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Zinc in PDB 4s26: Crystal Structure of Arabidopsis Thaliana Thic with Bound Imidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Zn (Monoclinic Crystal Form)

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

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana Thic with Bound Imidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Zn (Monoclinic 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 (Monoclinic Crystal Form), PDB code: 4s26 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) 48.26 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 175.911, 95.596, 71.414, 90.00, 104.22, 90.00
R / Rfree (%) 16.7 / 19.8

Other elements in 4s26:

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

Iron (Fe) 8 atoms
Chlorine (Cl) 2 atoms

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 (Monoclinic Crystal Form) (pdb code 4s26). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Arabidopsis Thaliana Thic with Bound Imidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Zn (Monoclinic Crystal Form), PDB code: 4s26:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4s26

Go back to Zinc Binding Sites List in 4s26
Zinc binding site 1 out of 2 in the Crystal Structure of Arabidopsis Thaliana Thic with Bound Imidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Zn (Monoclinic 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 (Monoclinic Crystal Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:21.7
occ:1.00
 O A:HOH962 2.1 15.0 1.0
NE2 A:HIS490 2.2 16.7 1.0
NE2 A:HIS426 2.2 14.1 1.0
O A:HOH961 2.2 17.7 1.0
O A:SAH703 2.2 20.4 1.0
N A:SAH703 2.3 17.8 1.0
C A:SAH703 2.9 20.7 1.0
CA A:SAH703 3.0 16.9 1.0
CD2 A:HIS490 3.1 19.4 1.0
CE1 A:HIS426 3.1 18.5 1.0
CE1 A:HIS490 3.2 19.2 1.0
CD2 A:HIS426 3.2 19.4 1.0
OXT A:SAH703 4.1 22.9 1.0
OE2 A:GLU489 4.1 23.1 1.0
O A:HOH963 4.1 24.1 1.0
ND1 A:HIS426 4.2 14.7 1.0
CG A:HIS490 4.2 17.9 1.0
O A:HOH927 4.3 22.4 1.0
O A:GLY388 4.3 18.3 1.0
ND1 A:HIS490 4.3 19.7 1.0
CG A:HIS426 4.3 16.6 1.0
O A:HOH1051 4.3 21.6 1.0
CB A:SAH703 4.4 21.6 1.0
CG A:GLU489 4.7 17.8 1.0
CA A:GLY388 4.8 16.1 1.0
CD2 A:LEU454 4.9 19.2 1.0
C A:GLY388 4.9 18.7 1.0
CD A:GLU489 4.9 21.0 1.0

Zinc binding site 2 out of 2 in 4s26

Go back to Zinc Binding Sites List in 4s26
Zinc binding site 2 out of 2 in the Crystal Structure of Arabidopsis Thaliana Thic with Bound Imidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Zn (Monoclinic Crystal Form)


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 Arabidopsis Thaliana Thic with Bound Imidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Zn (Monoclinic Crystal Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn705

b:17.6
occ:1.00
 OXT B:SAH704 2.1 16.9 1.0
NE2 B:HIS426 2.2 12.9 1.0
NE2 B:HIS490 2.2 11.1 1.0
O B:HOH1065 2.2 15.3 1.0
O B:HOH1064 2.3 17.2 1.0
N B:SAH704 2.4 16.3 1.0
C B:SAH704 2.9 21.8 1.0
CD2 B:HIS490 3.1 15.6 1.0
CE1 B:HIS426 3.1 14.8 1.0
CA B:SAH704 3.1 15.8 1.0
CD2 B:HIS426 3.2 14.0 1.0
CE1 B:HIS490 3.2 12.6 1.0
O B:SAH704 4.1 20.5 1.0
OE2 B:GLU489 4.1 24.1 1.0
ND1 B:HIS426 4.2 10.2 1.0
CG B:HIS490 4.3 11.1 1.0
O B:GLY388 4.3 15.3 1.0
ND1 B:HIS490 4.3 13.8 1.0
O B:HOH1066 4.3 20.2 1.0
CG B:HIS426 4.3 11.3 1.0
O B:HOH1053 4.3 23.8 1.0
O B:HOH1045 4.4 17.8 1.0
CB B:SAH704 4.5 18.2 1.0
CG B:GLU489 4.7 14.7 1.0
CA B:GLY388 4.8 14.2 1.0
CD B:GLU489 4.9 24.0 1.0
C B:GLY388 4.9 14.1 1.0
CD2 B:LEU454 4.9 23.2 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 Dec 16 05:46:43 2020

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