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Zinc in PDB 4hk7: Crystal Structure of Cordyceps Militaris Idcase in Complex with Uracil

Enzymatic activity of Crystal Structure of Cordyceps Militaris Idcase in Complex with Uracil

All present enzymatic activity of Crystal Structure of Cordyceps Militaris Idcase in Complex with Uracil:
4.1.1.66;

Protein crystallography data

The structure of Crystal Structure of Cordyceps Militaris Idcase in Complex with Uracil, PDB code: 4hk7 was solved by S.Xu, J.Zhu, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.73 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.333, 144.921, 77.310, 90.00, 97.14, 90.00
R / Rfree (%) 15.3 / 21

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Cordyceps Militaris Idcase in Complex with Uracil (pdb code 4hk7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Cordyceps Militaris Idcase in Complex with Uracil, PDB code: 4hk7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4hk7

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Zinc binding site 1 out of 6 in the Crystal Structure of Cordyceps Militaris Idcase in Complex with 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 in Complex with Uracil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:33.6
occ:1.00
 OD1 A:ASP323 2.2 28.3 1.0
NE2 A:HIS12 2.2 26.7 1.0
O4 A:URA403 2.2 29.2 1.0
NE2 A:HIS195 2.3 26.4 1.0
NE2 A:HIS14 2.3 24.1 1.0
CG A:ASP323 3.0 31.7 1.0
CD2 A:HIS12 3.1 24.7 1.0
CD2 A:HIS14 3.2 23.4 1.0
CD2 A:HIS195 3.2 27.8 1.0
OD2 A:ASP323 3.2 32.9 1.0
CE1 A:HIS12 3.3 25.3 1.0
CE1 A:HIS195 3.3 26.8 1.0
C4 A:URA403 3.4 32.7 1.0
CE1 A:HIS14 3.4 26.7 1.0
C5 A:URA403 4.0 33.5 1.0
CG A:HIS12 4.3 26.6 1.0
ND1 A:HIS12 4.4 26.4 1.0
CB A:ASP323 4.4 28.6 1.0
CG A:HIS14 4.4 25.8 1.0
CG A:HIS195 4.4 26.9 1.0
ND1 A:HIS195 4.4 25.4 1.0
NE2 A:HIS251 4.4 31.3 1.0
ND1 A:HIS14 4.4 27.4 1.0
N3 A:URA403 4.5 34.6 1.0
CA A:ASP323 4.7 25.5 1.0
CE1 A:HIS251 4.8 29.3 1.0
CD2 A:PHE326 4.8 30.1 1.0
CE2 A:PHE326 5.0 28.6 1.0

Zinc binding site 2 out of 6 in 4hk7

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Zinc binding site 2 out of 6 in the Crystal Structure of Cordyceps Militaris Idcase in Complex with 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 in Complex with Uracil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:52.1
occ:1.00
 NE2 A:HIS379 2.2 61.2 1.0
NE2 A:HIS384 2.5 36.8 1.0
CD2 A:HIS379 3.0 64.5 1.0
CE1 A:HIS384 3.1 36.5 1.0
CE1 A:HIS379 3.4 63.5 1.0
CD2 A:HIS384 3.6 34.8 1.0
CG A:HIS379 4.3 67.0 1.0
ND1 A:HIS384 4.4 37.5 1.0
ND1 A:HIS379 4.4 66.5 1.0
CG1 A:VAL128 4.6 41.4 1.0
CG A:HIS384 4.7 36.3 1.0

Zinc binding site 3 out of 6 in 4hk7

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Zinc binding site 3 out of 6 in the Crystal Structure of Cordyceps Militaris Idcase in Complex with 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 in Complex with Uracil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:34.3
occ:1.00
 NE2 B:HIS195 2.2 26.5 1.0
OD1 B:ASP323 2.2 30.0 1.0
NE2 B:HIS12 2.2 26.1 1.0
NE2 B:HIS14 2.3 27.7 1.0
O4 B:URA402 2.3 27.7 1.0
CD2 B:HIS12 3.1 26.9 1.0
CG B:ASP323 3.1 29.6 1.0
CD2 B:HIS14 3.1 28.0 1.0
CE1 B:HIS195 3.1 29.5 1.0
CD2 B:HIS195 3.3 26.7 1.0
OD2 B:ASP323 3.3 30.5 1.0
CE1 B:HIS12 3.3 25.6 1.0
CE1 B:HIS14 3.4 28.7 1.0
C4 B:URA402 3.4 32.0 1.0
C5 B:URA402 4.0 29.7 1.0
ND1 B:HIS195 4.3 30.6 1.0
CG B:HIS12 4.3 26.0 1.0
CG B:HIS14 4.3 29.4 1.0
CG B:HIS195 4.4 28.4 1.0
ND1 B:HIS12 4.4 26.3 1.0
ND1 B:HIS14 4.4 29.1 1.0
CB B:ASP323 4.5 26.3 1.0
NE2 B:HIS251 4.5 29.2 1.0
N3 B:URA402 4.6 31.4 1.0
CD2 B:PHE326 4.7 30.8 1.0
CA B:ASP323 4.8 26.0 1.0
CE2 B:PHE326 4.9 30.9 1.0
CE1 B:HIS251 4.9 29.3 1.0

Zinc binding site 4 out of 6 in 4hk7

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Zinc binding site 4 out of 6 in the Crystal Structure of Cordyceps Militaris Idcase in Complex with 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 in Complex with Uracil within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:28.6
occ:1.00
 NE2 C:HIS14 2.2 21.4 1.0
NE2 C:HIS195 2.2 20.1 1.0
O4 C:URA402 2.2 23.3 1.0
OD1 C:ASP323 2.2 27.1 1.0
NE2 C:HIS12 2.3 20.7 1.0
CG C:ASP323 3.1 28.6 1.0
CD2 C:HIS12 3.1 20.2 1.0
CD2 C:HIS14 3.1 23.8 1.0
CE1 C:HIS195 3.2 21.7 1.0
CD2 C:HIS195 3.2 21.8 1.0
CE1 C:HIS14 3.2 25.3 1.0
OD2 C:ASP323 3.3 32.0 1.0
C4 C:URA402 3.3 24.7 1.0
CE1 C:HIS12 3.4 20.7 1.0
C5 C:URA402 3.8 23.8 1.0
ND1 C:HIS195 4.3 23.8 1.0
CG C:HIS14 4.3 25.7 1.0
ND1 C:HIS14 4.3 27.1 1.0
CG C:HIS12 4.3 22.7 1.0
CG C:HIS195 4.4 24.0 1.0
ND1 C:HIS12 4.4 24.6 1.0
CB C:ASP323 4.4 24.0 1.0
NE2 C:HIS251 4.5 23.1 1.0
N3 C:URA402 4.5 24.3 1.0
CA C:ASP323 4.7 23.1 1.0
CD2 C:PHE326 4.8 22.3 1.0
CE1 C:HIS251 4.9 22.5 1.0

Zinc binding site 5 out of 6 in 4hk7

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Zinc binding site 5 out of 6 in the Crystal Structure of Cordyceps Militaris Idcase in Complex with Uracil


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

b:31.6
occ:1.00
 O4 D:URA403 2.2 25.8 1.0
NE2 D:HIS195 2.2 19.2 1.0
OD1 D:ASP323 2.2 25.6 1.0
NE2 D:HIS12 2.2 22.0 1.0
NE2 D:HIS14 2.3 19.5 1.0
CD2 D:HIS14 3.1 20.9 1.0
CG D:ASP323 3.1 28.6 1.0
CD2 D:HIS12 3.2 20.5 1.0
CE1 D:HIS195 3.2 19.5 1.0
CD2 D:HIS195 3.2 19.6 1.0
CE1 D:HIS12 3.3 20.2 1.0
C4 D:URA403 3.3 25.6 1.0
OD2 D:ASP323 3.4 30.0 1.0
CE1 D:HIS14 3.4 20.9 1.0
C5 D:URA403 3.9 25.4 1.0
CG D:HIS14 4.3 22.2 1.0
ND1 D:HIS195 4.3 20.3 1.0
CG D:HIS12 4.4 22.7 1.0
ND1 D:HIS12 4.4 24.9 1.0
CG D:HIS195 4.4 22.0 1.0
NE2 D:HIS251 4.4 25.9 1.0
ND1 D:HIS14 4.4 23.2 1.0
N3 D:URA403 4.5 24.1 1.0
CB D:ASP323 4.5 24.5 1.0
CD2 D:PHE326 4.8 23.4 1.0
CA D:ASP323 4.8 22.6 1.0
CE1 D:HIS251 4.9 25.4 1.0
CE2 D:PHE326 5.0 23.9 1.0

Zinc binding site 6 out of 6 in 4hk7

Go back to Zinc Binding Sites List in 4hk7
Zinc binding site 6 out of 6 in the Crystal Structure of Cordyceps Militaris Idcase in Complex with Uracil


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 Cordyceps Militaris Idcase in Complex with Uracil within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:37.8
occ:1.00
 NE2 D:HIS384 2.2 34.9 1.0
NE2 D:HIS379 2.2 41.5 1.0
CE1 D:HIS384 3.1 35.4 1.0
CE1 D:HIS379 3.2 37.7 1.0
CD2 D:HIS384 3.2 34.6 1.0
CD2 D:HIS379 3.2 38.5 1.0
ND1 D:HIS379 4.3 38.7 1.0
ND1 D:HIS384 4.3 39.5 1.0
CG D:HIS379 4.4 39.7 1.0
CG D:HIS384 4.4 38.2 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: Sun Oct 27 00:09:17 2024

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