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Iron in PDB 6j27: Crystal Structure of the Branched-Chain Polyamine Synthase From Thermus Thermophilus (Tth-Bpsa) in Complex with N4- Aminopropylspermidine and 5'-Methylthioadenosine

Enzymatic activity of Crystal Structure of the Branched-Chain Polyamine Synthase From Thermus Thermophilus (Tth-Bpsa) in Complex with N4- Aminopropylspermidine and 5'-Methylthioadenosine

All present enzymatic activity of Crystal Structure of the Branched-Chain Polyamine Synthase From Thermus Thermophilus (Tth-Bpsa) in Complex with N4- Aminopropylspermidine and 5'-Methylthioadenosine:
2.5.1.128;

Protein crystallography data

The structure of Crystal Structure of the Branched-Chain Polyamine Synthase From Thermus Thermophilus (Tth-Bpsa) in Complex with N4- Aminopropylspermidine and 5'-Methylthioadenosine, PDB code: 6j27 was solved by E.Mizohata, M.Toyoda, J.Fujita, T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.66
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.570, 158.606, 71.936, 90.00, 118.95, 90.00
R / Rfree (%) 16.7 / 20.6

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Branched-Chain Polyamine Synthase From Thermus Thermophilus (Tth-Bpsa) in Complex with N4- Aminopropylspermidine and 5'-Methylthioadenosine (pdb code 6j27). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of the Branched-Chain Polyamine Synthase From Thermus Thermophilus (Tth-Bpsa) in Complex with N4- Aminopropylspermidine and 5'-Methylthioadenosine, PDB code: 6j27:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6j27

Go back to Iron Binding Sites List in 6j27
Iron binding site 1 out of 2 in the Crystal Structure of the Branched-Chain Polyamine Synthase From Thermus Thermophilus (Tth-Bpsa) in Complex with N4- Aminopropylspermidine and 5'-Methylthioadenosine


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 the Branched-Chain Polyamine Synthase From Thermus Thermophilus (Tth-Bpsa) in Complex with N4- Aminopropylspermidine and 5'-Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:26.3
occ:0.90
 SG B:CYS100 2.3 31.6 1.0
SG A:CYS100 2.3 32.1 1.0
SG B:CYS97 2.3 34.0 1.0
SG A:CYS97 2.4 34.2 1.0
CB B:CYS97 3.2 33.7 1.0
CB A:CYS97 3.2 29.7 1.0
CB B:CYS100 3.3 29.9 1.0
CB A:CYS100 3.4 37.7 1.0
N B:CYS100 3.8 34.7 1.0
N A:CYS100 3.8 39.1 1.0
CA B:CYS100 4.2 31.9 1.0
CA A:CYS100 4.2 37.8 1.0
CB B:ALA99 4.3 43.4 1.0
CB A:ALA99 4.4 41.5 1.0
CA B:GLY104 4.6 28.5 1.0
C B:ALA99 4.6 40.3 1.0
CA A:CYS97 4.6 33.3 1.0
CA B:CYS97 4.6 34.4 1.0
C A:ALA99 4.6 46.6 1.0
O A:CYS97 4.6 35.6 1.0
N B:GLY104 4.7 28.9 1.0
CA A:GLY104 4.7 27.2 1.0
C A:CYS97 4.8 35.7 1.0
CA B:ALA99 4.8 41.0 1.0
N A:GLY104 4.8 26.3 1.0
C B:CYS97 4.8 37.4 1.0
CA A:ALA99 4.8 41.6 1.0
O B:CYS97 4.9 31.3 1.0
N A:ALA99 4.9 42.2 1.0
N B:ALA99 4.9 39.7 1.0

Iron binding site 2 out of 2 in 6j27

Go back to Iron Binding Sites List in 6j27
Iron binding site 2 out of 2 in the Crystal Structure of the Branched-Chain Polyamine Synthase From Thermus Thermophilus (Tth-Bpsa) in Complex with N4- Aminopropylspermidine and 5'-Methylthioadenosine


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 the Branched-Chain Polyamine Synthase From Thermus Thermophilus (Tth-Bpsa) in Complex with N4- Aminopropylspermidine and 5'-Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:22.1
occ:0.90
 SG C:CYS97 2.3 28.8 1.0
SG D:CYS100 2.3 25.6 1.0
SG D:CYS97 2.3 29.1 1.0
SG C:CYS100 2.3 25.9 1.0
CB D:CYS97 3.1 25.8 1.0
CB C:CYS97 3.1 28.7 1.0
CB C:CYS100 3.4 27.7 1.0
CB D:CYS100 3.4 27.5 1.0
N C:CYS100 3.8 31.0 1.0
N D:CYS100 3.9 30.0 1.0
CA C:CYS100 4.2 28.0 1.0
CA D:CYS100 4.3 27.6 1.0
CB C:ALA99 4.4 35.5 1.0
CB D:ALA99 4.5 38.6 1.0
CA D:CYS97 4.5 25.6 1.0
CA C:CYS97 4.6 27.0 1.0
CA C:GLY104 4.6 24.6 1.0
C C:ALA99 4.7 35.0 1.0
C D:ALA99 4.7 34.7 1.0
O D:CYS97 4.7 28.4 1.0
CA D:GLY104 4.7 23.6 1.0
N C:GLY104 4.8 23.5 1.0
N D:GLY104 4.8 22.8 1.0
C D:CYS97 4.8 30.3 1.0
O C:CYS97 4.8 34.1 1.0
C C:CYS97 4.8 32.6 1.0
N D:ALA99 4.9 32.8 1.0
CA C:ALA99 4.9 36.2 1.0
CA D:ALA99 4.9 34.1 1.0
N C:ALA99 5.0 35.6 1.0

Reference:

R.Hidese, M.Toyoda, K.I.Yoshino, W.Fukuda, G.A.Wihardja, S.Kimura, J.Fujita, M.Niitsu, T.Oshima, T.Imanaka, E.Mizohata, S.Fujiwara. The C-Terminal Flexible Region of Branched-Chain Polyamine Synthase Facilitates Substrate Specificity and Catalysis. Febs J. V. 286 3926 2019.
ISSN: ISSN 1742-464X
PubMed: 31162806
DOI: 10.1111/FEBS.14949
Page generated: Tue Aug 6 23:12:16 2024

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