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Sodium in PDB 6py9: Structural Elements That Modulate the Substrate Specificity of Plant Purple Acid Phosphatases

Enzymatic activity of Structural Elements That Modulate the Substrate Specificity of Plant Purple Acid Phosphatases

All present enzymatic activity of Structural Elements That Modulate the Substrate Specificity of Plant Purple Acid Phosphatases:
3.1.3.2;

Protein crystallography data

The structure of Structural Elements That Modulate the Substrate Specificity of Plant Purple Acid Phosphatases, PDB code: 6py9 was solved by D.Feder, G.Schenk, L.W.Guddat, R.P.Mcgeary, N.Mitic, A.Furtado, B.L.Schulz, R.J.Henry, S.Schmidt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.90 / 2.20
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 126.052, 126.052, 295.149, 90.00, 90.00, 120.00
R / Rfree (%) 16.7 / 22.8

Other elements in 6py9:

The structure of Structural Elements That Modulate the Substrate Specificity of Plant Purple Acid Phosphatases also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Vanadium (V) 9 atoms
Iron (Fe) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structural Elements That Modulate the Substrate Specificity of Plant Purple Acid Phosphatases (pdb code 6py9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structural Elements That Modulate the Substrate Specificity of Plant Purple Acid Phosphatases, PDB code: 6py9:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6py9

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Sodium binding site 1 out of 4 in the Structural Elements That Modulate the Substrate Specificity of Plant Purple Acid Phosphatases


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Elements That Modulate the Substrate Specificity of Plant Purple Acid Phosphatases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na512

b:17.3
occ:1.00
O D:HOH706 2.9 18.5 1.0
NZ A:LYS306 3.0 24.3 1.0
O D:HOH643 3.0 21.8 1.0
CE A:LYS306 3.2 21.6 1.0
N A:ARG258 3.2 21.5 1.0
O D:GLU299 3.5 26.7 1.0
CA A:GLY257 3.6 18.0 1.0
C A:GLY257 4.0 19.8 1.0
CE2 D:TYR253 4.0 17.1 1.0
O D:HOH726 4.1 20.4 1.0
CB A:ARG258 4.1 20.5 1.0
CB D:GLU299 4.2 24.4 0.4
CA A:ARG258 4.2 21.3 1.0
C D:GLU299 4.3 23.5 1.0
CB D:GLU299 4.3 24.0 0.6
CD2 D:TYR253 4.6 19.1 1.0
OG D:SER287 4.7 28.6 1.0
CD A:LYS306 4.7 25.3 1.0
CA D:GLU299 4.7 23.4 0.6
CA D:GLU299 4.8 23.4 0.4
O A:ARG258 4.8 27.8 1.0
CG D:GLU299 4.8 22.8 0.6
O D:SER252 4.9 22.5 1.0
OE1 D:GLU299 4.9 21.6 0.4
OE1 D:GLU299 4.9 25.1 0.6
OH D:TYR253 4.9 22.6 1.0
CG D:GLU299 4.9 26.5 0.4
CZ D:TYR253 4.9 20.8 1.0
OH D:TYR256 4.9 23.9 1.0
CB D:SER287 5.0 24.2 1.0

Sodium binding site 2 out of 4 in 6py9

Go back to Sodium Binding Sites List in 6py9
Sodium binding site 2 out of 4 in the Structural Elements That Modulate the Substrate Specificity of Plant Purple Acid Phosphatases


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Elements That Modulate the Substrate Specificity of Plant Purple Acid Phosphatases within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na512

b:30.4
occ:1.00
OE1 B:GLU299 2.6 30.4 1.0
OH B:TYR253 2.8 23.6 1.0
OG B:SER287 3.1 26.5 1.0
O C:HOH797 3.1 9.8 1.0
NE2 B:HIS323 3.3 27.1 1.0
CB B:SER287 3.3 20.7 1.0
CB B:GLU299 3.5 30.6 1.0
CD2 B:HIS323 3.6 26.6 1.0
CD B:GLU299 3.7 32.9 1.0
CZ B:TYR253 3.7 27.6 1.0
CE2 B:TYR253 3.7 24.3 1.0
O B:HOH647 4.1 36.0 1.0
CG B:GLU299 4.2 28.6 1.0
CE1 B:HIS323 4.2 28.4 1.0
O C:HOH755 4.3 26.4 1.0
CG B:HIS323 4.5 24.5 1.0
CA B:SER287 4.6 25.1 1.0
C B:GLU299 4.7 27.3 1.0
O B:GLU299 4.7 21.9 1.0
CA B:GLU299 4.7 27.2 1.0
CB C:ARG258 4.7 24.4 1.0
OE2 B:GLU299 4.7 32.4 1.0
ND1 B:HIS323 4.8 26.6 1.0
O C:HOH712 5.0 32.4 1.0

Sodium binding site 3 out of 4 in 6py9

Go back to Sodium Binding Sites List in 6py9
Sodium binding site 3 out of 4 in the Structural Elements That Modulate the Substrate Specificity of Plant Purple Acid Phosphatases


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structural Elements That Modulate the Substrate Specificity of Plant Purple Acid Phosphatases within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na514

b:15.7
occ:1.00
O A:HOH854 2.6 37.9 1.0
NZ D:LYS306 2.9 24.7 1.0
O A:HOH693 3.0 21.2 1.0
O A:HOH715 3.1 24.4 1.0
N D:ARG258 3.2 22.5 1.0
CE D:LYS306 3.4 22.9 1.0
O A:GLU299 3.4 27.8 1.0
CA D:GLY257 3.6 17.3 1.0
O A:HOH662 3.8 22.6 1.0
CE2 A:TYR253 3.8 19.2 1.0
C D:GLY257 3.9 24.0 1.0
CB D:ARG258 4.0 25.7 1.0
CA D:ARG258 4.2 22.7 1.0
CB A:GLU299 4.3 26.3 1.0
C A:GLU299 4.3 25.6 1.0
CD2 A:TYR253 4.3 19.4 1.0
O3 D:SO4509 4.7 24.8 0.6
CA A:GLU299 4.7 23.4 1.0
OE1 A:GLU299 4.7 23.6 1.0
OG A:SER287 4.7 24.5 1.0
O A:SER252 4.8 22.0 1.0
CZ A:TYR253 4.8 21.4 1.0
O D:ARG258 4.8 22.4 1.0
CD D:LYS306 4.9 25.9 1.0
N D:GLY257 5.0 16.3 1.0

Sodium binding site 4 out of 4 in 6py9

Go back to Sodium Binding Sites List in 6py9
Sodium binding site 4 out of 4 in the Structural Elements That Modulate the Substrate Specificity of Plant Purple Acid Phosphatases


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structural Elements That Modulate the Substrate Specificity of Plant Purple Acid Phosphatases within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na510

b:34.6
occ:1.00
OH C:TYR253 2.5 29.5 1.0
OE1 C:GLU299 2.9 28.7 1.0
OG C:SER287 3.0 28.4 1.0
O B:HOH794 3.1 7.3 1.0
CE2 C:TYR253 3.1 23.1 1.0
CZ C:TYR253 3.2 22.1 1.0
CB C:SER287 3.3 21.2 1.0
NE2 C:HIS323 3.4 29.9 1.0
CD2 C:HIS323 3.7 24.0 1.0
O B:HOH701 3.8 30.1 1.0
CB C:GLU299 3.9 22.2 1.0
CD C:GLU299 4.1 27.7 1.0
CE1 C:HIS323 4.2 29.8 1.0
CB B:ARG258 4.4 28.3 1.0
O C:HOH677 4.4 33.5 1.0
CD2 C:TYR253 4.5 22.6 1.0
CG C:GLU299 4.6 26.7 1.0
CE1 C:TYR253 4.6 22.4 1.0
CA C:SER287 4.6 25.1 1.0
CG C:HIS323 4.6 26.3 1.0
O C:GLU299 4.7 22.1 1.0
ND1 C:HIS323 4.8 25.8 1.0
O B:ARG258 4.9 22.0 1.0
C C:GLU299 4.9 29.0 1.0
N B:ARG258 5.0 23.1 1.0

Reference:

D.Feder, R.P.Mcgeary, N.Mitic, T.Lonhienne, A.Furtado, B.L.Schulz, R.J.Henry, S.Schmidt, L.W.Guddat, G.Schenk. Structural Elements That Modulate the Substrate Specificity of Plant Purple Acid Phosphatases: Avenues For Improved Phosphorus Acquisition in Crops. Plant Sci. V. 294 10445 2020.
ISSN: ISSN 0168-9452
PubMed: 32234228
DOI: 10.1016/J.PLANTSCI.2020.110445
Page generated: Tue Dec 15 12:47:35 2020

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