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Sodium in PDB 2r37: Crystal Structure of Human Glutathione Peroxidase 3 (Selenocysteine to Glycine Mutant)

Enzymatic activity of Crystal Structure of Human Glutathione Peroxidase 3 (Selenocysteine to Glycine Mutant)

All present enzymatic activity of Crystal Structure of Human Glutathione Peroxidase 3 (Selenocysteine to Glycine Mutant):
1.11.1.9;

Protein crystallography data

The structure of Crystal Structure of Human Glutathione Peroxidase 3 (Selenocysteine to Glycine Mutant), PDB code: 2r37 was solved by E.S.Pilka, K.Guo, O.Gileadi, A.Rojkowa, F.Von Delft, A.C.W.Pike, K.L.Kavanagh, C.Johannson, M.Sundstrom, C.H.Arrowsmith, J.Weigelt, A.M.Edwards, U.Oppermann, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.00 / 1.85
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.720, 61.308, 100.400, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 18.3

Other elements in 2r37:

The structure of Crystal Structure of Human Glutathione Peroxidase 3 (Selenocysteine to Glycine Mutant) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Glutathione Peroxidase 3 (Selenocysteine to Glycine Mutant) (pdb code 2r37). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Glutathione Peroxidase 3 (Selenocysteine to Glycine Mutant), PDB code: 2r37:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2r37

Go back to Sodium Binding Sites List in 2r37
Sodium binding site 1 out of 2 in the Crystal Structure of Human Glutathione Peroxidase 3 (Selenocysteine to Glycine Mutant)


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 Human Glutathione Peroxidase 3 (Selenocysteine to Glycine Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na237

b:24.5
occ:1.00
O A:LEU169 2.3 22.5 1.0
O A:SER166 2.3 25.3 1.0
O A:HOH413 2.3 29.1 1.0
O A:HOH412 2.4 31.6 1.0
O A:HOH417 2.4 36.6 1.0
O A:HOH300 2.6 42.9 1.0
O A:HOH431 3.3 54.4 1.0
C A:LEU169 3.4 23.4 1.0
C A:SER166 3.4 23.3 1.0
N A:LEU169 4.1 21.0 1.0
CA A:LEU169 4.1 18.2 1.0
CA A:SER166 4.2 26.2 1.0
CB A:SER166 4.2 27.4 1.0
N A:ASP167 4.3 22.4 1.0
CB A:LEU169 4.3 22.8 1.0
N A:PHE170 4.3 18.9 1.0
OE2 A:GLU172 4.3 37.0 1.0
O A:TRP171 4.4 20.2 1.0
CA A:ASP167 4.4 30.2 1.0
CA A:PHE170 4.5 20.3 1.0
C A:ASP167 4.5 28.8 1.0
O A:HOH432 4.6 51.0 1.0
O A:HOH433 4.7 48.4 1.0
N A:TRP171 4.7 20.9 1.0
O A:ASP167 4.7 32.9 1.0
OG A:SER166 4.8 29.9 1.0
N A:ARG168 5.0 23.4 1.0

Sodium binding site 2 out of 2 in 2r37

Go back to Sodium Binding Sites List in 2r37
Sodium binding site 2 out of 2 in the Crystal Structure of Human Glutathione Peroxidase 3 (Selenocysteine to Glycine Mutant)


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 Human Glutathione Peroxidase 3 (Selenocysteine to Glycine Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na237

b:26.9
occ:1.00
O B:SER166 2.3 26.4 1.0
O B:LEU169 2.3 25.7 1.0
O B:HOH382 2.4 31.7 1.0
O B:HOH381 2.4 30.6 1.0
O B:HOH257 2.4 34.5 1.0
O B:HOH411 2.7 47.1 1.0
C B:SER166 3.4 22.9 1.0
C B:LEU169 3.4 24.6 1.0
N B:LEU169 4.0 24.8 1.0
CA B:LEU169 4.1 26.4 1.0
O B:HOH412 4.2 53.5 1.0
CB B:LEU169 4.2 23.6 1.0
CA B:SER166 4.2 22.1 1.0
N B:ASP167 4.2 21.1 1.0
CB B:SER166 4.3 24.8 1.0
OE2 B:GLU172 4.3 29.6 1.0
CA B:ASP167 4.3 29.5 1.0
N B:PHE170 4.4 20.1 1.0
O B:TRP171 4.4 19.2 1.0
C B:ASP167 4.5 32.6 1.0
CA B:PHE170 4.5 21.9 1.0
O B:HOH413 4.5 53.4 1.0
OG B:SER166 4.7 31.7 1.0
N B:TRP171 4.8 22.6 1.0
O B:ASP167 4.8 28.5 1.0
N B:ARG168 4.9 26.4 1.0

Reference:

E.S.Pilka, K.Guo, O.Gileadi, A.Rojkowa, F.Von Delft, A.C.W.Pike, K.L.Kavanagh, C.Johannson, M.Sundstrom, C.H.Arrowsmith, J.Weigelt, A.M.Edwards, U.Oppermann. Crystal Structure of Human Glutathione Peroxidase 3 (Selenocysteine to Glycine Mutant). To Be Published.
Page generated: Tue Dec 15 05:55:46 2020

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