Atomistry » Zinc » PDB 4i7d-4ih7 » 4ih3
Atomistry »
  Zinc »
    PDB 4i7d-4ih7 »
      4ih3 »

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

Go back to Zinc Binding Sites List in 4ih3
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

Go back to Zinc Binding Sites List in 4ih3
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

Go back to Zinc Binding Sites List in 4ih3
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

Go back to Zinc Binding Sites List in 4ih3
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

Go back to Zinc Binding Sites List in 4ih3
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: Sun Oct 27 00:44:20 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy