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Iron in PDB 5xgk: Crystal Structure of Arabidopsis Thaliana 4-Hydroxyphenylpyruvate Dioxygenase (Athppd) Complexed with Its Substrate 4- Hydroxyphenylpyruvate Acid (Hppa)

Enzymatic activity of Crystal Structure of Arabidopsis Thaliana 4-Hydroxyphenylpyruvate Dioxygenase (Athppd) Complexed with Its Substrate 4- Hydroxyphenylpyruvate Acid (Hppa)

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana 4-Hydroxyphenylpyruvate Dioxygenase (Athppd) Complexed with Its Substrate 4- Hydroxyphenylpyruvate Acid (Hppa):
1.13.11.27;

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana 4-Hydroxyphenylpyruvate Dioxygenase (Athppd) Complexed with Its Substrate 4- Hydroxyphenylpyruvate Acid (Hppa), PDB code: 5xgk was solved by G.F.Yang, W.C.Yang, H.Y.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.24 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 95.606, 95.294, 98.000, 90.00, 92.10, 90.00
R / Rfree (%) 25.8 / 31.2

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Arabidopsis Thaliana 4-Hydroxyphenylpyruvate Dioxygenase (Athppd) Complexed with Its Substrate 4- Hydroxyphenylpyruvate Acid (Hppa) (pdb code 5xgk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Arabidopsis Thaliana 4-Hydroxyphenylpyruvate Dioxygenase (Athppd) Complexed with Its Substrate 4- Hydroxyphenylpyruvate Acid (Hppa), PDB code: 5xgk:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5xgk

Go back to Iron Binding Sites List in 5xgk
Iron binding site 1 out of 4 in the Crystal Structure of Arabidopsis Thaliana 4-Hydroxyphenylpyruvate Dioxygenase (Athppd) Complexed with Its Substrate 4- Hydroxyphenylpyruvate Acid (Hppa)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Arabidopsis Thaliana 4-Hydroxyphenylpyruvate Dioxygenase (Athppd) Complexed with Its Substrate 4- Hydroxyphenylpyruvate Acid (Hppa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:30.0
occ:1.00
 O4 A:TYF501 1.8 20.0 1.0
O1 A:TYF501 1.9 20.0 1.0
OE1 A:GLU394 2.1 25.7 1.0
O A:HOH601 2.3 21.6 1.0
NE2 A:HIS308 2.4 21.7 1.0
NE2 A:HIS226 2.7 22.9 1.0
C2 A:TYF501 2.8 20.0 1.0
C1 A:TYF501 2.8 20.0 1.0
CD A:GLU394 3.1 22.8 1.0
CE1 A:HIS308 3.2 20.9 1.0
OE2 A:GLU394 3.4 26.6 1.0
CD2 A:HIS226 3.5 20.6 1.0
CD2 A:HIS308 3.5 21.2 1.0
CE1 A:HIS226 3.7 24.1 1.0
C3 A:TYF501 3.9 20.0 1.0
CG2 A:VAL228 4.0 15.4 1.0
O2 A:TYF501 4.0 20.0 1.0
ND1 A:HIS308 4.4 24.2 1.0
CG A:GLU394 4.5 16.0 1.0
CB A:ALA310 4.5 23.6 1.0
CG A:HIS308 4.6 20.5 1.0
C5 A:TYF501 4.6 20.0 1.0
CE2 A:PHE381 4.6 30.3 1.0
CG A:HIS226 4.7 23.4 1.0
C4 A:TYF501 4.7 20.0 1.0
O A:PHE419 4.7 26.1 1.0
CB A:GLU394 4.8 21.5 1.0
ND1 A:HIS226 4.8 21.7 1.0
CZ A:PHE381 4.8 27.1 1.0
CD1 A:PHE419 4.9 25.2 1.0

Iron binding site 2 out of 4 in 5xgk

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Iron binding site 2 out of 4 in the Crystal Structure of Arabidopsis Thaliana 4-Hydroxyphenylpyruvate Dioxygenase (Athppd) Complexed with Its Substrate 4- Hydroxyphenylpyruvate Acid (Hppa)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Arabidopsis Thaliana 4-Hydroxyphenylpyruvate Dioxygenase (Athppd) Complexed with Its Substrate 4- Hydroxyphenylpyruvate Acid (Hppa) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:30.0
occ:1.00
 OE1 B:GLU394 2.2 29.4 1.0
NE2 B:HIS308 2.6 25.6 1.0
NE2 B:HIS226 2.7 25.4 1.0
CD B:GLU394 3.1 27.1 1.0
CE1 B:HIS308 3.3 25.1 1.0
OE2 B:GLU394 3.4 31.0 1.0
CE1 B:HIS226 3.6 23.3 1.0
CD2 B:HIS226 3.7 24.6 1.0
CD2 B:HIS308 3.7 23.5 1.0
O B:PHE419 4.0 31.4 1.0
CG2 B:VAL228 4.3 20.1 1.0
CE1 B:PHE381 4.4 34.2 1.0
ND1 B:HIS308 4.5 29.7 1.0
CG B:GLU394 4.5 21.4 1.0
CZ B:PHE381 4.6 35.3 1.0
CB B:PHE419 4.7 24.2 1.0
CG B:HIS308 4.7 26.7 1.0
ND1 B:HIS226 4.8 22.6 1.0
NE2 B:GLN379 4.8 35.6 1.0
CB B:ALA310 4.8 22.1 1.0
CG B:HIS226 4.8 24.1 1.0
CB B:GLU394 4.9 20.8 1.0

Iron binding site 3 out of 4 in 5xgk

Go back to Iron Binding Sites List in 5xgk
Iron binding site 3 out of 4 in the Crystal Structure of Arabidopsis Thaliana 4-Hydroxyphenylpyruvate Dioxygenase (Athppd) Complexed with Its Substrate 4- Hydroxyphenylpyruvate Acid (Hppa)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Arabidopsis Thaliana 4-Hydroxyphenylpyruvate Dioxygenase (Athppd) Complexed with Its Substrate 4- Hydroxyphenylpyruvate Acid (Hppa) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:30.0
occ:1.00
 O C:HOH613 2.4 23.0 1.0
OE1 C:GLU394 2.4 31.0 1.0
NE2 C:HIS226 2.5 17.2 1.0
NE2 C:HIS308 2.5 18.9 1.0
CE1 C:HIS308 3.2 20.5 1.0
CE1 C:HIS226 3.4 20.2 1.0
CD C:GLU394 3.4 27.7 1.0
CD2 C:HIS226 3.5 21.3 1.0
CD2 C:HIS308 3.6 22.8 1.0
OE2 C:GLU394 3.7 28.0 1.0
CG2 C:VAL228 4.1 19.5 1.0
O C:PHE419 4.1 28.9 1.0
CE2 C:PHE381 4.4 23.6 1.0
ND1 C:HIS308 4.4 26.7 1.0
ND1 C:HIS226 4.5 21.5 1.0
CG C:HIS226 4.6 21.9 1.0
CG C:HIS308 4.7 23.5 1.0
CB C:ALA310 4.7 19.1 1.0
CZ C:PHE381 4.7 17.6 1.0
CB C:PHE419 4.7 24.3 1.0
CG C:GLU394 4.7 16.5 1.0
CD2 C:PHE419 4.8 18.5 1.0
CB C:GLU394 4.9 18.6 1.0

Iron binding site 4 out of 4 in 5xgk

Go back to Iron Binding Sites List in 5xgk
Iron binding site 4 out of 4 in the Crystal Structure of Arabidopsis Thaliana 4-Hydroxyphenylpyruvate Dioxygenase (Athppd) Complexed with Its Substrate 4- Hydroxyphenylpyruvate Acid (Hppa)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Arabidopsis Thaliana 4-Hydroxyphenylpyruvate Dioxygenase (Athppd) Complexed with Its Substrate 4- Hydroxyphenylpyruvate Acid (Hppa) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:30.0
occ:1.00
 OE1 D:GLU394 2.3 29.3 1.0
NE2 D:HIS226 2.5 25.5 1.0
O D:HOH649 2.6 20.5 1.0
NE2 D:HIS308 2.8 23.0 1.0
CD D:GLU394 3.2 28.6 1.0
OE2 D:GLU394 3.3 34.0 1.0
CE1 D:HIS226 3.4 25.0 1.0
CD2 D:HIS226 3.4 21.4 1.0
CE1 D:HIS308 3.6 25.0 1.0
CD2 D:HIS308 3.7 24.0 1.0
O D:PHE419 4.0 38.8 1.0
CE2 D:PHE381 4.4 25.3 1.0
CB D:PHE419 4.4 28.7 1.0
CG2 D:VAL228 4.5 15.0 1.0
ND1 D:HIS226 4.5 22.9 1.0
CG D:GLU394 4.6 19.5 1.0
CG D:HIS226 4.6 23.4 1.0
CZ D:PHE381 4.7 27.9 1.0
CB D:ALA310 4.8 23.8 1.0
ND1 D:HIS308 4.8 28.7 1.0
CG D:HIS308 4.9 22.0 1.0
CD1 D:PHE419 4.9 28.8 1.0
NE2 D:GLN379 4.9 35.4 1.0
C D:PHE419 4.9 30.7 1.0
CB D:GLU394 4.9 19.6 1.0
CA D:PHE419 5.0 30.3 1.0

Reference:

H.Y.Lin, X.Chen, J.N.Chen, D.W.Wang, F.X.Wu, S.Y.Lin, C.G.Zhan, J.W.Wu, W.C.Yang, G.F.Yang. Crystal Structure of 4-Hydroxyphenylpyruvate Dioxygenase in Complex with Substrate Reveals A New Starting Point For Herbicide Discovery. Res V.2019 02414 2019.
ISSN: ESSN 2639-5274
PubMed: 31549053
DOI: 10.34133/2019/2602414
Page generated: Tue Aug 6 11:39:26 2024

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