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Sodium in PDB 4dpq: The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana in Complex with (S)-Lysine

Enzymatic activity of The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana in Complex with (S)-Lysine

All present enzymatic activity of The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana in Complex with (S)-Lysine:
4.2.1.52;

Protein crystallography data

The structure of The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana in Complex with (S)-Lysine, PDB code: 4dpq was solved by M.D.W.Griffin, J.M.Billakanti, J.A.Gerrard, R.C.J.Dobson, F.G.Pearce, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.64 / 2.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.480, 95.480, 174.500, 90.00, 90.00, 90.00
R / Rfree (%) 13.9 / 17.7

Sodium Binding Sites:

The binding sites of Sodium atom in the The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana in Complex with (S)-Lysine (pdb code 4dpq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana in Complex with (S)-Lysine, PDB code: 4dpq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4dpq

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Sodium binding site 1 out of 5 in the The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana in Complex with (S)-Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana in Complex with (S)-Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:27.9
occ:1.00
 O A:HOH588 2.3 34.5 1.0
O A:HOH542 2.3 25.0 1.0
O A:GLY347 2.4 24.5 1.0
O A:PHE345 2.4 22.1 1.0
O A:HOH553 2.5 28.2 1.0
O A:HOH545 2.5 25.6 1.0
C A:GLY347 3.4 29.2 1.0
N A:GLY347 3.4 22.0 1.0
NA A:NA402 3.4 42.2 1.0
C A:PHE345 3.6 22.7 1.0
C A:VAL346 3.6 20.2 1.0
CA A:VAL346 3.9 19.5 1.0
NH1 A:ARG342 4.0 22.4 1.0
CA A:GLY347 4.0 27.8 1.0
N A:VAL346 4.2 20.1 1.0
O A:VAL346 4.2 18.3 1.0
O A:HOH643 4.2 43.7 1.0
O A:HOH566 4.4 30.0 1.0
OE1 A:GLU348 4.5 65.2 1.0
O A:GLU343 4.5 21.2 1.0
N A:GLU348 4.5 33.8 1.0
CD A:GLU348 4.5 54.8 1.0
OE2 A:GLU348 4.6 55.9 1.0
O A:ARG342 4.7 26.6 1.0
CA A:PHE345 4.8 21.6 1.0
CZ A:ARG342 4.8 24.8 1.0
N A:PHE345 4.9 21.4 1.0
O A:HOH647 4.9 44.2 1.0
CA A:GLU348 4.9 34.8 1.0

Sodium binding site 2 out of 5 in 4dpq

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Sodium binding site 2 out of 5 in the The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana in Complex with (S)-Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana in Complex with (S)-Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:42.2
occ:1.00
 O A:HOH647 2.3 44.2 1.0
O A:GLU343 2.4 21.2 1.0
O A:HOH553 2.4 28.2 1.0
O A:HOH588 2.7 34.5 1.0
O A:HOH542 2.8 25.0 1.0
NA A:NA401 3.4 27.9 1.0
C A:GLU343 3.4 23.8 1.0
CA A:GLU343 3.9 23.6 1.0
CB A:GLU343 4.3 24.1 1.0
O A:PHE345 4.6 22.1 1.0
O A:HOH566 4.6 30.0 1.0
N A:HIS344 4.6 23.7 1.0
O A:HOH643 4.7 43.7 1.0
O A:HOH545 4.9 25.6 1.0

Sodium binding site 3 out of 5 in 4dpq

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Sodium binding site 3 out of 5 in the The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana in Complex with (S)-Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana in Complex with (S)-Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:33.1
occ:1.00
 O A:HOH525 2.2 22.2 1.0
O A:HOH543 2.3 25.1 1.0
O A:HOH565 2.3 29.9 1.0
O A:HOH532 2.4 23.2 1.0
O A:ARG252 2.7 21.7 1.0
O A:HOH589 3.7 34.8 1.0
C A:ARG252 3.9 19.4 1.0
O A:TRP253 3.9 26.7 1.0
CA A:GLY256 3.9 19.5 1.0
NH1 A:ARG252 3.9 22.2 1.0
N A:GLY256 4.2 18.1 1.0
C A:TRP253 4.2 24.3 1.0
CA A:TRP253 4.2 21.9 1.0
O A:HOH533 4.5 23.4 1.0
N A:TRP253 4.5 19.9 1.0
C A:GLY256 4.6 19.9 1.0
O A:ALA257 4.7 16.9 1.0
CE3 A:TRP253 4.8 17.9 1.0

Sodium binding site 4 out of 5 in 4dpq

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Sodium binding site 4 out of 5 in the The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana in Complex with (S)-Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana in Complex with (S)-Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:27.7
occ:1.00
 O B:HOH617 2.4 37.3 1.0
O B:HOH520 2.4 22.7 1.0
O B:GLY347 2.4 20.9 1.0
O B:PHE345 2.4 19.7 1.0
O B:HOH557 2.5 30.6 1.0
O B:HOH556 2.6 30.1 1.0
NA B:NA402 3.1 40.4 1.0
N B:GLY347 3.4 21.7 1.0
C B:GLY347 3.4 22.5 1.0
C B:PHE345 3.6 20.0 1.0
C B:VAL346 3.6 19.6 1.0
CA B:VAL346 3.9 18.9 1.0
CA B:GLY347 3.9 23.0 1.0
NH1 B:ARG342 4.0 26.6 1.0
O B:VAL346 4.2 17.9 1.0
N B:VAL346 4.2 19.4 1.0
O B:HOH580 4.2 32.5 1.0
O B:GLU343 4.3 25.4 1.0
O B:ARG342 4.5 22.4 1.0
N B:GLU348 4.5 26.2 1.0
OE2 B:GLU348 4.7 66.4 1.0
CD B:GLU348 4.7 58.0 1.0
CA B:PHE345 4.8 19.4 1.0
N B:PHE345 4.8 20.7 1.0
CA B:GLU348 4.9 30.9 1.0
C B:GLU343 5.0 28.0 1.0
CZ B:ARG342 5.0 26.2 1.0

Sodium binding site 5 out of 5 in 4dpq

Go back to Sodium Binding Sites List in 4dpq
Sodium binding site 5 out of 5 in the The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana in Complex with (S)-Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana in Complex with (S)-Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:40.4
occ:1.00
 O B:GLU343 2.3 25.4 1.0
O B:HOH520 2.5 22.7 1.0
O B:HOH617 2.5 37.3 1.0
O B:HOH556 2.7 30.1 1.0
O B:HOH629 2.7 41.8 1.0
NA B:NA401 3.1 27.7 1.0
C B:GLU343 3.3 28.0 1.0
CA B:GLU343 3.7 29.0 1.0
O B:HOH637 3.9 42.1 1.0
CB B:GLU343 4.2 30.5 1.0
O B:PHE345 4.4 19.7 1.0
O B:HOH580 4.5 32.5 1.0
N B:HIS344 4.5 24.9 1.0
O B:ARG342 4.6 22.4 1.0
O B:HOH557 4.9 30.6 1.0
N B:GLU343 4.9 26.3 1.0
CA B:HIS344 5.0 25.6 1.0

Reference:

M.D.W.Griffin, J.M.Billakanti, A.Wason, S.Keller, H.D.T.Mertens, S.C.Atkinson, R.C.J.Dobson, M.A.Perugini, J.A.Gerrard, F.G.Pearce. Characterisation of the First Enzymes Committed to Lysine Biosynthesis in Arabidopsis Thaliana Plos One V. 7 40318 2012.
ISSN: ESSN 1932-6203
PubMed: 22792278
DOI: 10.1371/JOURNAL.PONE.0040318
Page generated: Mon Oct 7 14:59:23 2024

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