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Sodium in PDB 3agc: F218V Mutant of the Substrate-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana

Enzymatic activity of F218V Mutant of the Substrate-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana

All present enzymatic activity of F218V Mutant of the Substrate-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana:
1.3.1.80;

Protein crystallography data

The structure of F218V Mutant of the Substrate-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana, PDB code: 3agc was solved by M.Sugishima, K.Fukuyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.089, 84.321, 131.518, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 27

Sodium Binding Sites:

The binding sites of Sodium atom in the F218V Mutant of the Substrate-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana (pdb code 3agc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the F218V Mutant of the Substrate-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana, PDB code: 3agc:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3agc

Go back to Sodium Binding Sites List in 3agc
Sodium binding site 1 out of 2 in the F218V Mutant of the Substrate-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of F218V Mutant of the Substrate-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1

b:29.0
occ:1.00
O A:VAL204 2.3 12.4 1.0
O A:HOH383 2.3 32.1 1.0
O A:HOH351 2.4 34.4 1.0
O A:LEU199 2.4 18.1 1.0
O A:LEU201 2.5 15.9 1.0
O A:HOH365 2.6 39.7 1.0
C A:VAL204 3.5 12.7 1.0
C A:LEU201 3.5 16.1 1.0
C A:LEU199 3.5 18.0 1.0
OD1 A:ASN205 4.1 14.2 1.0
C A:LYS200 4.2 17.9 1.0
O A:PRO202 4.2 14.9 1.0
N A:VAL204 4.2 12.9 1.0
CA A:PRO202 4.2 15.3 1.0
N A:LEU201 4.2 17.2 1.0
N A:PRO202 4.2 15.9 1.0
C A:PRO202 4.3 15.0 1.0
CA A:VAL204 4.3 12.7 1.0
O A:LYS200 4.3 18.1 1.0
CA A:LEU199 4.4 17.8 1.0
O A:HOH355 4.5 48.0 1.0
CA A:LEU201 4.5 16.6 1.0
N A:LYS200 4.5 18.1 1.0
N A:ASN205 4.5 12.6 1.0
CB A:VAL204 4.6 12.5 1.0
CA A:LYS200 4.6 18.3 1.0
CD1 A:LEU199 4.6 16.7 1.0
CA A:ASN205 4.7 12.7 1.0
CG A:ASN205 4.8 13.4 1.0

Sodium binding site 2 out of 2 in 3agc

Go back to Sodium Binding Sites List in 3agc
Sodium binding site 2 out of 2 in the F218V Mutant of the Substrate-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of F218V Mutant of the Substrate-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2

b:35.6
occ:1.00
O B:HOH328 2.3 30.0 1.0
O B:LEU199 2.3 17.1 1.0
O B:HOH329 2.3 33.5 1.0
O B:VAL204 2.4 16.0 1.0
O B:HOH327 2.4 33.5 1.0
O B:LEU201 2.5 18.3 1.0
C B:LEU199 3.4 17.3 1.0
C B:LEU201 3.5 18.1 1.0
C B:VAL204 3.6 16.2 1.0
O B:PRO202 4.1 17.7 1.0
CA B:PRO202 4.1 17.7 1.0
C B:LYS200 4.2 18.4 1.0
ND2 B:ASN205 4.2 15.3 1.0
O B:HOH340 4.2 42.0 1.0
CA B:LEU199 4.2 17.0 1.0
N B:PRO202 4.2 17.8 1.0
C B:PRO202 4.2 17.4 1.0
N B:LEU201 4.2 18.4 1.0
N B:VAL204 4.3 16.8 1.0
O B:LYS200 4.3 18.7 1.0
CA B:VAL204 4.3 16.4 1.0
N B:LYS200 4.5 17.8 1.0
CA B:LEU201 4.5 18.3 1.0
CB B:VAL204 4.6 16.3 1.0
N B:ASN205 4.6 15.7 1.0
CA B:LYS200 4.7 18.4 1.0
CD2 B:LEU199 4.7 16.8 1.0
CA B:ASN205 4.8 15.5 1.0
CB B:LEU199 4.8 17.2 1.0
CG B:ASN205 4.9 16.3 1.0
N B:GLU203 4.9 17.5 1.0

Reference:

M.Sugishima, Y.Okamoto, M.Noguchi, T.Kohchi, H.Tamiaki, K.Fukuyama. Crystal Structures of the Substrate-Bound Forms of Red Chlorophyll Catabolite Reductase: Implications For Site-Specific and Stereospecific Reaction J.Mol.Biol. V. 402 879 2010.
ISSN: ISSN 0022-2836
PubMed: 20727901
DOI: 10.1016/J.JMB.2010.08.021
Page generated: Tue Dec 15 06:02:07 2020

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