Atomistry » Iron » PDB 4ryx-4toe » 4s25
Atomistry »
  Iron »
    PDB 4ryx-4toe »
      4s25 »

Iron 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:

Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron where 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:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4s25

Go back to Iron Binding Sites List in 4s25
Iron binding site 1 out of 4 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 Iron with other atoms in the Fe 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:Fe701

b:10.5
occ:0.70
 FE1 A:SF4701 0.0 10.5 0.7
S4 A:SF4701 2.2 10.5 0.7
S2 A:SF4701 2.3 10.5 0.7
S3 A:SF4701 2.3 10.0 0.7
SG A:CYS570 2.3 14.9 1.0
FE4 A:SF4701 2.7 10.8 0.7
FE3 A:SF4701 2.8 10.8 0.7
FE2 A:SF4701 2.8 10.2 0.7
CB A:CYS570 3.4 14.2 1.0
N A:CYS570 3.4 14.7 1.0
CA A:CYS570 3.8 15.7 1.0
S1 A:SF4701 3.9 11.1 0.7
C A:PHE569 4.2 16.5 1.0
C A:CYS570 4.2 13.6 1.0
CB A:MET572 4.3 13.4 1.0
O A:CYS570 4.4 17.0 1.0
CL A:CL705 4.6 12.3 0.7
N A:CYS573 4.7 15.1 1.0
CH2 A:TRP538 4.7 12.7 1.0
CA A:PHE569 4.7 14.4 1.0
N A:MET572 4.7 14.2 1.0
SG A:CYS573 4.7 15.6 1.0
SG A:CYS578 4.9 14.8 1.0
CZ2 A:TRP538 5.0 12.3 1.0
N A:SER571 5.0 15.1 1.0
CA A:MET572 5.0 14.3 1.0

Iron binding site 2 out of 4 in 4s25

Go back to Iron Binding Sites List in 4s25
Iron binding site 2 out of 4 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 Iron with other atoms in the Fe binding site number 2 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:Fe701

b:10.2
occ:0.70
 FE2 A:SF4701 0.0 10.2 0.7
S3 A:SF4701 2.3 10.0 0.7
SG A:CYS573 2.3 15.6 1.0
S1 A:SF4701 2.3 11.1 0.7
S4 A:SF4701 2.3 10.5 0.7
FE3 A:SF4701 2.7 10.8 0.7
FE4 A:SF4701 2.8 10.8 0.7
FE1 A:SF4701 2.8 10.5 0.7
CB A:CYS573 3.3 15.4 1.0
S2 A:SF4701 3.9 10.5 0.7
O A:HOH1098 4.0 22.8 1.0
N A:CYS573 4.0 15.1 1.0
CB A:MET572 4.3 13.4 1.0
CA A:CYS573 4.3 15.5 1.0
CG A:MET572 4.4 13.1 1.0
CA A:CYS578 4.4 15.8 1.0
SG A:CYS578 4.6 14.8 1.0
SG A:CYS570 4.7 14.9 1.0
CB A:CYS578 4.8 14.4 1.0
C A:MET572 4.8 16.0 1.0
CL A:CL705 4.8 12.3 0.7
N A:SER579 4.9 15.1 1.0

Iron binding site 3 out of 4 in 4s25

Go back to Iron Binding Sites List in 4s25
Iron binding site 3 out of 4 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 Iron with other atoms in the Fe binding site number 3 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:Fe701

b:10.8
occ:0.70
 FE3 A:SF4701 0.0 10.8 0.7
S2 A:SF4701 2.2 10.5 0.7
S1 A:SF4701 2.3 11.1 0.7
S4 A:SF4701 2.3 10.5 0.7
SG A:CYS578 2.3 14.8 1.0
FE4 A:SF4701 2.7 10.8 0.7
FE2 A:SF4701 2.7 10.2 0.7
FE1 A:SF4701 2.8 10.5 0.7
CB A:CYS578 3.3 14.4 1.0
CA A:CYS578 3.8 15.8 1.0
S3 A:SF4701 3.8 10.0 0.7
CA A:PHE569 4.2 14.4 1.0
N A:CYS570 4.4 14.7 1.0
C A:CYS578 4.4 17.0 1.0
CE A:MET580 4.4 15.4 1.0
N A:SER579 4.5 15.1 1.0
CE1 A:PHE536 4.5 13.0 1.0
SG A:CYS573 4.6 15.6 1.0
C A:PHE569 4.6 16.5 1.0
CL A:CL705 4.7 12.3 0.7
CB A:CYS573 4.9 15.4 1.0
CZ A:PHE536 4.9 14.4 1.0
CB A:PHE569 4.9 15.5 1.0
N A:MET580 4.9 17.7 1.0
SG A:CYS570 5.0 14.9 1.0

Iron binding site 4 out of 4 in 4s25

Go back to Iron Binding Sites List in 4s25
Iron binding site 4 out of 4 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 Iron with other atoms in the Fe binding site number 4 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:Fe701

b:10.8
occ:0.70
 FE4 A:SF4701 0.0 10.8 0.7
S1 A:SF4701 2.3 11.1 0.7
CL A:CL705 2.3 12.3 0.7
S3 A:SF4701 2.3 10.0 0.7
S2 A:SF4701 2.3 10.5 0.7
FE3 A:SF4701 2.7 10.8 0.7
FE1 A:SF4701 2.7 10.5 0.7
FE2 A:SF4701 2.8 10.2 0.7
S4 A:SF4701 3.8 10.5 0.7
CE A:MET580 4.0 15.4 1.0
SG A:CYS570 4.7 14.9 1.0
SG A:CYS578 4.8 14.8 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: Mon Aug 5 10:08:08 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy