Atomistry » Sodium » PDB 6myw-6nfx » 6myw
Atomistry »
  Sodium »
    PDB 6myw-6nfx »
      6myw »

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

Go back to Sodium Binding Sites List in 6myw
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

Go back to Sodium Binding Sites List in 6myw
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

Go back to Sodium Binding Sites List in 6myw
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

Go back to Sodium Binding Sites List in 6myw
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

Go back to Sodium Binding Sites List in 6myw
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

Go back to Sodium Binding Sites List in 6myw
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

Go back to Sodium Binding Sites List in 6myw
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy