2-Keto-3-Deoxyarabonate Dehydratase An Enzyme Involved in An Alternative Bacterial Pathway of L-Arabinose Metabolism in Complex with Pyruvate To Be Published.
Page generated: Tue Dec 15 06:10:53 2020

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