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Iron 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:

Zinc (Zn) 2 atoms
Chlorine (Cl) 2 atoms

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 (Monoclinic Crystal Form) (pdb code 4s26). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron 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 Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4s26

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Iron binding site 1 out of 8 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 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 (Monoclinic Crystal Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:17.0
occ:1.00
 FE1 A:SF4701 0.0 17.0 1.0
S4 A:SF4701 2.2 20.5 1.0
S2 A:SF4701 2.3 19.9 1.0
S3 A:SF4701 2.3 19.8 1.0
SG A:CYS570 2.3 17.0 1.0
FE4 A:SF4701 2.7 17.6 1.0
FE3 A:SF4701 2.8 18.2 1.0
FE2 A:SF4701 2.8 18.9 1.0
CB A:CYS570 3.4 22.3 1.0
N A:CYS570 3.5 16.5 1.0
CA A:CYS570 3.9 17.8 1.0
S1 A:SF4701 3.9 18.8 1.0
CB A:MET572 4.2 18.3 1.0
C A:PHE569 4.3 14.8 1.0
C A:CYS570 4.3 14.2 1.0
O A:CYS570 4.4 20.0 1.0
CH2 A:TRP538 4.6 16.3 1.0
CL B:CL701 4.6 17.7 0.8
N A:CYS573 4.6 17.9 1.0
SG A:CYS573 4.7 21.4 1.0
N A:MET572 4.7 19.3 1.0
CA A:PHE569 4.7 15.2 1.0
CZ2 A:TRP538 4.9 18.3 1.0
SG A:CYS578 4.9 19.6 1.0
CA A:MET572 5.0 17.4 1.0
N A:SER571 5.0 16.8 1.0

Iron binding site 2 out of 8 in 4s26

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Iron binding site 2 out of 8 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 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 (Monoclinic Crystal Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:18.9
occ:1.00
 FE2 A:SF4701 0.0 18.9 1.0
S3 A:SF4701 2.3 19.8 1.0
SG A:CYS573 2.3 21.4 1.0
S4 A:SF4701 2.3 20.5 1.0
S1 A:SF4701 2.4 18.8 1.0
FE3 A:SF4701 2.7 18.2 1.0
FE4 A:SF4701 2.8 17.6 1.0
FE1 A:SF4701 2.8 17.0 1.0
SD B:SAH704 3.3 27.7 1.0
CB A:CYS573 3.4 18.4 1.0
CG B:SAH704 3.9 25.5 1.0
S2 A:SF4701 3.9 19.9 1.0
N A:CYS573 4.0 17.9 1.0
CB A:MET572 4.3 18.3 1.0
CA A:CYS573 4.4 18.9 1.0
CG A:MET572 4.4 20.3 1.0
CA A:CYS578 4.4 19.9 1.0
SG A:CYS578 4.7 19.6 1.0
CB A:CYS578 4.8 19.0 1.0
SG A:CYS570 4.8 17.0 1.0
CL B:CL701 4.8 17.7 0.8
C A:MET572 4.8 15.5 1.0
N A:SER579 4.8 18.8 1.0
O B:HOH1057 4.9 19.8 1.0

Iron binding site 3 out of 8 in 4s26

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Iron binding site 3 out of 8 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 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 (Monoclinic Crystal Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:18.2
occ:1.00
 FE3 A:SF4701 0.0 18.2 1.0
S2 A:SF4701 2.2 19.9 1.0
S1 A:SF4701 2.2 18.8 1.0
S4 A:SF4701 2.3 20.5 1.0
SG A:CYS578 2.3 19.6 1.0
FE4 A:SF4701 2.7 17.6 1.0
FE2 A:SF4701 2.7 18.9 1.0
FE1 A:SF4701 2.8 17.0 1.0
CB A:CYS578 3.2 19.0 1.0
CA A:CYS578 3.7 19.9 1.0
S3 A:SF4701 3.8 19.8 1.0
CA A:PHE569 4.2 15.2 1.0
CE A:MET580 4.3 16.9 1.0
CE1 A:PHE536 4.3 18.4 1.0
C A:CYS578 4.4 23.8 1.0
N A:SER579 4.4 18.8 1.0
N A:CYS570 4.4 16.5 1.0
SG A:CYS573 4.6 21.4 1.0
CZ A:PHE536 4.6 20.5 1.0
C A:PHE569 4.7 14.8 1.0
CL B:CL701 4.7 17.7 0.8
N A:MET580 4.9 18.6 1.0
CB A:CYS573 4.9 18.4 1.0
CB A:PHE569 5.0 20.4 1.0
SG A:CYS570 5.0 17.0 1.0

Iron binding site 4 out of 8 in 4s26

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Iron binding site 4 out of 8 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 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 (Monoclinic Crystal Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:17.6
occ:1.00
 FE4 A:SF4701 0.0 17.6 1.0
CL B:CL701 2.2 17.7 0.8
S1 A:SF4701 2.2 18.8 1.0
S3 A:SF4701 2.3 19.8 1.0
S2 A:SF4701 2.3 19.9 1.0
FE3 A:SF4701 2.7 18.2 1.0
FE1 A:SF4701 2.7 17.0 1.0
FE2 A:SF4701 2.8 18.9 1.0
CE A:MET580 3.7 16.9 1.0
S4 A:SF4701 3.9 20.5 1.0
CG B:SAH704 4.1 25.5 1.0
O B:HOH1066 4.2 20.2 1.0
O B:HOH1057 4.4 19.8 1.0
O B:HOH942 4.5 18.8 1.0
SD B:SAH704 4.7 27.7 1.0
SG A:CYS570 4.7 17.0 1.0
CA B:HIS490 4.8 11.9 1.0
SG A:CYS578 4.9 19.6 1.0

Iron binding site 5 out of 8 in 4s26

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Iron binding site 5 out of 8 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 Iron with other atoms in the Fe binding site number 5 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:Fe702

b:21.6
occ:1.00
 FE1 B:SF4702 0.0 21.6 1.0
SG B:CYS570 2.2 22.0 1.0
S4 B:SF4702 2.2 21.5 1.0
S2 B:SF4702 2.2 22.1 1.0
S3 B:SF4702 2.3 20.5 1.0
FE4 B:SF4702 2.7 22.4 1.0
FE3 B:SF4702 2.8 21.3 1.0
FE2 B:SF4702 2.8 22.8 1.0
CB B:CYS570 3.4 23.3 1.0
N B:CYS570 3.4 20.7 1.0
CA B:CYS570 3.8 20.5 1.0
S1 B:SF4702 3.9 22.2 1.0
CB B:MET572 4.1 20.0 1.0
C B:CYS570 4.2 17.7 1.0
C B:PHE569 4.3 19.8 1.0
O B:CYS570 4.4 23.6 1.0
CL A:CL705 4.6 22.0 0.8
CH2 B:TRP538 4.6 24.6 1.0
N B:CYS573 4.6 21.0 1.0
SG B:CYS573 4.7 22.0 1.0
N B:MET572 4.7 21.0 1.0
CA B:PHE569 4.7 22.5 1.0
CZ2 B:TRP538 4.9 28.8 1.0
CA B:MET572 4.9 23.0 1.0
N B:SER571 4.9 17.5 1.0
SG B:CYS578 5.0 24.0 1.0

Iron binding site 6 out of 8 in 4s26

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Iron binding site 6 out of 8 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 Iron with other atoms in the Fe binding site number 6 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:Fe702

b:22.8
occ:1.00
 FE2 B:SF4702 0.0 22.8 1.0
S3 B:SF4702 2.3 20.5 1.0
SG B:CYS573 2.3 22.0 1.0
S4 B:SF4702 2.3 21.5 1.0
S1 B:SF4702 2.3 22.2 1.0
FE3 B:SF4702 2.8 21.3 1.0
FE4 B:SF4702 2.8 22.4 1.0
FE1 B:SF4702 2.8 21.6 1.0
SD A:SAH703 3.2 27.9 1.0
CB B:CYS573 3.4 23.4 1.0
CG A:SAH703 3.8 28.3 1.0
S2 B:SF4702 3.9 22.1 1.0
N B:CYS573 4.0 21.0 1.0
CB B:MET572 4.2 20.0 1.0
CG B:MET572 4.3 22.2 1.0
CA B:CYS573 4.4 24.6 1.0
CA B:CYS578 4.5 23.7 1.0
SG B:CYS570 4.7 22.0 1.0
SG B:CYS578 4.7 24.0 1.0
CL A:CL705 4.8 22.0 0.8
CB B:CYS578 4.8 24.7 1.0
C B:MET572 4.8 19.8 1.0
N B:SER579 4.8 22.4 1.0
O A:HOH1065 5.0 20.6 1.0

Iron binding site 7 out of 8 in 4s26

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Iron binding site 7 out of 8 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 Iron with other atoms in the Fe binding site number 7 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:Fe702

b:21.3
occ:1.00
 FE3 B:SF4702 0.0 21.3 1.0
S2 B:SF4702 2.2 22.1 1.0
S1 B:SF4702 2.2 22.2 1.0
S4 B:SF4702 2.3 21.5 1.0
SG B:CYS578 2.3 24.0 1.0
FE4 B:SF4702 2.8 22.4 1.0
FE2 B:SF4702 2.8 22.8 1.0
FE1 B:SF4702 2.8 21.6 1.0
CB B:CYS578 3.2 24.7 1.0
CA B:CYS578 3.7 23.7 1.0
S3 B:SF4702 3.9 20.5 1.0
CA B:PHE569 4.2 22.5 1.0
CE B:MET580 4.3 19.0 1.0
C B:CYS578 4.3 26.8 1.0
N B:SER579 4.3 22.4 1.0
N B:CYS570 4.4 20.7 1.0
CE1 B:PHE536 4.4 23.4 1.0
SG B:CYS573 4.6 22.0 1.0
C B:PHE569 4.6 19.8 1.0
CZ B:PHE536 4.8 22.4 1.0
CL A:CL705 4.8 22.0 0.8
CB B:CYS573 4.8 23.4 1.0
N B:MET580 4.9 21.4 1.0
CB B:PHE569 4.9 22.1 1.0
SG B:CYS570 4.9 22.0 1.0
N B:CYS578 5.0 26.2 1.0

Iron binding site 8 out of 8 in 4s26

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Iron binding site 8 out of 8 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 Iron with other atoms in the Fe binding site number 8 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:Fe702

b:22.4
occ:1.00
 FE4 B:SF4702 0.0 22.4 1.0
CL A:CL705 2.2 22.0 0.8
S3 B:SF4702 2.2 20.5 1.0
S1 B:SF4702 2.2 22.2 1.0
S2 B:SF4702 2.3 22.1 1.0
FE1 B:SF4702 2.7 21.6 1.0
FE3 B:SF4702 2.8 21.3 1.0
FE2 B:SF4702 2.8 22.8 1.0
S4 B:SF4702 3.8 21.5 1.0
CE B:MET580 3.8 19.0 1.0
CG A:SAH703 3.9 28.3 1.0
O A:HOH963 4.3 24.1 1.0
O A:HOH1065 4.5 20.6 1.0
SD A:SAH703 4.5 27.9 1.0
O A:HOH957 4.5 22.1 1.0
SG B:CYS570 4.6 22.0 1.0
CA A:HIS490 4.8 17.2 1.0
SG B:CYS578 4.9 24.0 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 10:08:39 2024

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