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Sodium in PDB 6zxt: High Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase From Chlamydomonas Reinhardtii

Enzymatic activity of High Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase From Chlamydomonas Reinhardtii

All present enzymatic activity of High Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase From Chlamydomonas Reinhardtii:
5.3.1.6;

Protein crystallography data

The structure of High Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase From Chlamydomonas Reinhardtii, PDB code: 6zxt was solved by T.Le Moigne, P.Crozet, S.D.Lemaire, J.Henri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.89 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.152, 63.952, 80.909, 90.00, 96.13, 90.00
R / Rfree (%) 15.8 / 17.6

Sodium Binding Sites:

The binding sites of Sodium atom in the High Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase From Chlamydomonas Reinhardtii (pdb code 6zxt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the High Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase From Chlamydomonas Reinhardtii, PDB code: 6zxt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6zxt

Go back to Sodium Binding Sites List in 6zxt
Sodium binding site 1 out of 2 in the High Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase From Chlamydomonas Reinhardtii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase From Chlamydomonas Reinhardtii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:33.9
occ:1.00
O A:HOH450 2.7 46.8 1.0
HB3 A:ASN80 3.0 27.3 1.0
HA2 A:GLY51 3.8 24.7 1.0
CB A:ASN80 3.9 22.7 1.0
CG A:ASN80 4.2 26.1 1.0
HB2 A:ASN80 4.3 27.3 1.0
ND2 A:ASN80 4.6 26.8 1.0
OD1 A:ASN80 4.6 25.3 1.0
HD22 A:ASN80 4.6 32.2 1.0
O A:GLY51 4.6 24.8 1.0
O A:ASN80 4.6 23.5 1.0
CA A:GLY51 4.7 20.6 1.0
HA3 A:GLY51 4.9 24.7 1.0
HA A:ASN80 5.0 28.2 1.0
CA A:ASN80 5.0 23.5 1.0

Sodium binding site 2 out of 2 in 6zxt

Go back to Sodium Binding Sites List in 6zxt
Sodium binding site 2 out of 2 in the High Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase From Chlamydomonas Reinhardtii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase From Chlamydomonas Reinhardtii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:15.4
occ:1.00
H A:ALA133 2.5 20.6 1.0
H A:GLY131 2.6 20.6 1.0
HA2 A:GLY129 2.7 22.6 1.0
OE2 A:GLU137 3.1 20.0 1.0
O A:HOH586 3.1 37.0 1.0
HA3 A:GLY131 3.1 24.4 1.0
HB3 A:ALA133 3.1 24.2 1.0
O A:HOH547 3.2 18.0 1.0
H A:GLY132 3.3 21.1 1.0
N A:GLY131 3.3 17.2 1.0
H A:GLY129 3.3 20.2 1.0
N A:ALA133 3.4 17.1 1.0
CA A:GLY129 3.4 18.8 1.0
CA A:GLY131 3.5 20.3 1.0
N A:GLY132 3.5 17.5 1.0
C A:GLY131 3.6 20.4 1.0
OE1 A:GLU137 3.6 21.6 1.0
C A:GLY129 3.7 17.5 1.0
CD A:GLU137 3.7 18.8 1.0
N A:GLY129 3.8 16.8 1.0
CB A:ALA133 3.9 20.2 1.0
O A:HOH469 4.0 31.3 1.0
CA A:ALA133 4.0 18.4 1.0
N A:ARG130 4.1 19.3 1.0
O A:GLY129 4.1 18.7 1.0
HB A:THR58 4.2 18.8 1.0
H A:ARG130 4.2 23.2 1.0
HG21 A:THR58 4.2 21.1 1.0
HB2 A:ALA133 4.3 24.2 1.0
HA3 A:GLY129 4.3 22.6 1.0
C A:ALA133 4.3 18.1 1.0
O A:GLY131 4.4 24.3 1.0
C A:GLY132 4.4 19.4 1.0
N A:LEU134 4.4 17.1 0.8
HA2 A:GLY131 4.4 24.4 1.0
C A:ARG130 4.4 19.5 1.0
N A:LEU134 4.5 17.2 0.2
CA A:GLY132 4.5 18.9 1.0
HG23 A:THR58 4.6 21.1 1.0
HZ1 A:LYS128 4.6 20.1 1.0
HB1 A:ALA133 4.7 24.2 1.0
HB3 A:LYS128 4.7 19.8 1.0
CG2 A:THR58 4.8 17.6 1.0
O A:HOH464 4.8 25.8 1.0
CB A:THR58 4.9 15.7 1.0
CA A:ARG130 4.9 19.2 1.0
HZ3 A:LYS128 4.9 20.1 1.0
HA A:ALA133 5.0 22.0 1.0
O A:THR58 5.0 19.7 1.0

Reference:

T.Le Moigne, P.Crozet, S.D.Lemaire, J.Henri. High-Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase From Chlamydomonas Reinhardtii -An Enzyme Involved in the Photosynthetic Calvin-Benson Cycle. Int J Mol Sci V. 21 2020.
ISSN: ESSN 1422-0067
PubMed: 33096784
DOI: 10.3390/IJMS21207787
Page generated: Tue Dec 15 17:13:17 2020

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