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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

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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

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