Zinc in PDB 4ih3: 2.5 Angstroms X-Ray Crystal Structure of of Human 2-Amino-3- Carboxymuconate-6-Semialdehyde Decarboxylase in Complex with Dipicolinic Acid

Enzymatic activity of 2.5 Angstroms X-Ray Crystal Structure of of Human 2-Amino-3- Carboxymuconate-6-Semialdehyde Decarboxylase in Complex with Dipicolinic Acid

All present enzymatic activity of 2.5 Angstroms X-Ray Crystal Structure of of Human 2-Amino-3- Carboxymuconate-6-Semialdehyde Decarboxylase in Complex with Dipicolinic Acid:
4.1.1.45;

Protein crystallography data

The structure of 2.5 Angstroms X-Ray Crystal Structure of of Human 2-Amino-3- Carboxymuconate-6-Semialdehyde Decarboxylase in Complex with Dipicolinic Acid, PDB code: 4ih3 was solved by L.Huo, A.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.21 / 2.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.368, 100.655, 233.117, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 28.3

Zinc Binding Sites:

The binding sites of Zinc atom in the 2.5 Angstroms X-Ray Crystal Structure of of Human 2-Amino-3- Carboxymuconate-6-Semialdehyde Decarboxylase in Complex with Dipicolinic Acid (pdb code 4ih3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the 2.5 Angstroms X-Ray Crystal Structure of of Human 2-Amino-3- Carboxymuconate-6-Semialdehyde Decarboxylase in Complex with Dipicolinic Acid, PDB code: 4ih3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4ih3

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Zinc binding site 1 out of 6 in the 2.5 Angstroms X-Ray Crystal Structure of of Human 2-Amino-3- Carboxymuconate-6-Semialdehyde Decarboxylase in Complex with Dipicolinic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2.5 Angstroms X-Ray Crystal Structure of of Human 2-Amino-3- Carboxymuconate-6-Semialdehyde Decarboxylase in Complex with Dipicolinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:25.5
occ:1.00
 NE2 A:HIS6 2.0 25.5 1.0
OD1 A:ASP291 2.1 30.2 1.0
NE2 A:HIS174 2.1 20.9 1.0
NE2 A:HIS8 2.1 22.0 1.0
C4 A:PDC402 2.2 29.9 1.0
CD2 A:HIS6 2.9 21.9 1.0
C3 A:PDC402 3.0 33.5 1.0
CE1 A:HIS174 3.0 18.0 1.0
CE1 A:HIS6 3.1 22.2 1.0
CE1 A:HIS8 3.1 23.6 1.0
CG A:ASP291 3.1 30.6 1.0
CD2 A:HIS8 3.1 20.4 1.0
CD2 A:HIS174 3.1 24.8 1.0
C5 A:PDC402 3.4 27.3 1.0
OD2 A:ASP291 3.5 31.3 1.0
CG A:HIS6 4.1 22.4 1.0
ND1 A:HIS6 4.1 20.6 1.0
ND1 A:HIS174 4.2 21.8 1.0
ND1 A:HIS8 4.2 19.1 1.0
CG A:HIS8 4.3 23.0 1.0
CG A:HIS174 4.3 22.5 1.0
C2 A:PDC402 4.3 34.9 1.0
CB A:ASP291 4.4 21.8 1.0
CA A:ASP291 4.5 20.5 1.0
C6 A:PDC402 4.6 25.9 1.0
NE2 A:HIS224 4.6 29.2 1.0
CE1 A:HIS224 4.8 29.8 1.0
CG A:PRO77 5.0 22.8 1.0

Zinc binding site 2 out of 6 in 4ih3

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Zinc binding site 2 out of 6 in the 2.5 Angstroms X-Ray Crystal Structure of of Human 2-Amino-3- Carboxymuconate-6-Semialdehyde Decarboxylase in Complex with Dipicolinic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 2.5 Angstroms X-Ray Crystal Structure of of Human 2-Amino-3- Carboxymuconate-6-Semialdehyde Decarboxylase in Complex with Dipicolinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:22.0
occ:1.00
 NE2 B:HIS8 2.0 21.6 1.0
OD1 B:ASP291 2.1 36.3 1.0
NE2 B:HIS174 2.2 23.8 1.0
NE2 B:HIS6 2.2 26.3 1.0
C5 B:PDC402 2.4 31.0 1.0
C4 B:PDC402 2.4 34.5 1.0
CE1 B:HIS8 2.9 22.5 1.0
CG B:ASP291 3.0 30.8 1.0
CD2 B:HIS8 3.1 22.5 1.0
CE1 B:HIS6 3.1 24.2 1.0
CD2 B:HIS174 3.1 21.2 1.0
CE1 B:HIS174 3.2 19.4 1.0
CD2 B:HIS6 3.3 26.8 1.0
OD2 B:ASP291 3.3 26.9 1.0
C3 B:PDC402 3.8 30.9 1.0
C6 B:PDC402 3.9 39.3 1.0
ND1 B:HIS8 4.1 24.2 1.0
CG B:HIS8 4.2 22.0 1.0
ND1 B:HIS6 4.3 20.6 1.0
ND1 B:HIS174 4.3 18.3 1.0
CB B:ASP291 4.3 21.6 1.0
CG B:HIS174 4.3 20.4 1.0
CG B:HIS6 4.4 23.9 1.0
CE1 B:HIS224 4.5 22.9 1.0
CA B:ASP291 4.6 22.2 1.0
CG B:PRO77 4.7 20.1 1.0
C2 B:PDC402 4.8 26.7 1.0
O4 B:PDC402 4.8 37.9 1.0
C8 B:PDC402 4.8 37.1 1.0
NE2 B:HIS224 4.8 22.1 1.0
N1 B:PDC402 4.9 28.7 1.0
CD B:PRO77 5.0 24.9 1.0

Zinc binding site 3 out of 6 in 4ih3

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Zinc binding site 3 out of 6 in the 2.5 Angstroms X-Ray Crystal Structure of of Human 2-Amino-3- Carboxymuconate-6-Semialdehyde Decarboxylase in Complex with Dipicolinic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 2.5 Angstroms X-Ray Crystal Structure of of Human 2-Amino-3- Carboxymuconate-6-Semialdehyde Decarboxylase in Complex with Dipicolinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:25.5
occ:1.00
 NE2 C:HIS6 1.8 29.2 1.0
NE2 C:HIS174 2.1 29.4 1.0
OD1 C:ASP291 2.1 36.8 1.0
NE2 C:HIS8 2.1 26.5 1.0
CE1 C:HIS6 2.2 31.6 1.0
C4 C:PDC402 3.0 39.5 1.0
CD2 C:HIS174 3.1 29.4 1.0
CE1 C:HIS174 3.1 24.0 1.0
CD2 C:HIS6 3.1 29.1 1.0
CD2 C:HIS8 3.1 24.0 1.0
CE1 C:HIS8 3.1 27.9 1.0
CG C:ASP291 3.3 32.3 1.0
C5 C:PDC402 3.4 38.9 1.0
ND1 C:HIS6 3.5 25.6 1.0
O C:HOH533 3.9 40.3 1.0
CG C:HIS6 3.9 26.7 1.0
OD2 C:ASP291 4.0 32.0 1.0
C3 C:PDC402 4.1 33.1 1.0
ND1 C:HIS174 4.2 21.9 1.0
CG C:HIS174 4.2 22.3 1.0
ND1 C:HIS8 4.2 22.2 1.0
CG C:HIS8 4.3 23.8 1.0
CB C:ASP291 4.3 24.6 1.0
CA C:ASP291 4.6 22.7 1.0
CG C:PRO77 4.7 22.8 1.0
C6 C:PDC402 4.8 40.2 1.0
NE2 C:HIS224 4.9 32.4 1.0
CE1 C:HIS224 4.9 29.0 1.0

Zinc binding site 4 out of 6 in 4ih3

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Zinc binding site 4 out of 6 in the 2.5 Angstroms X-Ray Crystal Structure of of Human 2-Amino-3- Carboxymuconate-6-Semialdehyde Decarboxylase in Complex with Dipicolinic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 2.5 Angstroms X-Ray Crystal Structure of of Human 2-Amino-3- Carboxymuconate-6-Semialdehyde Decarboxylase in Complex with Dipicolinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:28.1
occ:1.00
 OD1 D:ASP291 2.1 34.3 1.0
NE2 D:HIS6 2.1 27.8 1.0
NE2 D:HIS174 2.2 29.3 1.0
CE1 D:HIS8 2.2 26.7 1.0
C5 D:PDC402 2.2 38.9 1.0
C4 D:PDC402 2.8 40.6 1.0
CD2 D:HIS6 3.0 25.2 1.0
CD2 D:HIS174 3.0 25.3 1.0
CE1 D:HIS6 3.1 23.8 1.0
NE2 D:HIS8 3.1 21.3 1.0
ND1 D:HIS8 3.2 28.3 1.0
CE1 D:HIS174 3.3 28.5 1.0
CG D:ASP291 3.3 35.0 1.0
C6 D:PDC402 3.4 43.8 1.0
O3 D:PDC402 3.6 48.1 1.0
C8 D:PDC402 3.8 51.4 1.0
OD2 D:ASP291 4.0 37.9 1.0
CG D:HIS6 4.1 26.6 1.0
ND1 D:HIS6 4.2 22.6 1.0
C3 D:PDC402 4.2 35.7 1.0
CG D:HIS174 4.2 23.6 1.0
CD2 D:HIS8 4.3 25.6 1.0
ND1 D:HIS174 4.3 27.3 1.0
CG D:HIS8 4.3 23.8 1.0
CB D:ASP291 4.3 30.8 1.0
CA D:ASP291 4.6 29.4 1.0
N1 D:PDC402 4.6 50.5 1.0
CG D:PRO77 4.6 21.8 1.0
C2 D:PDC402 4.9 40.5 1.0
O4 D:PDC402 4.9 48.6 1.0
CE1 D:HIS224 4.9 32.7 1.0
CD1 D:PHE294 5.0 29.2 1.0
CD D:PRO77 5.0 23.4 1.0

Zinc binding site 5 out of 6 in 4ih3

Go back to Zinc Binding Sites List in 4ih3
Zinc binding site 5 out of 6 in the 2.5 Angstroms X-Ray Crystal Structure of of Human 2-Amino-3- Carboxymuconate-6-Semialdehyde Decarboxylase in Complex with Dipicolinic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 2.5 Angstroms X-Ray Crystal Structure of of Human 2-Amino-3- Carboxymuconate-6-Semialdehyde Decarboxylase in Complex with Dipicolinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:31.7
occ:1.00
 NE2 E:HIS6 2.0 24.7 1.0
NE2 E:HIS174 2.1 29.1 1.0
OD1 E:ASP291 2.1 36.6 1.0
NE2 E:HIS8 2.1 30.7 1.0
CD2 E:HIS174 2.8 31.6 1.0
CE1 E:HIS6 2.8 32.8 1.0
C4 E:PDC402 3.0 43.0 1.0
CG E:ASP291 3.0 37.9 1.0
CD2 E:HIS8 3.0 30.7 1.0
CD2 E:HIS6 3.1 30.9 1.0
CE1 E:HIS174 3.2 31.6 1.0
CE1 E:HIS8 3.2 31.6 1.0
OD2 E:ASP291 3.4 41.5 1.0
C5 E:PDC402 3.7 32.4 1.0
ND1 E:HIS6 4.0 29.2 1.0
C3 E:PDC402 4.0 43.0 1.0
CG E:HIS174 4.0 25.1 1.0
CG E:HIS6 4.1 32.9 1.0
ND1 E:HIS174 4.1 27.7 1.0
CG E:HIS8 4.2 28.8 1.0
ND1 E:HIS8 4.3 29.5 1.0
CB E:ASP291 4.3 28.7 1.0
CA E:ASP291 4.5 32.9 1.0
NE2 E:HIS224 4.7 36.2 1.0
CE1 E:HIS224 4.8 33.0 1.0
CG E:PRO77 4.9 29.0 1.0

Zinc binding site 6 out of 6 in 4ih3

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Zinc binding site 6 out of 6 in the 2.5 Angstroms X-Ray Crystal Structure of of Human 2-Amino-3- Carboxymuconate-6-Semialdehyde Decarboxylase in Complex with Dipicolinic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 2.5 Angstroms X-Ray Crystal Structure of of Human 2-Amino-3- Carboxymuconate-6-Semialdehyde Decarboxylase in Complex with Dipicolinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:35.8
occ:1.00
 OD1 F:ASP291 2.0 40.9 1.0
NE2 F:HIS6 2.1 30.1 1.0
NE2 F:HIS8 2.1 39.0 1.0
NE2 F:HIS174 2.2 41.7 1.0
C4 F:PDC402 2.4 44.7 1.0
CE1 F:HIS6 2.9 34.0 1.0
CG F:ASP291 2.9 39.0 1.0
CE1 F:HIS8 3.0 38.4 1.0
C5 F:PDC402 3.1 49.9 1.0
CD2 F:HIS174 3.1 34.1 1.0
CD2 F:HIS8 3.1 33.0 1.0
CD2 F:HIS6 3.2 32.4 1.0
CE1 F:HIS174 3.2 34.6 1.0
OD2 F:ASP291 3.2 40.6 1.0
C3 F:PDC402 3.3 45.8 1.0
ND1 F:HIS6 4.0 29.8 1.0
ND1 F:HIS8 4.1 38.3 1.0
CG F:HIS6 4.2 32.5 1.0
CG F:HIS8 4.2 35.0 1.0
CG F:HIS174 4.3 29.2 1.0
ND1 F:HIS174 4.3 34.8 1.0
CB F:ASP291 4.3 30.6 1.0
C6 F:PDC402 4.3 54.9 1.0
C2 F:PDC402 4.6 42.7 1.0
CA F:ASP291 4.7 33.3 1.0
NE2 F:HIS224 4.8 43.3 1.0
CE1 F:HIS224 4.8 39.6 1.0
CD1 F:PHE294 4.8 41.9 1.0
CG F:PRO77 4.8 40.3 1.0
CE1 F:PHE294 5.0 41.1 1.0

Reference:

L.Huo, A.Liu. 2.5 Angstroms X-Ray Crystal Structure of of Human 2-Amino-3-Carboxymuconate-6-Semialdehyde Decarboxylase in Complex with Dipicolinic Acid To Be Published.
Page generated: Wed Dec 16 05:24:10 2020

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