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Sodium in PDB 4dpp: The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana

Enzymatic activity of The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana

All present enzymatic activity of The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana:
4.2.1.52;

Protein crystallography data

The structure of The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana, PDB code: 4dpp 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) 37.00 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.810, 95.810, 174.770, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 18.1

Sodium Binding Sites:

The binding sites of Sodium atom in the The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana (pdb code 4dpp). 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, PDB code: 4dpp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4dpp

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Sodium binding site 1 out of 5 in the The Structure of Dihydrodipicolinate Synthase 2 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 The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:35.2
occ:1.00
 O A:HOH553 2.2 30.2 1.0
O A:HOH550 2.4 29.1 1.0
O A:PHE345 2.4 24.2 1.0
O A:GLY347 2.5 22.4 1.0
O A:HOH541 2.5 28.4 1.0
O A:HOH598 2.5 36.8 1.0
NA A:NA402 3.1 38.1 1.0
N A:GLY347 3.4 22.9 1.0
C A:GLY347 3.5 24.1 1.0
C A:PHE345 3.5 24.4 1.0
C A:VAL346 3.6 23.8 1.0
CA A:VAL346 3.8 22.7 1.0
CA A:GLY347 4.1 24.4 1.0
NH1 A:ARG342 4.1 26.3 1.0
N A:VAL346 4.1 24.2 1.0
O A:VAL346 4.2 23.4 1.0
O A:GLU343 4.3 32.2 1.0
O A:HOH595 4.3 36.7 1.0
O A:HOH676 4.4 46.5 1.0
O A:HOH632 4.5 42.7 1.0
OE2 A:GLU348 4.6 57.7 1.0
O A:ARG342 4.6 28.4 1.0
N A:GLU348 4.6 25.1 1.0
CA A:PHE345 4.7 24.4 1.0
CD A:GLU348 4.7 53.4 1.0
N A:PHE345 4.8 25.9 1.0
CA A:GLU348 4.9 31.9 1.0
O A:HOH658 5.0 44.8 1.0
C A:GLU343 5.0 31.9 1.0
OE1 A:GLU348 5.0 68.6 1.0

Sodium binding site 2 out of 5 in 4dpp

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Sodium binding site 2 out of 5 in the The Structure of Dihydrodipicolinate Synthase 2 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 The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:38.1
occ:1.00
 O A:GLU343 2.3 32.2 1.0
O A:HOH690 2.3 49.3 1.0
O A:HOH658 2.4 44.8 1.0
O A:HOH553 2.5 30.2 1.0
O A:HOH550 2.5 29.1 1.0
O A:HOH598 2.6 36.8 1.0
NA A:NA401 3.1 35.2 1.0
C A:GLU343 3.3 31.9 1.0
CA A:GLU343 3.8 32.4 1.0
O A:PHE345 4.3 24.2 1.0
CB A:GLU343 4.4 30.9 1.0
N A:HIS344 4.4 27.8 1.0
O A:HOH595 4.5 36.7 1.0
O A:HOH632 4.6 42.7 1.0
O A:ARG342 4.7 28.4 1.0
O A:HOH541 4.8 28.4 1.0
CA A:HIS344 4.9 29.0 1.0

Sodium binding site 3 out of 5 in 4dpp

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Sodium binding site 3 out of 5 in the The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:41.0
occ:1.00
 O B:HOH705 2.0 49.0 1.0
O B:HOH680 2.4 44.9 1.0
O B:GLU343 2.4 23.1 1.0
O B:HOH538 2.4 26.8 1.0
O B:HOH564 2.5 31.2 1.0
O B:HOH640 2.5 39.7 1.0
NA B:NA402 3.1 31.2 1.0
C B:GLU343 3.3 21.9 1.0
CA B:GLU343 3.7 24.4 1.0
O B:PHE345 4.2 24.1 1.0
O B:HOH686 4.3 45.8 1.0
CB B:GLU343 4.4 28.3 1.0
N B:HIS344 4.5 22.4 1.0
O B:ARG342 4.5 25.9 1.0
O B:HOH543 4.9 27.3 1.0
O B:HOH635 4.9 38.7 1.0
CA B:HIS344 4.9 24.7 1.0
N B:GLU343 4.9 24.4 1.0
O B:GLY347 5.0 23.6 1.0

Sodium binding site 4 out of 5 in 4dpp

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Sodium binding site 4 out of 5 in the The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:31.2
occ:1.00
 O B:GLY347 2.4 23.6 1.0
O B:HOH640 2.4 39.7 1.0
O B:HOH538 2.4 26.8 1.0
O B:PHE345 2.5 24.1 1.0
O B:HOH543 2.5 27.3 1.0
O B:HOH564 2.6 31.2 1.0
NA B:NA401 3.1 41.0 1.0
N B:GLY347 3.4 21.8 1.0
C B:GLY347 3.4 29.2 1.0
C B:VAL346 3.6 20.1 1.0
C B:PHE345 3.6 25.2 1.0
CA B:VAL346 3.8 20.1 1.0
CA B:GLY347 4.0 24.2 1.0
NH1 B:ARG342 4.1 23.6 1.0
O B:HOH677 4.2 44.4 1.0
N B:VAL346 4.2 21.6 1.0
O B:VAL346 4.2 19.1 1.0
O B:HOH686 4.4 45.8 1.0
O B:HOH635 4.5 38.7 1.0
O B:GLU343 4.5 23.1 1.0
N B:GLU348 4.5 29.0 1.0
O B:HOH705 4.6 49.0 1.0
O B:ARG342 4.6 25.9 1.0
OE1 B:GLU348 4.6 67.4 1.0
OE2 B:GLU348 4.6 60.0 1.0
CD B:GLU348 4.7 54.7 1.0
O B:HOH680 4.8 44.9 1.0
CA B:PHE345 4.9 23.1 1.0
N B:PHE345 4.9 23.8 1.0
CZ B:ARG342 5.0 29.1 1.0

Sodium binding site 5 out of 5 in 4dpp

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Sodium binding site 5 out of 5 in the The Structure of Dihydrodipicolinate Synthase 2 From Arabidopsis Thaliana


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:35.8
occ:1.00
 O B:HOH597 2.2 35.4 1.0
O B:HOH563 2.3 31.1 1.0
O B:HOH518 2.4 23.1 1.0
O B:HOH542 2.5 27.1 1.0
O B:ARG252 2.7 22.9 1.0
NH1 B:ARG252 3.8 23.7 1.0
O B:HOH578 3.8 33.8 1.0
C B:ARG252 3.9 23.2 1.0
CA B:GLY256 4.0 23.0 1.0
O B:TRP253 4.0 27.2 1.0
CA B:TRP253 4.2 23.8 1.0
N B:GLY256 4.2 21.5 1.0
C B:TRP253 4.2 25.5 1.0
O B:HOH624 4.3 37.1 1.0
O B:HOH536 4.5 26.8 1.0
N B:TRP253 4.5 22.5 1.0
C B:GLY256 4.6 21.8 1.0
O B:ALA257 4.7 22.5 1.0
CE3 B:TRP253 4.7 18.5 1.0
N B:ALA257 5.0 19.9 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 14:58:44 2024

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