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Sodium in PDB 1lk5: Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii

Enzymatic activity of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii

All present enzymatic activity of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii:
5.3.1.6;

Protein crystallography data

The structure of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii, PDB code: 1lk5 was solved by K.Ishikawa, I.Matsui, F.Payan, C.Cambillau, H.Ishida, Y.Kawarabayasi, H.Kikuchi, A.Roussel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.548, 114.932, 119.017, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 21.5

Other elements in 1lk5:

The structure of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii also contains other interesting chemical elements:

Chlorine (Cl) 10 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii (pdb code 1lk5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii, PDB code: 1lk5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1lk5

Go back to Sodium Binding Sites List in 1lk5
Sodium binding site 1 out of 2 in the Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1011

b:14.1
occ:1.00
O A:ASN175 2.3 16.1 1.0
O B:ASN175 2.3 15.5 1.0
O A:HOH1024 2.3 20.5 1.0
O B:HOH1026 2.4 19.4 1.0
O B:HOH1016 2.5 13.9 1.0
O A:HOH1016 2.5 16.0 1.0
C A:ASN175 3.5 15.4 1.0
O B:HOH1044 3.5 17.0 1.0
C B:ASN175 3.5 16.0 1.0
O A:HOH1052 4.2 31.1 1.0
O A:HOH1143 4.3 32.0 1.0
O A:HOH1092 4.3 28.3 1.0
CA A:ASN175 4.3 16.1 1.0
CA B:ASN175 4.3 16.3 1.0
N B:GLY176 4.4 15.2 1.0
N A:GLY176 4.4 14.4 1.0
O B:HOH1025 4.5 25.2 1.0
CA B:GLY176 4.5 15.1 1.0
O A:HOH1070 4.5 26.1 1.0
CB B:ASN175 4.5 17.0 1.0
O B:HOH1057 4.5 28.6 1.0
CA A:GLY176 4.5 14.4 1.0
CB A:ASN175 4.6 16.1 1.0
O B:HOH1104 4.6 29.4 1.0
O A:HOH1194 4.6 26.0 1.0
OD1 B:ASN177 4.6 15.4 1.0
OD1 A:ASN177 4.7 14.6 1.0
ND2 A:ASN177 4.8 14.3 1.0
ND2 B:ASN177 4.9 15.1 1.0
O A:HOH1197 4.9 42.1 1.0
C B:GLY176 5.0 15.0 1.0
C A:GLY176 5.0 14.9 1.0

Sodium binding site 2 out of 2 in 1lk5

Go back to Sodium Binding Sites List in 1lk5
Sodium binding site 2 out of 2 in the Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1012

b:17.7
occ:1.00
O D:HOH1069 2.3 28.2 1.0
O D:ASN175 2.3 16.4 1.0
O C:ASN175 2.3 16.4 1.0
O C:HOH1047 2.4 28.7 1.0
O D:HOH1014 2.5 16.7 1.0
O C:HOH1039 2.5 20.8 1.0
O D:HOH1022 3.5 18.5 1.0
C D:ASN175 3.5 17.3 1.0
C C:ASN175 3.5 16.8 1.0
O A:HOH1143 4.2 32.0 1.0
O A:HOH1052 4.2 31.1 1.0
O C:HOH1113 4.4 29.6 1.0
O D:HOH1047 4.4 31.4 1.0
N D:GLY176 4.4 16.5 1.0
CA D:ASN175 4.4 17.9 1.0
CA C:ASN175 4.4 17.0 1.0
N C:GLY176 4.5 16.1 1.0
CA D:GLY176 4.5 16.0 1.0
CA C:GLY176 4.5 16.1 1.0
O C:HOH1074 4.5 39.3 1.0
O C:HOH1055 4.5 28.3 1.0
OD1 C:ASN177 4.6 14.5 1.0
OD1 D:ASN177 4.6 14.7 1.0
CB D:ASN175 4.6 18.3 1.0
CB C:ASN175 4.7 16.8 1.0
ND2 D:ASN177 4.7 17.4 1.0
O D:HOH1121 4.7 37.8 1.0
ND2 C:ASN177 4.7 15.4 1.0
C D:GLY176 4.9 16.0 1.0
C C:GLY176 4.9 16.2 1.0
CG D:ASN177 4.9 15.3 1.0
CG C:ASN177 5.0 15.3 1.0

Reference:

K.Ishikawa, I.Matsui, F.Payan, C.Cambillau, H.Ishida, Y.Kawarabayasi, H.Kikuchi, A.Roussel. A Hyperthermostable D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii Characterization and Three-Dimensional Structure. Structure V. 10 877 2002.
ISSN: ISSN 0969-2126
PubMed: 12057201
DOI: 10.1016/S0969-2126(02)00779-7
Page generated: Tue Dec 15 05:29:24 2020

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