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Sodium in PDB 8qeu: Crystal Structure of Ornithine Transcarbamylase From Arabidopsis Thaliana (Atotc) in Complex with Ornithine

Enzymatic activity of Crystal Structure of Ornithine Transcarbamylase From Arabidopsis Thaliana (Atotc) in Complex with Ornithine

All present enzymatic activity of Crystal Structure of Ornithine Transcarbamylase From Arabidopsis Thaliana (Atotc) in Complex with Ornithine:
2.1.3.3;

Protein crystallography data

The structure of Crystal Structure of Ornithine Transcarbamylase From Arabidopsis Thaliana (Atotc) in Complex with Ornithine, PDB code: 8qeu was solved by M.Nielipinski, A.Pietrzyk-Brzezinska, B.Sekula, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.02 / 1.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 89.307, 155.38, 189.541, 90, 90, 90
R / Rfree (%) 11.9 / 15.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Ornithine Transcarbamylase From Arabidopsis Thaliana (Atotc) in Complex with Ornithine (pdb code 8qeu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Ornithine Transcarbamylase From Arabidopsis Thaliana (Atotc) in Complex with Ornithine, PDB code: 8qeu:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8qeu

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Sodium binding site 1 out of 4 in the Crystal Structure of Ornithine Transcarbamylase From Arabidopsis Thaliana (Atotc) in Complex with Ornithine


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 Ornithine Transcarbamylase From Arabidopsis Thaliana (Atotc) in Complex with Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:33.8
occ:1.00
 O A:HOH840 2.7 36.5 1.0
O A:HOH811 2.9 32.9 1.0
O A:ASP302 3.0 28.9 1.0
O A:HOH679 3.0 31.8 1.0
N A:ALA306 3.0 23.7 1.0
C A:GLU303 3.5 21.5 1.0
N A:GLU305 3.5 21.4 1.0
CB A:ALA306 3.5 24.5 1.0
CA A:GLU303 3.5 21.9 1.0
O A:GLU303 3.7 22.8 1.0
CB A:GLU305 3.8 26.9 1.0
CA A:ALA306 3.9 22.1 1.0
CA A:GLU305 3.9 22.6 1.0
C A:GLU305 3.9 21.1 1.0
N A:ALA304 3.9 20.8 1.0
C A:ASP302 4.0 23.6 1.0
O A:HOH524 4.0 45.5 1.0
O A:HOH924 4.0 53.7 1.0
N A:GLU303 4.2 22.6 1.0
C A:ALA304 4.4 20.1 1.0
O A:HOH510 4.6 56.7 1.0
O A:HOH772 4.7 52.6 1.0
O A:HOH822 4.7 37.6 1.0
CB A:GLU303 4.8 22.1 1.0
CA A:ALA304 4.8 21.7 1.0
CG A:GLU305 4.8 32.6 1.0

Sodium binding site 2 out of 4 in 8qeu

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Sodium binding site 2 out of 4 in the Crystal Structure of Ornithine Transcarbamylase From Arabidopsis Thaliana (Atotc) in Complex with Ornithine


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 Ornithine Transcarbamylase From Arabidopsis Thaliana (Atotc) in Complex with Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na411

b:30.4
occ:1.00
 O3 A:SO4405 2.5 22.8 1.0
NH2 A:ARG174 2.7 18.4 1.0
O A:HOH571 2.7 29.2 1.0
NE2 A:HIS201 2.8 15.1 1.0
OG1 A:THR126 2.9 15.1 1.0
O4 A:SO4405 2.9 17.7 1.0
NH1 A:ARG361 3.0 16.7 1.0
S A:SO4405 3.1 20.6 1.0
NE A:ORN401 3.1 22.5 1.0
O1 A:SO4405 3.3 25.7 1.0
CE1 A:HIS201 3.6 14.5 1.0
CD A:ORN401 3.7 24.6 1.0
CZ A:ARG174 3.8 19.2 1.0
CD2 A:HIS201 3.9 16.0 1.0
CZ A:ARG361 4.0 15.9 1.0
NH1 A:ARG174 4.1 17.2 1.0
NH2 A:ARG361 4.1 16.4 1.0
CB A:THR126 4.2 14.3 1.0
OE1 A:GLN204 4.2 15.1 1.0
N A:THR126 4.5 14.4 1.0
O2 A:SO4405 4.5 18.0 1.0
CG A:ORN401 4.6 22.0 1.0
CB A:ARG125 4.7 15.4 1.0
CD1 A:LEU196 4.7 10.1 0.5
CA A:THR126 4.9 13.6 1.0
ND1 A:HIS201 4.9 13.6 1.0
CD2 A:LEU196 4.9 20.5 0.5
NE A:ARG174 5.0 20.5 1.0

Sodium binding site 3 out of 4 in 8qeu

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Sodium binding site 3 out of 4 in the Crystal Structure of Ornithine Transcarbamylase From Arabidopsis Thaliana (Atotc) in Complex with Ornithine


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 Ornithine Transcarbamylase From Arabidopsis Thaliana (Atotc) in Complex with Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na407

b:23.7
occ:1.00
 O B:HOH601 2.7 19.0 1.0
O4 B:SO4405 2.9 17.1 0.9
NE2 B:HIS201 3.0 14.0 1.0
OG1 B:THR126 3.0 13.2 1.0
NH1 B:ARG361 3.0 14.6 1.0
O3 B:SO4405 3.1 14.5 0.9
O B:HOH547 3.3 18.4 1.0
NE B:ORN401 3.4 17.6 1.0
S B:SO4405 3.4 14.6 0.9
CE1 B:HIS201 3.8 13.9 1.0
O2 B:SO4405 3.9 16.2 0.9
O B:HOH647 4.0 22.6 1.0
CD2 B:HIS201 4.0 14.4 1.0
CZ B:ARG361 4.1 13.3 1.0
CD B:ORN401 4.2 19.5 1.0
OE1 B:GLN204 4.2 12.8 1.0
CG B:ORN401 4.2 19.9 1.0
NH2 B:ARG361 4.3 14.1 1.0
CB B:THR126 4.4 12.8 1.0
CD1 B:LEU196 4.4 20.7 0.5
N B:THR126 4.5 13.6 1.0
CB B:ARG125 4.6 15.2 1.0
O1 B:SO4405 4.8 15.2 0.9
CA B:THR126 5.0 12.4 1.0
ND1 B:HIS201 5.0 13.4 1.0

Sodium binding site 4 out of 4 in 8qeu

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Sodium binding site 4 out of 4 in the Crystal Structure of Ornithine Transcarbamylase From Arabidopsis Thaliana (Atotc) in Complex with Ornithine


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 Ornithine Transcarbamylase From Arabidopsis Thaliana (Atotc) in Complex with Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na411

b:27.4
occ:1.00
 NH1 C:ARG174 2.4 9.6 0.5
O C:HOH663 2.7 23.2 1.0
O4 C:SO4405 2.8 29.0 1.0
OG1 C:THR126 2.9 15.1 1.0
NE2 C:HIS201 2.9 14.7 1.0
O3 C:SO4405 3.0 18.9 1.0
NH1 C:ARG361 3.0 14.3 1.0
NE C:ORN401 3.3 21.8 1.0
S C:SO4405 3.4 21.1 1.0
CZ C:ARG174 3.6 14.9 0.5
CD C:ORN401 3.7 24.9 1.0
CE1 C:HIS201 3.7 14.6 1.0
O1 C:SO4405 3.8 27.9 1.0
NH2 C:ARG174 3.9 12.8 0.5
CD2 C:HIS201 4.0 15.1 1.0
CZ C:ARG361 4.0 14.4 1.0
NH2 C:ARG361 4.2 15.0 1.0
OE1 C:GLN204 4.2 14.1 1.0
CB C:THR126 4.3 14.7 1.0
N C:THR126 4.5 14.2 1.0
CG C:ORN401 4.5 24.8 1.0
CB C:ARG125 4.6 17.3 1.0
NE C:ARG174 4.7 19.1 0.5
O2 C:SO4405 4.7 19.0 1.0
CD1 C:LEU196 4.8 13.6 0.5
ND1 C:HIS201 4.9 13.2 1.0
CA C:THR126 4.9 14.0 1.0

Reference:

M.Nielipinski, A.Pietrzyk-Brzezinska, A.Wlodawer, B.Sekula. Structural Analysis and Molecular Substrate Recognition Properties of Arabidopsis Thaliana Ornithine Transcarbamylase, the Molecular Target of Phaseolotoxin Produced By Pseudomonas Syringae Front Plant Sci 2023.
ISSN: ESSN 1664-462X
DOI: 10.3389/FPLS.2023.1297956
Page generated: Wed Oct 9 13:09:54 2024

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