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Sodium in PDB 6myw: Gluconobacter Ene-Reductase (Gluer) Mutant - T36A

Protein crystallography data

The structure of Gluconobacter Ene-Reductase (Gluer) Mutant - T36A, PDB code: 6myw was solved by S.E.Garfinkle, P.Jeffrey, T.K.Hyster, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.28 / 1.16
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 99.475, 45.154, 163.744, 90.00, 107.67, 90.00
R / Rfree (%) 12.3 / 14.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Gluconobacter Ene-Reductase (Gluer) Mutant - T36A (pdb code 6myw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Gluconobacter Ene-Reductase (Gluer) Mutant - T36A, PDB code: 6myw:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 6myw

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Sodium binding site 1 out of 7 in the Gluconobacter Ene-Reductase (Gluer) Mutant - T36A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Gluconobacter Ene-Reductase (Gluer) Mutant - T36A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:32.8
occ:1.00
 O B:HOH784 2.5 18.5 1.0
O B:HOH804 3.1 29.3 1.0
O B:HOH891 3.8 19.2 1.0
CE B:LYS317 3.9 17.9 1.0
CG2 B:THR296 4.3 19.2 1.0
NZ B:LYS317 4.3 18.5 1.0
CB B:THR296 4.3 15.4 1.0
CD1 B:LEU334 4.5 18.5 1.0
CA B:THR296 4.6 12.7 1.0
O B:HOH772 4.8 13.2 1.0

Sodium binding site 2 out of 7 in 6myw

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Sodium binding site 2 out of 7 in the Gluconobacter Ene-Reductase (Gluer) Mutant - T36A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Gluconobacter Ene-Reductase (Gluer) Mutant - T36A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:18.4
occ:1.00
 OG1 B:THR121 2.7 8.8 1.0
O B:THR187 2.8 10.4 1.0
OG B:SER117 2.8 8.2 1.0
OG B:SER118 3.4 8.7 1.0
O B:SER119 3.4 8.3 1.0
CG2 B:THR121 3.5 9.6 1.0
CB B:THR121 3.6 8.4 1.0
CB B:THR187 3.7 8.5 1.0
N B:SER119 3.7 8.5 1.0
C B:THR187 3.7 8.6 1.0
CB B:SER117 3.9 8.0 1.0
CA B:THR187 4.0 8.8 1.0
C B:SER119 4.0 8.3 1.0
CA B:SER119 4.1 8.1 1.0
CB B:SER119 4.1 8.7 1.0
CD B:ARG104 4.3 7.8 1.0
CG2 B:THR187 4.3 9.3 1.0
CB B:GLU181 4.4 6.7 1.0
N B:SER118 4.5 7.4 1.0
NH1 B:ARG104 4.5 9.1 1.0
N B:THR121 4.6 8.6 1.0
OE1 B:GLU181 4.6 7.9 1.0
CG B:GLU181 4.6 7.5 1.0
CB B:SER118 4.6 8.7 1.0
CA B:THR121 4.7 8.4 1.0
O B:GLU181 4.7 9.1 1.0
C B:SER118 4.7 8.1 1.0
OG1 B:THR187 4.7 8.9 1.0
N B:ASN188 4.8 8.5 1.0
CA B:SER118 4.8 7.7 1.0
NE B:ARG104 4.9 9.0 1.0
OG B:SER119 4.9 9.3 1.0
CZ B:ARG104 5.0 8.5 1.0

Sodium binding site 3 out of 7 in 6myw

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Sodium binding site 3 out of 7 in the Gluconobacter Ene-Reductase (Gluer) Mutant - T36A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Gluconobacter Ene-Reductase (Gluer) Mutant - T36A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na406

b:36.6
occ:1.00
 O C:HOH771 2.8 16.4 1.0
CB C:SER74 3.9 9.7 1.0
CA C:SER74 4.7 9.3 1.0
N C:ASP75 4.7 10.8 0.4
N C:ASP75 4.7 10.1 0.6
OG C:SER74 4.7 9.8 1.0
O C:HOH577 4.8 20.5 1.0

Sodium binding site 4 out of 7 in 6myw

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Sodium binding site 4 out of 7 in the Gluconobacter Ene-Reductase (Gluer) Mutant - T36A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Gluconobacter Ene-Reductase (Gluer) Mutant - T36A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na407

b:14.7
occ:1.00
 OG1 C:THR231 2.7 10.3 1.0
O C:GLY229 2.8 9.8 1.0
O C:HOH553 2.8 9.9 1.0
NH2 C:ARG184 3.0 8.2 1.0
O C:ASN228 3.2 9.6 1.0
O C:SER226 3.5 9.2 1.0
NH1 C:ARG184 3.5 9.1 1.0
CB C:THR231 3.6 9.8 1.0
OG C:SER226 3.6 8.2 1.0
CB C:SER226 3.7 8.6 1.0
CZ C:ARG184 3.7 7.9 1.0
C C:GLY229 3.7 9.2 1.0
C C:ASN228 3.8 8.7 1.0
NH2 C:ARG261 4.0 10.9 1.0
N C:THR231 4.1 9.4 1.0
C C:SER226 4.1 8.2 1.0
N C:GLY229 4.3 9.1 1.0
CA C:GLY229 4.3 10.2 1.0
N C:ASN228 4.4 9.0 1.0
CA C:THR231 4.4 9.7 1.0
CA C:SER226 4.4 8.1 1.0
C C:ASP230 4.4 10.9 1.0
O C:HOH671 4.6 13.0 1.0
CG2 C:THR231 4.7 10.5 1.0
N C:ASP230 4.8 9.6 1.0
CA C:ASN228 4.8 9.7 1.0
CD C:PRO263 4.9 11.6 1.0
O C:ASP230 4.9 11.7 1.0
CG C:PRO263 4.9 14.6 1.0
C C:PRO227 4.9 10.3 1.0
N C:PRO227 5.0 8.2 1.0
NE C:ARG184 5.0 8.8 1.0

Sodium binding site 5 out of 7 in 6myw

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Sodium binding site 5 out of 7 in the Gluconobacter Ene-Reductase (Gluer) Mutant - T36A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Gluconobacter Ene-Reductase (Gluer) Mutant - T36A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na408

b:34.4
occ:1.00
 O C:HOH649 2.6 20.6 1.0
O C:HOH858 2.9 20.5 1.0
O C:HOH905 3.8 30.0 1.0
CD C:LYS82 3.8 11.1 1.0
CE C:LYS82 4.0 12.1 1.0
CG C:LYS82 4.2 9.8 1.0
O C:HOH576 4.3 15.6 1.0
NZ C:LYS82 4.4 14.0 1.0
O C:HOH589 4.5 12.4 1.0
O C:HOH972 4.5 29.9 1.0
CB C:LYS82 4.7 9.4 1.0
O C:ARG163 4.8 10.1 1.0

Sodium binding site 6 out of 7 in 6myw

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Sodium binding site 6 out of 7 in the Gluconobacter Ene-Reductase (Gluer) Mutant - T36A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Gluconobacter Ene-Reductase (Gluer) Mutant - T36A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na409

b:15.4
occ:1.00
 O C:ARG201 2.7 9.1 1.0
N C:LEU205 3.0 8.1 1.0
CB C:PHE182 3.5 7.7 1.0
CB C:LEU205 3.5 9.1 1.0
CD2 C:LEU183 3.5 10.0 1.0
O C:HOH690 3.6 8.9 1.0
CG C:LEU183 3.7 8.2 1.0
CB C:PHE204 3.7 9.1 1.0
O C:ILE179 3.7 7.9 1.0
CA C:LEU205 3.8 8.3 1.0
N C:PHE204 3.8 8.2 1.0
C C:ARG201 3.8 9.4 1.0
C C:ILE202 3.8 7.9 1.0
O C:ILE202 3.9 8.8 1.0
C C:PHE204 3.9 8.3 1.0
CA C:ILE202 3.9 9.4 1.0
N C:LEU183 3.9 7.3 1.0
CG2 C:ILE179 3.9 7.9 1.0
CA C:PHE204 4.0 8.4 1.0
C C:PHE182 4.2 8.0 1.0
CA C:LEU183 4.3 7.8 1.0
N C:ILE202 4.3 9.4 1.0
CA C:PHE182 4.5 6.9 1.0
N C:ARG203 4.5 8.4 1.0
CG C:PHE182 4.5 7.8 1.0
CB C:LEU183 4.5 7.8 1.0
CD2 C:PHE204 4.7 8.7 1.0
CG C:PHE204 4.7 8.9 1.0
C C:ILE179 4.7 6.7 1.0
CD1 C:LEU183 4.7 9.2 1.0
O C:PHE182 4.7 8.0 1.0
C C:ARG203 4.7 8.5 1.0
CG C:LEU205 4.9 9.1 1.0
CA C:ILE179 4.9 7.0 1.0
O C:PHE204 5.0 8.6 1.0

Sodium binding site 7 out of 7 in 6myw

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Sodium binding site 7 out of 7 in the Gluconobacter Ene-Reductase (Gluer) Mutant - T36A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Gluconobacter Ene-Reductase (Gluer) Mutant - T36A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na410

b:37.3
occ:1.00
 O C:HOH967 2.7 21.6 1.0
O C:HOH868 3.8 21.9 1.0
O C:HOH918 4.3 27.2 1.0

Reference:

K.F.Biegasiewicz, S.J.Cooper, X.Gao, D.G.Oblinsky, J.H.Kim, S.E.Garfinkle, L.A.Joyce, B.A.Sandoval, G.D.Scholes, T.K.Hyster. Photoexcitation of Flavoenzymes Enables A Stereoselective Radical Cyclization. Science V. 364 1166 2019.
ISSN: ESSN 1095-9203
PubMed: 31221855
DOI: 10.1126/SCIENCE.AAW1143
Page generated: Tue Oct 8 12:08:15 2024

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