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Zinc in PDB 5gja: Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa

Enzymatic activity of Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa:
1.14.17.4;

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa, PDB code: 5gja was solved by X.Z.Sun, Y.X.Li, W.R.He, C.G.Ji, P.X.Xia, Y.C.Wang, S.Du, H.J.Li, N.Raikhel, J.Y.Xiao, H.W.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.59 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.455, 95.343, 95.892, 90.06, 89.48, 89.99
R / Rfree (%) 17.1 / 21.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa (pdb code 5gja). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa, PDB code: 5gja:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5gja

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Zinc binding site 1 out of 8 in the Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:22.2
occ:1.00
 O1 A:6PC402 2.0 22.0 1.0
OD1 A:ASP182 2.0 25.5 1.0
NE2 A:HIS237 2.1 14.1 1.0
NE2 A:HIS180 2.2 22.2 1.0
N2 A:6PC402 2.3 23.6 1.0
C2 A:6PC402 2.7 22.2 1.0
CG A:ASP182 2.8 19.6 1.0
C1 A:6PC402 2.8 22.4 1.0
OD2 A:ASP182 3.0 14.7 1.0
CD2 A:HIS237 3.1 19.5 1.0
CD2 A:HIS180 3.1 16.2 1.0
CE1 A:HIS237 3.1 18.8 1.0
CE1 A:HIS180 3.2 24.5 1.0
C3 A:6PC402 3.4 26.4 1.0
O A:HOH552 3.9 38.0 1.0
O2 A:6PC402 3.9 25.3 1.0
CB A:ASP182 4.2 16.4 1.0
O A:HOH513 4.2 45.7 1.0
C6 A:6PC402 4.2 21.9 1.0
ND1 A:HIS237 4.2 14.2 1.0
CG A:HIS237 4.2 16.6 1.0
CG A:HIS180 4.2 18.1 1.0
ND1 A:HIS180 4.3 19.5 1.0
CA A:ASP182 4.6 19.1 1.0
N A:ASP182 4.6 16.1 1.0
C4 A:6PC402 4.6 17.8 1.0
CE2 A:PHE253 4.8 30.2 1.0
C5 A:6PC402 4.9 18.6 1.0
CD2 A:LEU177 5.0 27.2 1.0

Zinc binding site 2 out of 8 in 5gja

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Zinc binding site 2 out of 8 in the Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:20.8
occ:1.00
 OD1 B:ASP182 2.0 21.2 1.0
O2 B:6PC402 2.1 26.8 1.0
CE1 B:HIS180 2.2 26.0 1.0
NE2 B:HIS237 2.2 17.0 1.0
N2 B:6PC402 2.2 20.3 1.0
CG B:ASP182 2.8 22.7 1.0
C2 B:6PC402 2.8 26.7 1.0
C1 B:6PC402 2.9 18.7 1.0
OD2 B:ASP182 3.0 21.2 1.0
CD2 B:HIS237 3.0 17.3 1.0
NE2 B:HIS180 3.1 27.1 1.0
ND1 B:HIS180 3.1 23.3 1.0
CE1 B:HIS237 3.2 24.9 1.0
C3 B:6PC402 3.3 22.4 1.0
O1 B:6PC402 4.0 27.5 1.0
O B:HOH622 4.1 35.0 1.0
CB B:ASP182 4.2 17.3 1.0
CG B:HIS237 4.2 19.8 1.0
CD2 B:HIS180 4.2 18.5 1.0
C6 B:6PC402 4.3 23.0 1.0
CG B:HIS180 4.3 26.7 1.0
ND1 B:HIS237 4.3 22.5 1.0
O B:HOH515 4.3 39.2 1.0
C4 B:6PC402 4.5 23.5 1.0
CA B:ASP182 4.6 21.9 1.0
N B:ASP182 4.7 22.8 1.0
CE2 B:PHE253 4.8 37.8 1.0
C5 B:6PC402 4.9 22.1 1.0
CD2 B:LEU177 4.9 19.4 1.0

Zinc binding site 3 out of 8 in 5gja

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Zinc binding site 3 out of 8 in the Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:21.5
occ:1.00
 OD2 C:ASP182 2.0 25.7 1.0
O1 C:6PC402 2.0 25.0 1.0
NE2 C:HIS237 2.1 17.2 1.0
NE2 C:HIS180 2.2 26.3 1.0
N2 C:6PC402 2.3 22.3 1.0
CG C:ASP182 2.8 23.5 1.0
C2 C:6PC402 2.8 28.4 1.0
OD1 C:ASP182 2.9 22.1 1.0
C1 C:6PC402 2.9 23.3 1.0
CD2 C:HIS180 3.0 18.6 1.0
CD2 C:HIS237 3.0 17.4 1.0
CE1 C:HIS237 3.2 23.9 1.0
CE1 C:HIS180 3.2 28.0 1.0
C3 C:6PC402 3.4 23.6 1.0
O2 C:6PC402 4.0 27.2 1.0
CB C:ASP182 4.2 24.9 1.0
CG C:HIS180 4.2 23.4 1.0
CG C:HIS237 4.2 21.7 1.0
ND1 C:HIS180 4.2 22.2 1.0
ND1 C:HIS237 4.2 19.7 1.0
C6 C:6PC402 4.3 23.0 1.0
O C:HOH540 4.3 43.2 1.0
O C:HOH514 4.4 37.8 1.0
CA C:ASP182 4.6 17.4 1.0
C4 C:6PC402 4.6 26.0 1.0
N C:ASP182 4.6 24.0 1.0
CE2 C:PHE253 4.8 37.3 1.0
C5 C:6PC402 5.0 18.8 1.0

Zinc binding site 4 out of 8 in 5gja

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Zinc binding site 4 out of 8 in the Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:21.7
occ:1.00
 O2 D:6PC402 1.9 21.3 1.0
OD1 D:ASP182 2.0 23.9 1.0
CE1 D:HIS237 2.1 17.2 1.0
NE2 D:HIS180 2.2 28.8 1.0
N2 D:6PC402 2.3 23.3 1.0
C2 D:6PC402 2.7 27.0 1.0
CG D:ASP182 2.7 23.8 1.0
C1 D:6PC402 2.8 25.2 1.0
OD2 D:ASP182 2.9 17.4 1.0
NE2 D:HIS237 3.0 22.0 1.0
CD2 D:HIS180 3.1 18.3 1.0
ND1 D:HIS237 3.1 19.7 1.0
CE1 D:HIS180 3.2 29.1 1.0
C3 D:6PC402 3.4 23.6 1.0
O D:HOH532 3.8 35.1 1.0
O1 D:6PC402 3.9 30.1 1.0
CB D:ASP182 4.2 12.9 1.0
C6 D:6PC402 4.2 22.8 1.0
CD2 D:HIS237 4.2 14.9 1.0
CG D:HIS180 4.2 23.4 1.0
ND1 D:HIS180 4.2 25.2 1.0
O D:HOH514 4.2 38.9 1.0
CG D:HIS237 4.3 21.9 1.0
C4 D:6PC402 4.6 20.4 1.0
CA D:ASP182 4.6 15.7 1.0
N D:ASP182 4.7 17.0 1.0
CE2 D:PHE253 4.8 26.8 1.0
C5 D:6PC402 4.9 17.4 1.0
CD2 D:LEU177 5.0 24.7 1.0

Zinc binding site 5 out of 8 in 5gja

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Zinc binding site 5 out of 8 in the Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:25.1
occ:1.00
 O2 E:6PC402 2.0 27.3 1.0
OD1 E:ASP182 2.1 25.7 1.0
CE1 E:HIS180 2.2 27.6 1.0
NE2 E:HIS237 2.2 20.4 1.0
N2 E:6PC402 2.2 24.3 1.0
C2 E:6PC402 2.7 30.1 1.0
C1 E:6PC402 2.8 25.2 1.0
CG E:ASP182 2.8 26.9 1.0
OD2 E:ASP182 3.0 23.9 1.0
NE2 E:HIS180 3.0 34.1 1.0
CD2 E:HIS237 3.1 20.4 1.0
ND1 E:HIS180 3.1 21.2 1.0
CE1 E:HIS237 3.2 22.5 1.0
C3 E:6PC402 3.3 25.1 1.0
O1 E:6PC402 4.0 31.1 1.0
O E:HOH561 4.0 34.2 1.0
C6 E:6PC402 4.2 22.7 1.0
CD2 E:HIS180 4.2 21.9 1.0
CB E:ASP182 4.2 23.8 1.0
ND1 E:HIS237 4.3 23.3 1.0
CG E:HIS180 4.3 32.8 1.0
CG E:HIS237 4.3 23.8 1.0
O E:HOH526 4.5 36.7 1.0
C4 E:6PC402 4.6 26.5 1.0
CA E:ASP182 4.6 23.5 1.0
N E:ASP182 4.7 21.0 1.0
CE2 E:PHE253 4.9 37.6 1.0
C5 E:6PC402 4.9 21.3 1.0

Zinc binding site 6 out of 8 in 5gja

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Zinc binding site 6 out of 8 in the Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:23.3
occ:1.00
 O2 F:6PC402 2.0 24.3 1.0
NE2 F:HIS237 2.1 18.0 1.0
OD1 F:ASP182 2.2 24.3 1.0
NE2 F:HIS180 2.2 22.7 1.0
N2 F:6PC402 2.2 22.4 1.0
C2 F:6PC402 2.7 27.1 1.0
CG F:ASP182 2.8 20.9 1.0
OD2 F:ASP182 2.8 19.8 1.0
C1 F:6PC402 2.8 20.7 1.0
CD2 F:HIS180 3.0 18.8 1.0
CE1 F:HIS237 3.1 21.9 1.0
CD2 F:HIS237 3.1 19.2 1.0
CE1 F:HIS180 3.2 21.4 1.0
C3 F:6PC402 3.3 26.1 1.0
O1 F:6PC402 4.0 29.4 1.0
O F:HOH602 4.2 35.0 1.0
ND1 F:HIS237 4.2 19.2 1.0
CG F:HIS237 4.2 19.1 1.0
CB F:ASP182 4.2 18.2 1.0
CG F:HIS180 4.2 19.7 1.0
C6 F:6PC402 4.2 19.0 1.0
ND1 F:HIS180 4.3 20.7 1.0
O F:HOH510 4.3 37.5 1.0
C4 F:6PC402 4.5 22.4 1.0
N F:ASP182 4.6 18.7 1.0
CA F:ASP182 4.6 19.8 1.0
C5 F:6PC402 4.9 17.3 1.0
NZ F:LYS291 4.9 55.5 1.0
CD2 F:LEU177 4.9 25.2 1.0
CE2 F:PHE253 5.0 27.1 1.0

Zinc binding site 7 out of 8 in 5gja

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Zinc binding site 7 out of 8 in the Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn401

b:21.0
occ:1.00
 O1 G:6PC402 2.0 18.7 1.0
OD2 G:ASP182 2.1 24.2 1.0
NE2 G:HIS180 2.1 27.8 1.0
CE1 G:HIS237 2.1 17.8 1.0
N2 G:6PC402 2.2 19.2 1.0
C2 G:6PC402 2.7 25.7 1.0
CG G:ASP182 2.8 20.8 1.0
C1 G:6PC402 2.8 19.9 1.0
OD1 G:ASP182 3.0 23.5 1.0
CD2 G:HIS180 3.0 20.1 1.0
ND1 G:HIS237 3.1 19.6 1.0
NE2 G:HIS237 3.1 27.6 1.0
CE1 G:HIS180 3.1 22.0 1.0
C3 G:6PC402 3.3 18.7 1.0
O2 G:6PC402 4.0 25.1 1.0
ND1 G:HIS180 4.2 22.0 1.0
CG G:HIS180 4.2 22.1 1.0
CB G:ASP182 4.2 17.2 1.0
C6 G:6PC402 4.2 19.8 1.0
CG G:HIS237 4.3 18.8 1.0
CD2 G:HIS237 4.3 18.2 1.0
C4 G:6PC402 4.6 21.7 1.0
CA G:ASP182 4.6 21.9 1.0
N G:ASP182 4.7 19.7 1.0
C5 G:6PC402 4.9 16.5 1.0
NZ G:LYS291 4.9 52.3 1.0
CE1 G:PHE253 5.0 32.0 1.0
CD2 G:LEU177 5.0 27.6 1.0

Zinc binding site 8 out of 8 in 5gja

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Zinc binding site 8 out of 8 in the Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Arabidopsis Thaliana ACO2 in Complex with 2-Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn401

b:22.9
occ:1.00
 O1 H:6PC402 2.0 25.3 1.0
OD2 H:ASP182 2.1 19.0 1.0
NE2 H:HIS237 2.1 20.6 1.0
N2 H:6PC402 2.2 20.2 1.0
NE2 H:HIS180 2.2 29.6 1.0
C2 H:6PC402 2.7 30.8 1.0
CG H:ASP182 2.8 20.8 1.0
C1 H:6PC402 2.8 22.5 1.0
OD1 H:ASP182 2.8 18.8 1.0
CD2 H:HIS237 3.0 21.3 1.0
CD2 H:HIS180 3.1 21.1 1.0
CE1 H:HIS237 3.2 22.8 1.0
CE1 H:HIS180 3.2 28.4 1.0
C3 H:6PC402 3.3 18.5 1.0
O2 H:6PC402 3.9 32.0 1.0
O H:HOH538 4.0 36.4 1.0
CB H:ASP182 4.2 18.6 1.0
C6 H:6PC402 4.2 18.6 1.0
CG H:HIS237 4.2 21.4 1.0
ND1 H:HIS237 4.2 23.6 1.0
CG H:HIS180 4.2 27.7 1.0
ND1 H:HIS180 4.3 22.3 1.0
O H:HOH513 4.4 32.1 1.0
C4 H:6PC402 4.5 19.8 1.0
CA H:ASP182 4.6 20.3 1.0
N H:ASP182 4.7 19.4 1.0
C5 H:6PC402 4.9 15.1 1.0
CE1 H:PHE253 4.9 29.7 1.0

Reference:

Y.X.Li, J.Y.Xiao. Pyrazinamide and Derivatives Block Ethylene Biosynthesis By Inhibiting Acc Oxidase Nat Commun 2017.
ISSN: ESSN 2041-1723
DOI: 10.1038/NCOMMS15758
Page generated: Sun Oct 27 17:00:25 2024

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