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Zinc in PDB 4s25: Crystal Structure of Arabidopsis Thaliana Thic with Bound Imidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Zn (Trigonal Crystal Form)

Enzymatic activity of Crystal Structure of Arabidopsis Thaliana Thic with Bound Imidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Zn (Trigonal Crystal Form)

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana Thic with Bound Imidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Zn (Trigonal Crystal Form):
4.1.99.17;

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana Thic with Bound Imidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Zn (Trigonal Crystal Form), PDB code: 4s25 was solved by M.K.Fenwick, A.P.Mehta, Y.Zhang, S.Abdelwahed, T.P.Begley, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.54 / 1.45
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 107.477, 107.477, 87.643, 90.00, 90.00, 120.00
R / Rfree (%) 14.2 / 16.2

Other elements in 4s25:

The structure of Crystal Structure of Arabidopsis Thaliana Thic with Bound Imidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Zn (Trigonal Crystal Form) also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Arabidopsis Thaliana Thic with Bound Imidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Zn (Trigonal Crystal Form) (pdb code 4s25). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Arabidopsis Thaliana Thic with Bound Imidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Zn (Trigonal Crystal Form), PDB code: 4s25:

Zinc binding site 1 out of 1 in 4s25

Go back to Zinc Binding Sites List in 4s25
Zinc binding site 1 out of 1 in the Crystal Structure of Arabidopsis Thaliana Thic with Bound Imidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Zn (Trigonal Crystal Form)


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 Arabidopsis Thaliana Thic with Bound Imidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Zn (Trigonal Crystal Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:10.4
occ:1.00
 OXT A:SAH703 2.1 11.2 1.0
NE2 A:HIS490 2.1 8.8 1.0
NE2 A:HIS426 2.2 8.3 1.0
O A:HOH1149 2.2 11.1 1.0
N A:SAH703 2.2 10.3 1.0
O A:HOH1148 2.2 11.4 1.0
C A:SAH703 2.9 15.2 1.0
CA A:SAH703 3.0 11.9 1.0
CD2 A:HIS490 3.1 9.1 1.0
CE1 A:HIS426 3.1 9.2 1.0
CE1 A:HIS490 3.2 9.2 1.0
CD2 A:HIS426 3.2 7.2 1.0
O A:SAH703 4.1 14.0 1.0
OE2 A:GLU489 4.1 12.3 1.0
ND1 A:HIS426 4.2 8.8 1.0
O A:HOH898 4.2 13.2 1.0
CG A:HIS490 4.2 8.6 1.0
ND1 A:HIS490 4.2 9.7 1.0
O A:GLY388 4.2 8.4 1.0
O A:HOH1312 4.3 15.5 1.0
CG A:HIS426 4.3 6.4 1.0
CB A:SAH703 4.4 17.9 1.0
O A:HOH870 4.4 11.9 1.0
CG A:GLU489 4.8 8.6 1.0
CA A:GLY388 4.8 7.7 1.0
C A:GLY388 4.9 7.4 1.0
CD2 A:LEU454 4.9 14.8 1.0
CD A:GLU489 4.9 11.4 1.0

Reference:

M.K.Fenwick, A.P.Mehta, Y.Zhang, S.H.Abdelwahed, T.P.Begley, S.E.Ealick. Non-Canonical Active Site Architecture of the Radical Sam Thiamin Pyrimidine Synthase. Nat Commun V. 6 6480.
ISSN: ESSN 2041-1723
PubMed: 25813242
DOI: 10.1038/NCOMMS7480
Page generated: Wed Aug 20 22:17:39 2025

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