Atomistry » Zinc » PDB 4rvo-4tpj » 4s26
Atomistry »
  Zinc »
    PDB 4rvo-4tpj »
      4s26 »

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: Sun Oct 27 07:29:02 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy