Atomistry » Zinc » PDB 4l5u-4le6 » 4lal
Atomistry »
  Zinc »
    PDB 4l5u-4le6 »
      4lal »

Zinc in PDB 4lal: Crystal Structure of Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil

Protein crystallography data

The structure of Crystal Structure of Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil, PDB code: 4lal was solved by S.Xu, W.Li, J.Zhu, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.96 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 192.266, 54.301, 143.776, 90.00, 121.04, 90.00
R / Rfree (%) 17.5 / 22

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil (pdb code 4lal). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil, PDB code: 4lal:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4lal

Go back to Zinc Binding Sites List in 4lal
Zinc binding site 1 out of 4 in the Crystal Structure of Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil


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 Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:37.7
occ:1.00
O53 A:5CU402 2.0 33.0 1.0
O4 A:5CU402 2.0 31.7 1.0
NE2 A:HIS195 2.3 23.4 1.0
NE2 A:HIS14 2.3 21.6 1.0
NE2 A:HIS12 2.5 22.5 1.0
C51 A:5CU402 3.0 37.8 1.0
C4 A:5CU402 3.0 37.8 1.0
CE1 A:HIS195 3.1 23.5 1.0
CD2 A:HIS14 3.2 22.0 1.0
CD2 A:HIS12 3.3 22.7 1.0
CD2 A:HIS195 3.3 23.5 1.0
CE1 A:HIS14 3.4 22.3 1.0
C5 A:5CU402 3.4 39.1 1.0
CE1 A:HIS12 3.6 23.2 1.0
O52 A:5CU402 4.1 33.5 1.0
N3 A:5CU402 4.2 37.5 1.0
ND1 A:HIS195 4.2 23.1 1.0
NE2 A:HIS251 4.3 24.3 1.0
CG A:HIS14 4.4 22.4 1.0
CG A:HIS195 4.4 22.9 1.0
ND1 A:HIS14 4.4 22.4 1.0
CG A:HIS12 4.5 22.9 1.0
CB A:ALA323 4.6 24.7 1.0
ND1 A:HIS12 4.6 23.7 1.0
CA A:ALA323 4.7 24.2 1.0
CD2 A:PHE326 4.7 20.5 1.0
CE1 A:HIS251 4.8 24.5 1.0
C6 A:5CU402 4.8 40.2 1.0
CE2 A:PHE326 4.9 20.9 1.0

Zinc binding site 2 out of 4 in 4lal

Go back to Zinc Binding Sites List in 4lal
Zinc binding site 2 out of 4 in the Crystal Structure of Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil


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 Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:38.8
occ:1.00
O52 B:5CU402 1.9 36.8 1.0
O4 B:5CU402 2.0 28.8 1.0
NE2 B:HIS195 2.2 21.8 1.0
NE2 B:HIS14 2.3 25.5 1.0
NE2 B:HIS12 2.5 20.9 1.0
C51 B:5CU402 3.0 39.0 1.0
C4 B:5CU402 3.0 37.8 1.0
CE1 B:HIS195 3.1 21.9 1.0
CD2 B:HIS14 3.1 25.0 1.0
CD2 B:HIS195 3.3 21.6 1.0
CD2 B:HIS12 3.3 21.2 1.0
C5 B:5CU402 3.4 39.2 1.0
CE1 B:HIS14 3.4 25.6 1.0
CE1 B:HIS12 3.6 21.6 1.0
O53 B:5CU402 4.0 35.1 1.0
N3 B:5CU402 4.2 37.9 1.0
ND1 B:HIS195 4.2 21.6 1.0
NE2 B:HIS251 4.3 27.2 1.0
CG B:HIS14 4.3 25.4 1.0
CG B:HIS195 4.4 21.2 1.0
ND1 B:HIS14 4.4 25.8 1.0
CG B:HIS12 4.5 21.9 1.0
ND1 B:HIS12 4.6 22.4 1.0
CB B:ALA323 4.6 27.0 1.0
CD2 B:PHE326 4.7 23.7 1.0
CA B:ALA323 4.7 26.1 1.0
C6 B:5CU402 4.8 39.5 1.0
CE1 B:HIS251 4.9 27.8 1.0
CE2 B:PHE326 5.0 23.8 1.0

Zinc binding site 3 out of 4 in 4lal

Go back to Zinc Binding Sites List in 4lal
Zinc binding site 3 out of 4 in the Crystal Structure of Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil


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 Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:36.5
occ:1.00
O53 C:5CU402 2.0 31.4 1.0
O4 C:5CU402 2.0 31.4 1.0
NE2 C:HIS195 2.3 21.7 1.0
NE2 C:HIS14 2.4 21.2 1.0
NE2 C:HIS12 2.4 23.7 1.0
C51 C:5CU402 3.0 37.5 1.0
C4 C:5CU402 3.0 39.9 1.0
CD2 C:HIS14 3.2 21.9 1.0
CD2 C:HIS12 3.2 23.3 1.0
CD2 C:HIS195 3.3 21.9 1.0
CE1 C:HIS195 3.3 22.6 1.0
C5 C:5CU402 3.4 39.6 1.0
CE1 C:HIS12 3.5 23.3 1.0
CE1 C:HIS14 3.5 21.3 1.0
O52 C:5CU402 4.1 34.9 1.0
N3 C:5CU402 4.2 39.7 1.0
NE2 C:HIS251 4.2 24.7 1.0
CG C:HIS14 4.4 22.4 1.0
ND1 C:HIS195 4.4 22.7 1.0
CG C:HIS195 4.4 22.1 1.0
CG C:HIS12 4.5 23.8 1.0
ND1 C:HIS14 4.5 22.4 1.0
ND1 C:HIS12 4.5 23.9 1.0
CB C:ALA323 4.6 25.6 1.0
CE1 C:HIS251 4.7 24.7 1.0
CA C:ALA323 4.7 25.3 1.0
CD2 C:PHE326 4.7 28.0 1.0
C6 C:5CU402 4.8 39.7 1.0
CE2 C:PHE326 5.0 28.3 1.0

Zinc binding site 4 out of 4 in 4lal

Go back to Zinc Binding Sites List in 4lal
Zinc binding site 4 out of 4 in the Crystal Structure of Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil


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 Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:42.3
occ:1.00
O4 D:5CU402 2.0 38.0 1.0
O52 D:5CU402 2.0 36.4 1.0
NE2 D:HIS195 2.2 26.7 1.0
NE2 D:HIS14 2.4 27.1 1.0
NE2 D:HIS12 2.4 26.0 1.0
C4 D:5CU402 3.0 42.4 1.0
C51 D:5CU402 3.0 40.0 1.0
CE1 D:HIS195 3.0 28.3 1.0
CD2 D:HIS14 3.1 26.6 1.0
CD2 D:HIS12 3.3 26.7 1.0
CD2 D:HIS195 3.3 27.1 1.0
C5 D:5CU402 3.4 42.1 1.0
CE1 D:HIS12 3.5 27.2 1.0
CE1 D:HIS14 3.5 26.7 1.0
O53 D:5CU402 4.1 35.5 1.0
N3 D:5CU402 4.2 41.6 1.0
ND1 D:HIS195 4.2 28.8 1.0
NE2 D:HIS251 4.3 28.4 1.0
CG D:HIS14 4.4 26.4 1.0
CG D:HIS195 4.4 27.5 1.0
ND1 D:HIS14 4.5 26.8 1.0
CG D:HIS12 4.5 27.9 1.0
ND1 D:HIS12 4.5 27.7 1.0
CB D:ALA323 4.6 32.6 1.0
CE1 D:HIS251 4.7 27.8 1.0
CA D:ALA323 4.7 31.3 1.0
CD2 D:PHE326 4.8 27.6 1.0
C6 D:5CU402 4.8 43.2 1.0
CE2 D:PHE326 5.0 27.8 1.0

Reference:

S.Xu, W.Li, J.Zhu, R.Wang, Z.Li, G.L.Xu, J.Ding. Crystal Structures of Isoorotate Decarboxylases Reveal A Novel Catalytic Mechanism of 5-Carboxyl-Uracil Decarboxylation and Shed Light on the Search For Dna Decarboxylase. Cell Res. V. 23 1296 2013.
ISSN: ISSN 1001-0602
PubMed: 23917530
DOI: 10.1038/CR.2013.107
Page generated: Wed Dec 16 05:31:38 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy