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Sodium in PDB 3sn4: Crystal Structure of Putative L-Alanine-Dl-Glutamate Epimerase From Burkholderia Xenovorans Strain LB400 Bound to Magnesium and Alpha- Ketoglutarate

Protein crystallography data

The structure of Crystal Structure of Putative L-Alanine-Dl-Glutamate Epimerase From Burkholderia Xenovorans Strain LB400 Bound to Magnesium and Alpha- Ketoglutarate, PDB code: 3sn4 was solved by J.B.Bonanno, Y.Patskovsky, R.Toro, M.Dickey, K.T.Bain, B.Wu, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgx Research Center For Structuralgenomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.86
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 105.040, 105.040, 144.363, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20.1

Other elements in 3sn4:

The structure of Crystal Structure of Putative L-Alanine-Dl-Glutamate Epimerase From Burkholderia Xenovorans Strain LB400 Bound to Magnesium and Alpha- Ketoglutarate also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Putative L-Alanine-Dl-Glutamate Epimerase From Burkholderia Xenovorans Strain LB400 Bound to Magnesium and Alpha- Ketoglutarate (pdb code 3sn4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Putative L-Alanine-Dl-Glutamate Epimerase From Burkholderia Xenovorans Strain LB400 Bound to Magnesium and Alpha- Ketoglutarate, PDB code: 3sn4:

Sodium binding site 1 out of 1 in 3sn4

Go back to Sodium Binding Sites List in 3sn4
Sodium binding site 1 out of 1 in the Crystal Structure of Putative L-Alanine-Dl-Glutamate Epimerase From Burkholderia Xenovorans Strain LB400 Bound to Magnesium and Alpha- Ketoglutarate


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 Putative L-Alanine-Dl-Glutamate Epimerase From Burkholderia Xenovorans Strain LB400 Bound to Magnesium and Alpha- Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:31.5
occ:1.00
O A:HOH414 2.5 24.6 1.0
O A:HOH415 2.6 36.0 1.0
O A:THR268 2.7 20.8 1.0
OH A:TYR247 2.9 22.5 1.0
CE1 A:TYR247 3.6 23.8 1.0
CZ A:TYR247 3.6 22.5 1.0
OG1 A:THR268 3.7 21.8 1.0
C A:THR268 3.7 19.7 1.0
CB A:THR268 3.8 19.4 1.0
CE2 A:PHE270 4.3 22.4 1.0
O A:HOH456 4.3 23.8 1.0
CA A:THR268 4.4 19.7 1.0
CD2 A:PHE270 4.5 21.3 1.0
N A:LEU269 4.6 19.3 1.0
OE1 A:GLU274 4.7 21.6 1.0
CD2 A:LEU269 4.7 17.4 1.0
CA A:LEU269 4.7 18.7 1.0
CD1 A:TYR247 4.8 22.5 1.0
CE2 A:TYR247 4.8 22.4 1.0
CZ3 A:TRP293 4.9 21.8 1.0

Reference:

J.B.Bonanno, Y.Patskovsky, R.Toro, M.Dickey, K.T.Bain, B.Wu, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of Putative L-Alanine-Dl-Glutamate Epimerase From Burkholderia Xenovorans Strain LB400 Bound to Magnesium and Alpha-Ketoglutarate To Be Published.
Page generated: Tue Dec 15 06:24:53 2020

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