Atomistry » Iron » PDB 5xbp-5xxi » 5xgk
Atomistry »
  Iron »
    PDB 5xbp-5xxi »
      5xgk »

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

Go back to Iron Binding Sites List in 5xgk
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: Sun Dec 13 16:17:15 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