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Sodium in PDB 8agq: Crystal Structure of Anthocyanin-Related GSTF8 From Populus Trichocarpa in Complex with (-)-Catechin and Glutathione

Enzymatic activity of Crystal Structure of Anthocyanin-Related GSTF8 From Populus Trichocarpa in Complex with (-)-Catechin and Glutathione

All present enzymatic activity of Crystal Structure of Anthocyanin-Related GSTF8 From Populus Trichocarpa in Complex with (-)-Catechin and Glutathione:
2.5.1.18;

Protein crystallography data

The structure of Crystal Structure of Anthocyanin-Related GSTF8 From Populus Trichocarpa in Complex with (-)-Catechin and Glutathione, PDB code: 8agq was solved by M.Eichenberger, S.Hueppi, T.Schwander, P.Mittl, M.R.Buller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.50 / 1.09
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 89.948, 55.447, 54.787, 90, 113.55, 90
R / Rfree (%) 13.2 / 14.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Anthocyanin-Related GSTF8 From Populus Trichocarpa in Complex with (-)-Catechin and Glutathione (pdb code 8agq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Anthocyanin-Related GSTF8 From Populus Trichocarpa in Complex with (-)-Catechin and Glutathione, PDB code: 8agq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 8agq

Go back to Sodium Binding Sites List in 8agq
Sodium binding site 1 out of 5 in the Crystal Structure of Anthocyanin-Related GSTF8 From Populus Trichocarpa in Complex with (-)-Catechin and Glutathione


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 Anthocyanin-Related GSTF8 From Populus Trichocarpa in Complex with (-)-Catechin and Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:16.3
occ:1.00
 HZ2 A:TRP99 3.0 10.1 1.0
O A:HOH588 3.0 13.5 1.0
O A:HOH511 3.1 19.8 1.0
HD3 A:ARG150 3.2 11.5 1.0
HB2 A:ARG150 3.7 10.6 1.0
O A:HOH607 3.8 32.3 1.0
CZ2 A:TRP99 3.9 10.0 1.0
CD A:ARG150 4.2 11.4 1.0
HZ2 A:LYS149 4.2 17.5 0.5
HE22 A:GLN98 4.3 10.3 0.0
HE1 A:TRP99 4.3 10.1 1.0
HG11 A:VAL146 4.4 12.3 1.0
HG12 A:VAL146 4.5 12.3 1.0
HH2 A:TRP99 4.5 10.1 1.0
CB A:ARG150 4.5 10.4 1.0
HD2 A:ARG150 4.6 11.5 1.0
CH2 A:TRP99 4.7 10.9 1.0
HZ3 A:LYS149 4.7 17.5 0.5
CE2 A:TRP99 4.7 9.4 1.0
HA A:ARG150 4.7 11.5 1.0
HH11 A:ARG150 4.8 14.9 0.0
CG1 A:VAL146 4.8 11.7 1.0
CG A:ARG150 4.8 10.2 1.0
O A:HOH657 4.8 22.3 1.0
HG13 A:VAL146 4.8 12.3 1.0
NZ A:LYS149 4.8 18.0 0.5
HG2 A:ARG150 4.8 13.1 1.0
NE1 A:TRP99 4.8 9.8 1.0
NE2 A:GLN98 4.9 10.7 1.0
HE21 A:GLN98 5.0 10.3 0.0

Sodium binding site 2 out of 5 in 8agq

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Sodium binding site 2 out of 5 in the Crystal Structure of Anthocyanin-Related GSTF8 From Populus Trichocarpa in Complex with (-)-Catechin and Glutathione


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 Anthocyanin-Related GSTF8 From Populus Trichocarpa in Complex with (-)-Catechin and Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:19.6
occ:1.00
 HH12 A:ARG68 2.4 12.2 0.0
H3 A:GSH301 2.6 11.7 1.0
O A:HOH694 2.8 31.9 1.0
O A:HOH617 2.8 16.9 1.0
HN11 A:GSH301 2.9 11.7 1.0
HB12 A:GSH301 3.1 11.7 1.0
N1 A:GSH301 3.2 11.7 1.0
NH1 A:ARG68 3.2 12.6 1.0
HH21 A:ARG68 3.5 11.1 1.0
O A:HOH435 3.5 22.3 1.0
HB13 A:GSH301 3.7 11.7 1.0
CB1 A:GSH301 3.7 11.5 1.0
HD21 A:ASN108 3.8 13.3 0.0
HH11 A:ARG68 3.8 12.2 0.0
O12 A:GSH301 3.8 11.6 1.0
NH2 A:ARG68 3.8 11.2 1.0
HN12 A:GSH301 3.9 11.7 1.0
CZ A:ARG68 3.9 10.5 1.0
CA1 A:GSH301 4.0 11.8 1.0
O A:HOH650 4.1 37.5 1.0
HD22 A:ASN108 4.2 13.3 0.0
ND2 A:ASN108 4.2 13.9 1.0
C1 A:GSH301 4.4 10.6 1.0
HH22 A:ARG68 4.4 11.1 1.0
O A:HOH461 4.5 24.6 1.0
O A:HOH406 4.6 32.6 1.0
HG A:CYS13 4.6 13.7 0.0
HA1 A:GSH301 4.8 11.9 1.0
HH12 A:ARG16 4.9 11.1 0.0

Sodium binding site 3 out of 5 in 8agq

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Sodium binding site 3 out of 5 in the Crystal Structure of Anthocyanin-Related GSTF8 From Populus Trichocarpa in Complex with (-)-Catechin and Glutathione


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Anthocyanin-Related GSTF8 From Populus Trichocarpa in Complex with (-)-Catechin and Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:40.0
occ:1.00
 O A:HOH647 2.6 23.8 1.0
HD3 A:ARG134 2.8 20.4 0.5
HD2 A:ARG134 2.8 20.4 0.5
O A:HOH411 2.8 39.8 1.0
NE A:ARG134 3.0 36.9 0.5
CD A:ARG134 3.0 20.9 0.5
HE A:ARG134 3.1 27.0 0.5
CZ A:ARG134 3.6 54.7 0.5
HG2 A:ARG134 3.9 14.8 0.5
HH11 A:ARG134 4.0 37.4 0.0
HH22 A:ARG134 4.1 36.5 0.5
NH2 A:ARG134 4.2 65.9 0.5
NH1 A:ARG134 4.2 42.5 0.5
O A:HOH653 4.4 41.2 1.0
CG A:ARG134 4.5 18.2 0.5
O A:HOH631 4.7 14.7 1.0
HH12 A:ARG134 4.7 37.4 0.0
HG2 A:ARG134 4.8 18.2 0.5
CG A:ARG134 4.8 14.2 0.5
HB2 A:ARG134 5.0 17.3 0.5
HG3 A:ARG134 5.0 18.2 0.5

Sodium binding site 4 out of 5 in 8agq

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Sodium binding site 4 out of 5 in the Crystal Structure of Anthocyanin-Related GSTF8 From Populus Trichocarpa in Complex with (-)-Catechin and Glutathione


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Anthocyanin-Related GSTF8 From Populus Trichocarpa in Complex with (-)-Catechin and Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:42.4
occ:1.00
 O A:HOH664 2.7 31.1 1.0
O A:HOH482 2.7 20.9 1.0
O A:HOH612 2.8 13.6 1.0
HG11 A:VAL10 3.3 12.6 1.0
HB3 A:ALA9 3.4 12.1 1.0
HG13 A:VAL10 3.6 12.6 1.0
HA A:ALA212 3.8 13.4 1.0
CG1 A:VAL10 3.9 12.7 1.0
O A:ALA212 3.9 19.1 1.0
O A:HOH680 4.2 32.0 0.5
CB A:ALA9 4.3 12.2 1.0
O A:HOH496 4.3 13.3 1.0
HG12 A:VAL10 4.3 12.6 1.0
O A:HOH710 4.4 24.4 1.0
H A:VAL10 4.5 12.6 1.0
O A:HOH499 4.5 28.3 1.0
C A:ALA212 4.5 13.4 1.0
HB2 A:ALA9 4.6 12.1 1.0
CA A:ALA212 4.6 13.4 1.0
O A:LEU211 4.6 15.2 1.0
HB1 A:ALA9 4.7 12.1 1.0
O A:HOH695 4.7 20.1 1.0
H A:ALA9 4.8 10.7 1.0
N A:VAL10 4.9 9.9 1.0
HG23 A:VAL10 5.0 12.6 1.0

Sodium binding site 5 out of 5 in 8agq

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Sodium binding site 5 out of 5 in the Crystal Structure of Anthocyanin-Related GSTF8 From Populus Trichocarpa in Complex with (-)-Catechin and Glutathione


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Anthocyanin-Related GSTF8 From Populus Trichocarpa in Complex with (-)-Catechin and Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na307

b:15.6
occ:1.00
 H A:GLU66 2.1 12.2 1.0
HE21 A:GLN49 2.2 10.4 0.0
O A:PRO55 2.7 10.5 1.0
HB2 A:PHE65 2.8 12.2 1.0
O11 A:GSH301 2.8 10.6 1.0
HA A:GLU66 2.9 10.4 1.0
N A:GLU66 3.0 9.5 1.0
NE2 A:GLN49 3.0 10.8 1.0
HD2 A:PRO55 3.3 10.4 1.0
HE22 A:GLN49 3.4 10.4 0.0
CA A:GLU66 3.5 9.4 1.0
HD2 A:PHE65 3.5 12.2 1.0
HG3 A:GLN49 3.6 11.8 1.0
HA1 A:GSH301 3.6 11.9 1.0
H A:SER67 3.6 10.4 1.0
CB A:PHE65 3.7 10.1 1.0
N A:PRO55 3.8 9.4 1.0
C A:PRO55 3.8 9.2 1.0
C1 A:GSH301 3.9 10.6 1.0
HG12 A:GSH301 3.9 11.9 1.0
CD A:PRO55 4.0 10.0 1.0
C A:VAL54 4.0 9.6 1.0
CD A:GLN49 4.0 10.8 1.0
C A:PHE65 4.1 9.9 1.0
HG13 A:GSH301 4.1 11.9 1.0
HA A:PHE65 4.1 12.0 1.0
HG2 A:PRO55 4.1 10.9 1.0
N A:SER67 4.1 8.9 1.0
CG A:GLN49 4.2 10.5 1.0
HG2 A:GLU66 4.2 11.2 1.0
HG2 A:GLN49 4.2 11.8 1.0
CA A:PHE65 4.2 9.5 1.0
HB2 A:GLN53 4.2 11.9 1.0
CA1 A:GSH301 4.2 11.8 1.0
C A:GLU66 4.2 9.3 1.0
HB3 A:PHE65 4.2 12.2 1.0
O A:VAL54 4.2 10.7 1.0
CD2 A:PHE65 4.3 10.4 1.0
CA A:PRO55 4.4 9.7 1.0
CG1 A:GSH301 4.4 11.7 1.0
O A:HOH526 4.5 13.3 1.0
HA A:VAL54 4.5 14.0 1.0
O A:GLN53 4.5 11.0 1.0
CG A:PHE65 4.5 10.2 1.0
CG A:PRO55 4.6 10.9 1.0
CD A:GLU66 4.6 10.8 1.0
HD12 A:ILE70 4.6 12.0 1.0
OE2 A:GLU66 4.7 12.7 1.0
CG A:GLU66 4.7 11.0 1.0
CB A:GLU66 4.7 9.6 1.0
CA A:VAL54 4.7 9.5 1.0
HB3 A:GLN53 4.7 11.9 1.0
C A:GLN53 4.8 10.1 1.0
HD3 A:PRO55 4.8 10.4 1.0
HA A:VAL56 4.9 14.4 1.0
N A:VAL54 4.9 10.3 1.0
HB3 A:SER67 4.9 10.4 1.0
CB A:GLN53 4.9 11.0 1.0
N A:VAL56 4.9 10.1 1.0
O12 A:GSH301 5.0 11.6 1.0

Reference:

M.Eichenberger, S.Hueppi, T.Schwander, P.Mittl, M.R.Buller, J.Kreuzer, M.Naesby. The Catalytic Role of Glutathione Transferases in Anthocyanin Biosynthesis To Be Published.
Page generated: Thu Dec 28 11:32:19 2023

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