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Iron in PDB 4s28: Crystal Structure of Arabidopsis Thaliana Thic with Bound Aminoimidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Fe

Enzymatic activity of Crystal Structure of Arabidopsis Thaliana Thic with Bound Aminoimidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Fe

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana Thic with Bound Aminoimidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Fe:
4.1.99.17;

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana Thic with Bound Aminoimidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Fe, PDB code: 4s28 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) 40.99 / 1.25
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 107.071, 107.071, 87.677, 90.00, 90.00, 120.00
R / Rfree (%) 11.6 / 13.7

Other elements in 4s28:

The structure of Crystal Structure of Arabidopsis Thaliana Thic with Bound Aminoimidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Fe also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Arabidopsis Thaliana Thic with Bound Aminoimidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Fe (pdb code 4s28). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Crystal Structure of Arabidopsis Thaliana Thic with Bound Aminoimidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Fe, PDB code: 4s28:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 4s28

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Iron binding site 1 out of 5 in the Crystal Structure of Arabidopsis Thaliana Thic with Bound Aminoimidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Fe


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 Aminoimidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:11.3
occ:0.70
 FE1 A:SF4701 0.0 11.3 0.7
S4 A:SF4701 2.3 11.6 0.7
SG A:CYS570 2.3 14.6 1.0
S2 A:SF4701 2.3 11.8 0.7
S3 A:SF4701 2.3 11.6 0.7
FE4 A:SF4701 2.7 11.7 0.7
FE3 A:SF4701 2.8 11.4 0.7
FE2 A:SF4701 2.8 11.4 0.7
CB A:CYS570 3.3 15.3 1.0
N A:CYS570 3.4 16.1 1.0
CA A:CYS570 3.8 15.6 1.0
S1 A:SF4701 3.9 12.0 0.7
C A:CYS570 4.2 15.1 1.0
C A:PHE569 4.2 16.4 1.0
CB A:MET572 4.2 14.2 1.0
O A:CYS570 4.4 15.8 1.0
CL A:CL705 4.5 14.0 0.7
CH2 A:TRP538 4.6 14.1 1.0
N A:CYS573 4.7 15.0 1.0
N A:MET572 4.7 14.8 1.0
CA A:PHE569 4.7 17.0 1.0
SG A:CYS573 4.8 15.3 1.0
SG A:CYS578 4.9 15.1 1.0
CZ2 A:TRP538 4.9 14.0 1.0
N A:SER571 5.0 15.2 1.0
CA A:MET572 5.0 14.2 1.0

Iron binding site 2 out of 5 in 4s28

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Iron binding site 2 out of 5 in the Crystal Structure of Arabidopsis Thaliana Thic with Bound Aminoimidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Fe


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 Aminoimidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:11.4
occ:0.70
 FE2 A:SF4701 0.0 11.4 0.7
S3 A:SF4701 2.3 11.6 0.7
S1 A:SF4701 2.3 12.0 0.7
SG A:CYS573 2.3 15.3 1.0
S4 A:SF4701 2.3 11.6 0.7
FE3 A:SF4701 2.7 11.4 0.7
FE4 A:SF4701 2.8 11.7 0.7
FE1 A:SF4701 2.8 11.3 0.7
CB A:CYS573 3.3 15.1 1.0
S2 A:SF4701 3.9 11.8 0.7
N A:CYS573 4.0 15.0 1.0
O A:HOH1144 4.1 37.5 1.0
CB A:MET572 4.3 14.2 1.0
CA A:CYS573 4.3 15.5 1.0
CG A:MET572 4.4 14.5 1.0
CA A:CYS578 4.4 16.2 1.0
SG A:CYS578 4.6 15.1 1.0
SG A:CYS570 4.7 14.6 1.0
CB A:CYS578 4.7 15.8 1.0
C A:MET572 4.8 14.2 1.0
CL A:CL705 4.8 14.0 0.7
N A:SER579 4.8 17.0 1.0

Iron binding site 3 out of 5 in 4s28

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Iron binding site 3 out of 5 in the Crystal Structure of Arabidopsis Thaliana Thic with Bound Aminoimidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Fe


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 Aminoimidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:11.4
occ:0.70
 FE3 A:SF4701 0.0 11.4 0.7
S2 A:SF4701 2.3 11.8 0.7
S1 A:SF4701 2.3 12.0 0.7
S4 A:SF4701 2.3 11.6 0.7
SG A:CYS578 2.3 15.1 1.0
FE4 A:SF4701 2.7 11.7 0.7
FE2 A:SF4701 2.7 11.4 0.7
FE1 A:SF4701 2.8 11.3 0.7
CB A:CYS578 3.2 15.8 1.0
CA A:CYS578 3.7 16.2 1.0
S3 A:SF4701 3.9 11.6 0.7
CA A:PHE569 4.1 17.0 1.0
N A:CYS570 4.4 16.1 1.0
C A:CYS578 4.4 15.8 1.0
N A:SER579 4.4 17.0 1.0
CE A:MET580 4.4 15.8 1.0
CE1 A:PHE536 4.5 15.6 1.0
SG A:CYS573 4.6 15.3 1.0
C A:PHE569 4.6 16.4 1.0
CL A:CL705 4.7 14.0 0.7
CB A:CYS573 4.8 15.1 1.0
N A:MET580 4.8 16.8 1.0
CZ A:PHE536 4.8 16.6 1.0
CB A:PHE569 4.9 17.8 1.0
SG A:CYS570 5.0 14.6 1.0
N A:CYS578 5.0 17.0 1.0

Iron binding site 4 out of 5 in 4s28

Go back to Iron Binding Sites List in 4s28
Iron binding site 4 out of 5 in the Crystal Structure of Arabidopsis Thaliana Thic with Bound Aminoimidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Fe


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 Aminoimidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:11.7
occ:0.70
 FE4 A:SF4701 0.0 11.7 0.7
CL A:CL705 2.2 14.0 0.7
S1 A:SF4701 2.2 12.0 0.7
S3 A:SF4701 2.3 11.6 0.7
S2 A:SF4701 2.3 11.8 0.7
FE1 A:SF4701 2.7 11.3 0.7
FE3 A:SF4701 2.7 11.4 0.7
FE2 A:SF4701 2.8 11.4 0.7
S4 A:SF4701 3.8 11.6 0.7
CE A:MET580 4.0 15.8 1.0
SG A:CYS570 4.6 14.6 1.0
SG A:CYS578 4.8 15.1 1.0

Iron binding site 5 out of 5 in 4s28

Go back to Iron Binding Sites List in 4s28
Iron binding site 5 out of 5 in the Crystal Structure of Arabidopsis Thaliana Thic with Bound Aminoimidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Fe


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 Aminoimidazole Ribonucleotide, S-Adenosylhomocysteine, FE4S4 Cluster and Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe704

b:9.6
occ:1.00
 OXT A:SAH703 2.0 13.0 0.5
OXT A:SAH703 2.1 11.0 0.5
NE2 A:HIS490 2.2 9.5 1.0
NE2 A:HIS426 2.2 8.3 1.0
O A:HOH1195 2.2 11.0 1.0
N A:SAH703 2.2 9.8 0.5
O A:HOH1194 2.2 11.1 1.0
N A:SAH703 2.4 14.1 0.5
C A:SAH703 2.8 13.6 0.5
C A:SAH703 2.9 10.1 0.5
CA A:SAH703 3.0 13.3 0.5
CE1 A:HIS426 3.1 8.3 1.0
CA A:SAH703 3.1 10.0 0.5
CD2 A:HIS490 3.1 9.3 1.0
CE1 A:HIS490 3.2 9.5 1.0
CD2 A:HIS426 3.2 8.4 1.0
O A:SAH703 4.0 16.1 0.5
O A:SAH703 4.1 11.0 0.5
OE2 A:GLU489 4.1 11.4 1.0
O A:HOH899 4.2 13.2 1.0
ND1 A:HIS426 4.2 8.3 1.0
ND1 A:HIS490 4.3 9.6 1.0
O A:GLY388 4.3 9.4 1.0
CG A:HIS490 4.3 9.4 1.0
CG A:HIS426 4.3 8.1 1.0
CB A:SAH703 4.4 13.2 0.5
O A:HOH871 4.4 12.8 1.0
CB A:SAH703 4.4 13.7 0.5
CG A:GLU489 4.8 9.9 1.0
CA A:GLY388 4.8 9.2 1.0
C A:GLY388 4.9 8.7 1.0
CD2 A:LEU454 4.9 14.1 1.0
CD A:GLU489 4.9 11.0 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 10:11:00 2024

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