Atomistry » Sodium » PDB 4def-4dxz » 4dpp
Atomistry »
  Sodium »
    PDB 4def-4dxz »
      4dpp »

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

Go back to Sodium Binding Sites List in 4dpp
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

Go back to Sodium Binding Sites List in 4dpp
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

Go back to Sodium Binding Sites List in 4dpp
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

Go back to Sodium Binding Sites List in 4dpp
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

Go back to Sodium Binding Sites List in 4dpp
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: Tue Dec 15 06:37:06 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy