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Iron in PDB 5xnc: Crystal Structure of the Branched-Chain Polyamine Synthase (Bpsa) in Complex with N4-Aminopropylspermidine and 5-Methylthioadenosine

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

All present enzymatic activity of Crystal Structure of the Branched-Chain Polyamine Synthase (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 (Bpsa) in Complex with N4-Aminopropylspermidine and 5-Methylthioadenosine, PDB code: 5xnc was solved by E.Mizohata, K.M.Tse, J.Fujita, T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.53 / 1.84
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 137.533, 50.978, 402.428, 90.00, 93.69, 90.00
R / Rfree (%) 16.1 / 20.7

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Branched-Chain Polyamine Synthase (Bpsa) in Complex with N4-Aminopropylspermidine and 5-Methylthioadenosine (pdb code 5xnc). 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 the Branched-Chain Polyamine Synthase (Bpsa) in Complex with N4-Aminopropylspermidine and 5-Methylthioadenosine, PDB code: 5xnc:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5xnc

Go back to Iron Binding Sites List in 5xnc
Iron binding site 1 out of 4 in the Crystal Structure of the Branched-Chain Polyamine Synthase (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 (Bpsa) in Complex with N4-Aminopropylspermidine and 5-Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe406

b:30.3
occ:0.80
 SG B:CYS91 2.3 37.5 1.0
SG A:CYS94 2.3 37.6 1.0
SG B:CYS94 2.3 39.2 1.0
SG A:CYS91 2.3 35.1 1.0
CB A:CYS91 3.0 36.1 1.0
CB B:CYS91 3.1 37.7 1.0
CB A:CYS94 3.2 39.2 1.0
CB B:CYS94 3.3 38.9 1.0
N B:CYS94 3.6 37.8 1.0
N A:CYS94 3.7 36.7 1.0
CA B:CYS94 4.0 39.0 1.0
CA A:CYS94 4.1 38.2 1.0
CA A:CYS91 4.5 36.9 1.0
CA B:CYS91 4.5 38.0 1.0
CB B:HIS93 4.6 51.7 1.0
C B:HIS93 4.6 43.4 1.0
C A:HIS93 4.7 44.5 1.0
C A:CYS91 4.9 38.3 1.0
C B:CYS94 4.9 36.0 1.0
CA B:HIS93 4.9 46.0 1.0
C B:CYS91 4.9 39.0 1.0
C A:CYS94 4.9 39.1 1.0
N B:HIS93 5.0 43.4 1.0
CB A:HIS93 5.0 52.7 1.0

Iron binding site 2 out of 4 in 5xnc

Go back to Iron Binding Sites List in 5xnc
Iron binding site 2 out of 4 in the Crystal Structure of the Branched-Chain Polyamine Synthase (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 (Bpsa) in Complex with N4-Aminopropylspermidine and 5-Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe403

b:43.8
occ:0.80
 SG D:CYS91 2.2 53.9 1.0
SG D:CYS94 2.3 53.6 1.0
SG C:CYS94 2.3 50.6 1.0
SG C:CYS91 2.3 50.2 1.0
CB C:CYS91 3.0 49.9 1.0
CB D:CYS91 3.0 51.3 1.0
CB C:CYS94 3.2 52.6 1.0
CB D:CYS94 3.2 56.5 1.0
N C:CYS94 3.7 55.5 1.0
N D:CYS94 3.7 58.3 1.0
CA C:CYS94 4.0 53.4 1.0
CA D:CYS94 4.1 56.6 1.0
CA C:CYS91 4.4 51.2 1.0
CA D:CYS91 4.4 52.9 1.0
C D:HIS93 4.7 64.1 1.0
C C:HIS93 4.7 57.6 1.0
CB C:HIS93 4.8 69.8 1.0
CB D:HIS93 4.8 72.0 1.0
C D:CYS91 4.9 53.4 1.0
C D:CYS94 4.9 54.5 1.0
C C:CYS91 4.9 49.5 1.0
C C:CYS94 4.9 50.1 1.0
O D:CYS91 4.9 52.6 1.0
O C:CYS91 5.0 49.4 1.0

Iron binding site 3 out of 4 in 5xnc

Go back to Iron Binding Sites List in 5xnc
Iron binding site 3 out of 4 in the Crystal Structure of the Branched-Chain Polyamine Synthase (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 3 of Crystal Structure of the Branched-Chain Polyamine Synthase (Bpsa) in Complex with N4-Aminopropylspermidine and 5-Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe403

b:50.9
occ:0.80
 SG F:CYS91 2.3 61.4 1.0
SG E:CYS91 2.3 59.9 1.0
SG F:CYS94 2.3 61.6 1.0
SG E:CYS94 2.3 59.8 1.0
CB E:CYS91 3.1 63.5 1.0
CB F:CYS91 3.1 54.0 1.0
CB F:CYS94 3.2 66.4 1.0
CB E:CYS94 3.3 63.5 1.0
N E:CYS94 3.7 61.1 1.0
N F:CYS94 3.7 69.4 1.0
CA E:CYS94 4.0 64.2 1.0
CA F:CYS94 4.1 64.3 1.0
CA E:CYS91 4.5 61.9 1.0
CB E:HIS93 4.5 79.2 1.0
CA F:CYS91 4.5 57.2 1.0
CB F:HIS93 4.6 78.6 1.0
C E:HIS93 4.7 65.8 1.0
C F:HIS93 4.7 71.7 1.0
C E:CYS91 4.8 62.1 1.0
O E:CYS91 4.8 61.2 1.0
C E:CYS94 4.8 63.4 1.0
C F:CYS94 4.9 62.9 1.0
CA E:HIS93 4.9 71.5 1.0
N E:HIS93 5.0 67.2 1.0
C F:CYS91 5.0 56.5 1.0

Iron binding site 4 out of 4 in 5xnc

Go back to Iron Binding Sites List in 5xnc
Iron binding site 4 out of 4 in the Crystal Structure of the Branched-Chain Polyamine Synthase (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 4 of Crystal Structure of the Branched-Chain Polyamine Synthase (Bpsa) in Complex with N4-Aminopropylspermidine and 5-Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe403

b:46.5
occ:0.40
 SG G:CYS94 2.3 57.1 1.0
SG G:CYS91 2.3 54.8 1.0
CB G:CYS91 3.0 56.9 1.0
CB G:CYS94 3.3 61.3 1.0
N G:CYS94 3.7 59.8 1.0
CA G:CYS94 4.1 57.4 1.0
CA G:CYS91 4.4 54.5 1.0
C G:HIS93 4.8 63.1 1.0
C G:CYS91 4.9 56.7 1.0
C G:CYS94 5.0 60.6 1.0

Reference:

R.Hidese, K.M.Tse, S.Kimura, E.Mizohata, J.Fujita, Y.Horai, N.Umezawa, T.Higuchi, M.Niitsu, T.Oshima, T.Imanaka, T.Inoue, S.Fujiwara. Active Site Geometry of A Novel Aminopropyltransferase For Biosynthesis of Hyperthermophile-Specific Branched-Chain Polyamine. Febs J. V. 284 3684 2017.
ISSN: ISSN 1742-4658
PubMed: 28881427
DOI: 10.1111/FEBS.14262
Page generated: Sun Dec 13 16:17:30 2020

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