Zinc in PDB 6vj7: 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: 6vj7
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)
|
40.76 /
2.60
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
125.704,
125.704,
298.151,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
21.3 /
27.4
|
Other elements in 6vj7:
The structure of Structural Elements That Modulate the Substrate Specificity of Plant Purple Acid Phosphatases also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Structural Elements That Modulate the Substrate Specificity of Plant Purple Acid Phosphatases
(pdb code 6vj7). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Structural Elements That Modulate the Substrate Specificity of Plant Purple Acid Phosphatases, PDB code: 6vj7:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6vj7
Go back to
Zinc Binding Sites List in 6vj7
Zinc 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 Zinc with other atoms in the Zn 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:Zn501
b:42.3
occ:0.58
|
O2G
|
A:ANP526
|
2.2
|
33.8
|
0.6
|
CD2
|
A:HIS323
|
2.2
|
31.4
|
1.0
|
OD1
|
A:ASN201
|
2.3
|
37.0
|
1.0
|
NE2
|
A:HIS286
|
2.4
|
30.4
|
1.0
|
O1G
|
A:ANP526
|
2.6
|
31.0
|
0.6
|
OD2
|
A:ASP164
|
2.8
|
30.7
|
1.0
|
PG
|
A:ANP526
|
2.9
|
30.6
|
0.6
|
CD2
|
A:HIS286
|
3.2
|
28.8
|
1.0
|
CG
|
A:ASN201
|
3.2
|
36.8
|
1.0
|
CG
|
A:HIS323
|
3.2
|
35.9
|
1.0
|
NE2
|
A:HIS323
|
3.3
|
32.5
|
1.0
|
CA
|
A:HIS323
|
3.4
|
27.3
|
1.0
|
CE1
|
A:HIS286
|
3.5
|
27.2
|
1.0
|
CG
|
A:ASP164
|
3.5
|
32.4
|
1.0
|
FE
|
A:FE502
|
3.6
|
30.9
|
0.7
|
CB
|
A:HIS323
|
3.7
|
28.2
|
1.0
|
ND2
|
A:ASN201
|
3.7
|
37.3
|
1.0
|
OD1
|
A:ASP164
|
3.8
|
36.5
|
1.0
|
O3G
|
A:ANP526
|
3.8
|
34.5
|
0.6
|
OD2
|
A:ASP135
|
3.9
|
32.2
|
1.0
|
O
|
A:HIS323
|
4.2
|
38.3
|
1.0
|
N3B
|
A:ANP526
|
4.3
|
41.9
|
0.6
|
C
|
A:HIS323
|
4.3
|
34.7
|
1.0
|
CB
|
A:ASN201
|
4.3
|
31.9
|
1.0
|
N
|
A:HIS323
|
4.3
|
29.0
|
1.0
|
ND1
|
A:HIS323
|
4.4
|
37.2
|
1.0
|
CE1
|
A:HIS323
|
4.4
|
34.2
|
1.0
|
CG
|
A:HIS286
|
4.4
|
29.4
|
1.0
|
N
|
A:ASN201
|
4.4
|
33.8
|
1.0
|
ND1
|
A:HIS286
|
4.5
|
26.9
|
1.0
|
OH
|
A:TYR253
|
4.5
|
30.9
|
1.0
|
CD2
|
A:HIS202
|
4.6
|
31.9
|
1.0
|
CB
|
A:ASP164
|
4.7
|
32.5
|
1.0
|
CA
|
A:ASN201
|
4.9
|
34.0
|
1.0
|
CG
|
A:ASP135
|
4.9
|
29.6
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6vj7
Go back to
Zinc Binding Sites List in 6vj7
Zinc 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 Zinc with other atoms in the Zn 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:Zn501
b:69.3
occ:1.00
|
OD2
|
B:ASP164
|
2.7
|
38.6
|
1.0
|
OD1
|
B:ASN201
|
2.7
|
38.2
|
1.0
|
ND1
|
B:HIS323
|
2.7
|
42.7
|
1.0
|
FE
|
B:FE502
|
2.9
|
37.2
|
0.7
|
O
|
B:HIS323
|
3.2
|
36.0
|
1.0
|
NE2
|
B:HIS286
|
3.3
|
38.4
|
1.0
|
CE1
|
B:HIS323
|
3.4
|
38.6
|
1.0
|
CA
|
B:HIS323
|
3.4
|
33.0
|
1.0
|
CG
|
B:ASN201
|
3.5
|
37.5
|
1.0
|
OD1
|
B:ASP135
|
3.6
|
36.1
|
1.0
|
ND2
|
B:ASN201
|
3.6
|
28.4
|
1.0
|
CG
|
B:HIS323
|
3.7
|
40.3
|
1.0
|
C
|
B:HIS323
|
3.7
|
36.3
|
1.0
|
CG
|
B:ASP164
|
3.9
|
39.1
|
1.0
|
NE2
|
B:HIS325
|
4.0
|
36.1
|
1.0
|
CD2
|
B:HIS202
|
4.0
|
40.1
|
1.0
|
CE1
|
B:HIS286
|
4.1
|
37.1
|
1.0
|
NE2
|
B:HIS296
|
4.1
|
38.8
|
1.0
|
CB
|
B:HIS323
|
4.1
|
36.5
|
1.0
|
NE2
|
B:HIS202
|
4.3
|
42.0
|
1.0
|
OD1
|
B:ASP164
|
4.4
|
40.3
|
1.0
|
CD2
|
B:HIS286
|
4.4
|
36.4
|
1.0
|
N
|
B:HIS323
|
4.4
|
30.9
|
1.0
|
NE2
|
B:HIS323
|
4.5
|
37.8
|
1.0
|
CE1
|
B:HIS325
|
4.6
|
33.7
|
1.0
|
CD2
|
B:HIS323
|
4.7
|
38.0
|
1.0
|
CE1
|
B:HIS296
|
4.7
|
31.9
|
1.0
|
CG
|
B:ASP135
|
4.8
|
37.3
|
1.0
|
CD2
|
B:HIS325
|
4.8
|
33.5
|
1.0
|
CD2
|
B:HIS296
|
4.8
|
33.1
|
1.0
|
OH
|
B:TYR167
|
4.9
|
39.0
|
1.0
|
CB
|
B:ASN201
|
5.0
|
31.8
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6vj7
Go back to
Zinc Binding Sites List in 6vj7
Zinc 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 Zinc with other atoms in the Zn 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
|
C:Zn702
b:35.4
occ:0.54
|
O1G
|
C:ANP730
|
1.8
|
34.2
|
0.6
|
NE2
|
C:HIS286
|
2.1
|
34.8
|
1.0
|
OD1
|
C:ASN201
|
2.2
|
36.4
|
1.0
|
CD2
|
C:HIS323
|
2.4
|
36.7
|
1.0
|
OD2
|
C:ASP164
|
2.8
|
40.6
|
1.0
|
CG
|
C:HIS323
|
3.0
|
32.9
|
1.0
|
CG
|
C:ASN201
|
3.0
|
33.4
|
1.0
|
CE1
|
C:HIS286
|
3.1
|
32.2
|
1.0
|
CD2
|
C:HIS286
|
3.1
|
31.6
|
1.0
|
CA
|
C:HIS323
|
3.2
|
31.5
|
1.0
|
NE2
|
C:HIS323
|
3.3
|
42.6
|
1.0
|
PG
|
C:ANP730
|
3.3
|
37.7
|
0.6
|
ND2
|
C:ASN201
|
3.3
|
34.0
|
1.0
|
CB
|
C:HIS323
|
3.4
|
32.2
|
1.0
|
FE
|
C:FE703
|
3.5
|
33.8
|
0.8
|
CG
|
C:ASP164
|
3.6
|
40.2
|
1.0
|
OD1
|
C:ASP135
|
3.7
|
36.4
|
1.0
|
OD1
|
C:ASP164
|
3.9
|
34.9
|
1.0
|
O3G
|
C:ANP730
|
4.0
|
35.5
|
0.6
|
O
|
C:HIS323
|
4.0
|
30.5
|
1.0
|
ND1
|
C:HIS323
|
4.0
|
34.1
|
1.0
|
N
|
C:HIS323
|
4.1
|
31.4
|
1.0
|
C
|
C:HIS323
|
4.1
|
34.0
|
1.0
|
CE1
|
C:HIS323
|
4.2
|
33.2
|
1.0
|
N3B
|
C:ANP730
|
4.2
|
42.4
|
0.6
|
ND1
|
C:HIS286
|
4.2
|
30.4
|
1.0
|
CG
|
C:HIS286
|
4.2
|
31.8
|
1.0
|
O2G
|
C:ANP730
|
4.3
|
38.8
|
0.6
|
CB
|
C:ASN201
|
4.4
|
28.4
|
1.0
|
N
|
C:ASN201
|
4.4
|
33.6
|
1.0
|
CB
|
C:ASP164
|
4.7
|
37.7
|
1.0
|
CD2
|
C:HIS202
|
4.8
|
38.7
|
1.0
|
OH
|
C:TYR253
|
4.8
|
33.3
|
1.0
|
CG
|
C:ASP135
|
4.9
|
35.7
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6vj7
Go back to
Zinc Binding Sites List in 6vj7
Zinc 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 Zinc with other atoms in the Zn 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
|
D:Zn702
b:38.4
occ:0.58
|
O2G
|
D:ANP736
|
1.8
|
30.3
|
0.7
|
OD1
|
D:ASN201
|
2.1
|
34.7
|
1.0
|
NE2
|
D:HIS286
|
2.2
|
32.8
|
1.0
|
ND1
|
D:HIS323
|
2.2
|
33.5
|
1.0
|
OD2
|
D:ASP164
|
2.5
|
30.8
|
1.0
|
CD2
|
D:HIS286
|
3.0
|
34.3
|
1.0
|
CG
|
D:ASN201
|
3.0
|
35.4
|
1.0
|
CE1
|
D:HIS323
|
3.1
|
33.2
|
1.0
|
PG
|
D:ANP736
|
3.2
|
34.4
|
0.7
|
CG
|
D:HIS323
|
3.2
|
33.4
|
1.0
|
CE1
|
D:HIS286
|
3.2
|
33.1
|
1.0
|
CA
|
D:HIS323
|
3.3
|
30.1
|
1.0
|
ND2
|
D:ASN201
|
3.3
|
34.0
|
1.0
|
FE
|
D:FE703
|
3.5
|
35.4
|
0.8
|
CB
|
D:HIS323
|
3.6
|
33.5
|
1.0
|
CG
|
D:ASP164
|
3.6
|
34.1
|
1.0
|
N3B
|
D:ANP736
|
3.6
|
37.2
|
0.7
|
OD1
|
D:ASP135
|
4.0
|
31.7
|
1.0
|
O
|
D:HIS323
|
4.0
|
31.9
|
1.0
|
OD1
|
D:ASP164
|
4.0
|
36.2
|
1.0
|
O1G
|
D:ANP736
|
4.1
|
40.9
|
0.7
|
O3G
|
D:ANP736
|
4.1
|
35.2
|
0.7
|
C
|
D:HIS323
|
4.1
|
34.0
|
1.0
|
CG
|
D:HIS286
|
4.2
|
35.1
|
1.0
|
NE2
|
D:HIS323
|
4.2
|
33.2
|
1.0
|
N
|
D:HIS323
|
4.2
|
29.2
|
1.0
|
ND1
|
D:HIS286
|
4.3
|
36.1
|
1.0
|
CD2
|
D:HIS323
|
4.3
|
30.9
|
1.0
|
CD2
|
D:HIS202
|
4.3
|
35.4
|
1.0
|
CB
|
D:ASN201
|
4.4
|
34.1
|
1.0
|
N
|
D:ASN201
|
4.5
|
34.6
|
1.0
|
OH
|
D:TYR253
|
4.6
|
31.5
|
1.0
|
CB
|
D:ASP164
|
4.8
|
32.1
|
1.0
|
NE2
|
D:HIS202
|
4.8
|
38.6
|
1.0
|
CG
|
D:ASP135
|
4.9
|
31.2
|
1.0
|
NE2
|
D:HIS296
|
5.0
|
37.3
|
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 Oct 29 09:03:20 2024
|