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Zinc in PDB 4ofc: 2.0 Angstroms X-Ray Crystal Structure of Human 2-Amino-3- Carboxymuconate-6-Semialdehye Decarboxylase

Enzymatic activity of 2.0 Angstroms X-Ray Crystal Structure of Human 2-Amino-3- Carboxymuconate-6-Semialdehye Decarboxylase

All present enzymatic activity of 2.0 Angstroms X-Ray Crystal Structure of Human 2-Amino-3- Carboxymuconate-6-Semialdehye Decarboxylase:
4.1.1.45;

Protein crystallography data

The structure of 2.0 Angstroms X-Ray Crystal Structure of Human 2-Amino-3- Carboxymuconate-6-Semialdehye Decarboxylase, PDB code: 4ofc was solved by L.Huo, F.Liu, H.Iwaki, L.Chen, Y.Hasegawa, A.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.11 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.704, 101.082, 232.820, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24.1

Zinc Binding Sites:

The binding sites of Zinc atom in the 2.0 Angstroms X-Ray Crystal Structure of Human 2-Amino-3- Carboxymuconate-6-Semialdehye Decarboxylase (pdb code 4ofc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the 2.0 Angstroms X-Ray Crystal Structure of Human 2-Amino-3- Carboxymuconate-6-Semialdehye Decarboxylase, PDB code: 4ofc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4ofc

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Zinc binding site 1 out of 6 in the 2.0 Angstroms X-Ray Crystal Structure of Human 2-Amino-3- Carboxymuconate-6-Semialdehye Decarboxylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2.0 Angstroms X-Ray Crystal Structure of Human 2-Amino-3- Carboxymuconate-6-Semialdehye Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:23.3
occ:1.00
 NE2 A:HIS8 2.2 17.8 1.0
NE2 A:HIS174 2.2 16.4 1.0
NE2 A:HIS6 2.3 19.1 1.0
OD1 A:ASP291 2.4 22.5 1.0
O A:HOH557 2.5 28.7 1.0
CD2 A:HIS174 3.0 17.2 1.0
CD2 A:HIS8 3.0 17.3 1.0
CG A:ASP291 3.1 25.5 1.0
CD2 A:HIS6 3.2 17.6 1.0
OD2 A:ASP291 3.3 30.3 1.0
CE1 A:HIS6 3.3 16.5 1.0
CE1 A:HIS8 3.3 19.6 1.0
CE1 A:HIS174 3.3 16.6 1.0
CG A:HIS174 4.2 16.7 1.0
CG A:HIS8 4.3 16.5 1.0
CB A:ASP291 4.3 20.2 1.0
ND1 A:HIS8 4.4 16.4 1.0
ND1 A:HIS174 4.4 15.2 1.0
CG A:HIS6 4.4 18.8 1.0
ND1 A:HIS6 4.4 18.9 1.0
CA A:ASP291 4.5 17.1 1.0
CE1 A:HIS224 4.7 23.3 1.0
O A:HOH633 4.7 28.1 1.0
NE2 A:HIS224 4.7 26.6 1.0
CG A:PRO77 5.0 22.4 1.0
CD1 A:PHE294 5.0 19.0 1.0

Zinc binding site 2 out of 6 in 4ofc

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Zinc binding site 2 out of 6 in the 2.0 Angstroms X-Ray Crystal Structure of Human 2-Amino-3- Carboxymuconate-6-Semialdehye Decarboxylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 2.0 Angstroms X-Ray Crystal Structure of Human 2-Amino-3- Carboxymuconate-6-Semialdehye Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:20.7
occ:1.00
 NE2 B:HIS8 2.1 14.8 1.0
NE2 B:HIS174 2.3 16.0 1.0
OD1 B:ASP291 2.3 19.0 1.0
NE2 B:HIS6 2.4 15.3 1.0
O B:HOH546 2.9 29.7 1.0
CD2 B:HIS174 3.1 15.8 1.0
CD2 B:HIS8 3.1 16.4 1.0
CE1 B:HIS8 3.1 15.6 1.0
CG B:ASP291 3.2 27.4 1.0
CD2 B:HIS6 3.2 15.0 1.0
CE1 B:HIS6 3.4 17.9 1.0
CE1 B:HIS174 3.4 17.8 1.0
OD2 B:ASP291 3.8 34.0 1.0
ND1 B:HIS8 4.2 14.7 1.0
CG B:HIS8 4.2 14.3 1.0
CB B:ASP291 4.3 19.0 1.0
CG B:HIS174 4.3 15.2 1.0
CG B:HIS6 4.4 15.2 1.0
ND1 B:HIS174 4.4 15.9 1.0
ND1 B:HIS6 4.4 14.5 1.0
CA B:ASP291 4.6 16.9 1.0
CE1 B:HIS224 4.6 21.3 1.0
O B:HOH508 4.7 32.4 1.0
CG B:PRO77 4.8 18.1 1.0
NE2 B:HIS224 4.8 24.5 1.0
O B:HOH663 4.9 31.9 1.0

Zinc binding site 3 out of 6 in 4ofc

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Zinc binding site 3 out of 6 in the 2.0 Angstroms X-Ray Crystal Structure of Human 2-Amino-3- Carboxymuconate-6-Semialdehye Decarboxylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 2.0 Angstroms X-Ray Crystal Structure of Human 2-Amino-3- Carboxymuconate-6-Semialdehye Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:25.1
occ:1.00
 NE2 C:HIS8 2.3 18.7 1.0
NE2 C:HIS174 2.3 21.2 1.0
NE2 C:HIS6 2.3 22.3 1.0
OD1 C:ASP291 2.4 22.0 1.0
O C:HOH542 2.5 35.6 1.0
CD2 C:HIS174 3.0 20.8 1.0
CD2 C:HIS8 3.1 21.0 1.0
CG C:ASP291 3.2 27.2 1.0
CE1 C:HIS6 3.3 21.9 1.0
CD2 C:HIS6 3.3 17.5 1.0
CE1 C:HIS8 3.4 21.6 1.0
CE1 C:HIS174 3.4 19.9 1.0
OD2 C:ASP291 3.6 31.1 1.0
CG C:HIS174 4.3 18.3 1.0
CG C:HIS8 4.3 16.9 1.0
CB C:ASP291 4.3 18.5 1.0
ND1 C:HIS6 4.4 18.6 1.0
ND1 C:HIS8 4.4 20.9 1.0
CG C:HIS6 4.4 18.2 1.0
ND1 C:HIS174 4.4 20.2 1.0
NE2 C:HIS224 4.4 21.5 1.0
CA C:ASP291 4.6 19.7 1.0
O C:HOH613 4.7 31.0 1.0
O B:HOH676 4.7 30.2 1.0
CG C:PRO77 4.8 23.0 1.0
CE1 C:HIS224 4.9 24.5 1.0

Zinc binding site 4 out of 6 in 4ofc

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Zinc binding site 4 out of 6 in the 2.0 Angstroms X-Ray Crystal Structure of Human 2-Amino-3- Carboxymuconate-6-Semialdehye Decarboxylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 2.0 Angstroms X-Ray Crystal Structure of Human 2-Amino-3- Carboxymuconate-6-Semialdehye Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:26.3
occ:1.00
 NE2 D:HIS8 2.3 21.6 1.0
NE2 D:HIS174 2.3 19.7 1.0
NE2 D:HIS6 2.4 23.6 1.0
OD1 D:ASP291 2.4 24.3 1.0
O D:HOH636 2.5 32.7 1.0
O D:HOH639 2.6 33.2 1.0
CD2 D:HIS174 3.0 18.1 1.0
CD2 D:HIS8 3.1 23.2 1.0
CG D:ASP291 3.1 28.3 1.0
CD2 D:HIS6 3.2 20.6 1.0
CE1 D:HIS8 3.4 20.7 1.0
CE1 D:HIS174 3.4 19.8 1.0
CE1 D:HIS6 3.4 23.5 1.0
OD2 D:ASP291 3.5 36.6 1.0
CG D:HIS174 4.3 17.6 1.0
CG D:HIS8 4.3 20.6 1.0
CB D:ASP291 4.3 23.3 1.0
ND1 D:HIS8 4.4 19.8 1.0
ND1 D:HIS174 4.4 19.5 1.0
CG D:HIS6 4.4 19.4 1.0
ND1 D:HIS6 4.5 23.9 1.0
CA D:ASP291 4.6 23.1 1.0
CE1 D:HIS224 4.7 22.8 1.0
O D:HOH580 4.7 34.4 1.0
CG D:PRO77 4.7 20.6 1.0
NE2 D:HIS224 4.8 29.2 1.0

Zinc binding site 5 out of 6 in 4ofc

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Zinc binding site 5 out of 6 in the 2.0 Angstroms X-Ray Crystal Structure of Human 2-Amino-3- Carboxymuconate-6-Semialdehye Decarboxylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 2.0 Angstroms X-Ray Crystal Structure of Human 2-Amino-3- Carboxymuconate-6-Semialdehye Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:29.1
occ:1.00
 NE2 E:HIS8 2.2 23.8 1.0
NE2 E:HIS174 2.3 21.9 1.0
NE2 E:HIS6 2.3 23.5 1.0
OD1 E:ASP291 2.4 27.4 1.0
O E:HOH613 2.8 38.8 1.0
CD2 E:HIS174 3.0 20.9 1.0
CD2 E:HIS8 3.0 23.2 1.0
CD2 E:HIS6 3.3 20.8 1.0
CG E:ASP291 3.3 34.6 1.0
CE1 E:HIS6 3.3 23.8 1.0
CE1 E:HIS8 3.4 26.3 1.0
CE1 E:HIS174 3.5 22.2 1.0
OD2 E:ASP291 3.7 39.2 1.0
CG E:HIS8 4.3 22.6 1.0
CG E:HIS174 4.3 21.2 1.0
CB E:ASP291 4.3 26.5 1.0
ND1 E:HIS8 4.4 27.0 1.0
CG E:HIS6 4.4 20.0 1.0
ND1 E:HIS6 4.4 23.3 1.0
ND1 E:HIS174 4.4 21.4 1.0
CA E:ASP291 4.6 24.8 1.0
NE2 E:HIS224 4.6 28.2 1.0
CG E:PRO77 4.8 25.4 1.0
CE1 E:HIS224 4.9 27.3 1.0

Zinc binding site 6 out of 6 in 4ofc

Go back to Zinc Binding Sites List in 4ofc
Zinc binding site 6 out of 6 in the 2.0 Angstroms X-Ray Crystal Structure of Human 2-Amino-3- Carboxymuconate-6-Semialdehye Decarboxylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 2.0 Angstroms X-Ray Crystal Structure of Human 2-Amino-3- Carboxymuconate-6-Semialdehye Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:33.1
occ:1.00
 NE2 F:HIS6 2.3 28.3 1.0
NE2 F:HIS8 2.3 26.4 1.0
NE2 F:HIS174 2.3 28.6 1.0
OD2 F:ASP291 2.6 34.6 1.0
CG F:ASP291 3.0 33.0 1.0
OD1 F:ASP291 3.0 39.4 1.0
CD2 F:HIS174 3.0 25.5 1.0
CD2 F:HIS8 3.1 29.0 1.0
CE1 F:HIS6 3.2 26.6 1.0
CD2 F:HIS6 3.2 24.8 1.0
CE1 F:HIS8 3.4 27.8 1.0
CE1 F:HIS174 3.4 28.2 1.0
CG F:HIS174 4.3 23.4 1.0
CB F:ASP291 4.3 24.7 1.0
CG F:HIS8 4.3 26.2 1.0
ND1 F:HIS6 4.4 25.0 1.0
CG F:HIS6 4.4 23.0 1.0
ND1 F:HIS8 4.4 30.3 1.0
ND1 F:HIS174 4.4 27.9 1.0
CA F:ASP291 4.6 24.4 1.0
CE1 F:HIS224 4.6 29.3 1.0
NE2 F:HIS224 4.7 33.0 1.0
CD1 F:PHE294 4.8 37.6 1.0
CG F:PRO77 4.9 32.3 1.0
CE1 F:PHE294 4.9 34.0 1.0

Reference:

L.Huo, F.Liu, H.Iwaki, L.Chen, Y.Hasegawa, A.Liu. Human A-Amino-Beta-Carboxymuconate-E-Semialdehyde Decarboxylase (Acmsd): A Structural and Mechanistic Unveiling Protein Sci. 2014.
ISSN: ESSN 1469-896X
Page generated: Sun Oct 27 03:42:02 2024

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