Iron in PDB 8fsi: The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam
Enzymatic activity of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam
All present enzymatic activity of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam:
1.97.1.4;
Protein crystallography data
The structure of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam, PDB code: 8fsi
was solved by
J.D.Moody,
A.Galambas,
C.M.Lawrence,
J.B.Broderick,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.77 /
1.46
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
46.405,
59.094,
83.545,
90,
90,
90
|
R / Rfree (%)
|
15.1 /
17.3
|
Other elements in 8fsi:
The structure of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam
(pdb code 8fsi). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam, PDB code: 8fsi:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 8fsi
Go back to
Iron Binding Sites List in 8fsi
Iron binding site 1 out
of 4 in the The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:13.0
occ:1.00
|
FE1
|
A:SF4301
|
0.0
|
13.0
|
1.0
|
S3
|
A:SF4301
|
2.2
|
12.8
|
1.0
|
SG
|
A:CYS33
|
2.3
|
12.9
|
1.0
|
S2
|
A:SF4301
|
2.3
|
13.8
|
1.0
|
S4
|
A:SF4301
|
2.3
|
15.2
|
1.0
|
FE3
|
A:SF4301
|
2.7
|
14.1
|
1.0
|
FE4
|
A:SF4301
|
2.7
|
12.7
|
1.0
|
FE2
|
A:SF4301
|
2.8
|
14.5
|
1.0
|
HB2
|
A:CYS33
|
2.9
|
17.6
|
1.0
|
CB
|
A:CYS33
|
3.2
|
14.6
|
1.0
|
HZ2
|
A:LYS131
|
3.2
|
17.9
|
1.0
|
H
|
A:CYS33
|
3.3
|
17.3
|
1.0
|
HE3
|
A:LYS131
|
3.4
|
16.2
|
1.0
|
HZ1
|
A:LYS131
|
3.5
|
17.9
|
1.0
|
NZ
|
A:LYS131
|
3.7
|
15.0
|
1.0
|
HB2
|
A:MET31
|
3.7
|
17.9
|
1.0
|
HB3
|
A:CYS33
|
3.8
|
17.6
|
1.0
|
S1
|
A:SF4301
|
3.9
|
13.9
|
1.0
|
HB2
|
A:CYS36
|
3.9
|
18.8
|
1.0
|
HB3
|
A:MET31
|
3.9
|
17.9
|
1.0
|
O
|
A:SAM302
|
4.0
|
14.3
|
1.0
|
N
|
A:CYS33
|
4.0
|
14.4
|
1.0
|
CE
|
A:LYS131
|
4.0
|
13.5
|
1.0
|
CA
|
A:CYS33
|
4.3
|
14.5
|
1.0
|
CB
|
A:MET31
|
4.3
|
14.9
|
1.0
|
HZ3
|
A:LYS131
|
4.5
|
17.9
|
1.0
|
HD3
|
A:LYS131
|
4.5
|
15.5
|
1.0
|
SG
|
A:CYS36
|
4.6
|
16.0
|
1.0
|
HG13
|
A:VAL142
|
4.6
|
22.7
|
1.0
|
CB
|
A:CYS36
|
4.7
|
15.7
|
1.0
|
HN1
|
A:SAM302
|
4.7
|
17.2
|
1.0
|
HE1
|
A:TYR35
|
4.7
|
17.3
|
1.0
|
SG
|
A:CYS29
|
4.7
|
12.8
|
1.0
|
HD22
|
A:ASN106
|
4.7
|
19.8
|
1.0
|
HA
|
A:CYS36
|
4.7
|
18.8
|
1.0
|
HE2
|
A:LYS131
|
4.8
|
16.2
|
1.0
|
HO2'
|
A:SAM302
|
4.8
|
19.7
|
1.0
|
H2'
|
A:SAM302
|
4.8
|
16.0
|
1.0
|
N
|
A:SAM302
|
4.9
|
14.3
|
1.0
|
HA
|
A:CYS33
|
4.9
|
17.4
|
1.0
|
CD
|
A:LYS131
|
4.9
|
12.9
|
1.0
|
HE1
|
A:TRP42
|
4.9
|
22.1
|
1.0
|
C
|
A:MET31
|
5.0
|
13.7
|
1.0
|
H
|
A:ARG32
|
5.0
|
17.5
|
1.0
|
N
|
A:ARG32
|
5.0
|
14.6
|
1.0
|
|
Iron binding site 2 out
of 4 in 8fsi
Go back to
Iron Binding Sites List in 8fsi
Iron binding site 2 out
of 4 in the The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:14.5
occ:1.00
|
FE2
|
A:SF4301
|
0.0
|
14.5
|
1.0
|
O
|
A:SAM302
|
2.2
|
14.3
|
1.0
|
N
|
A:SAM302
|
2.3
|
14.3
|
1.0
|
S3
|
A:SF4301
|
2.3
|
12.8
|
1.0
|
S4
|
A:SF4301
|
2.3
|
15.2
|
1.0
|
S1
|
A:SF4301
|
2.4
|
13.9
|
1.0
|
HN1
|
A:SAM302
|
2.5
|
17.2
|
1.0
|
FE4
|
A:SF4301
|
2.8
|
12.7
|
1.0
|
FE1
|
A:SF4301
|
2.8
|
13.0
|
1.0
|
FE3
|
A:SF4301
|
2.9
|
14.1
|
1.0
|
HN2
|
A:SAM302
|
2.9
|
17.2
|
1.0
|
C
|
A:SAM302
|
3.0
|
13.8
|
1.0
|
CA
|
A:SAM302
|
3.1
|
14.7
|
1.0
|
HG2
|
A:SAM302
|
3.3
|
16.1
|
1.0
|
HZ1
|
A:LYS131
|
3.3
|
17.9
|
1.0
|
SD
|
A:SAM302
|
3.5
|
16.7
|
1.0
|
CG
|
A:SAM302
|
3.7
|
13.4
|
1.0
|
HE2
|
A:SAM302
|
3.8
|
20.3
|
1.0
|
H2'
|
A:SAM302
|
3.8
|
16.0
|
1.0
|
CB
|
A:SAM302
|
3.9
|
14.2
|
1.0
|
HA
|
A:SAM302
|
3.9
|
17.6
|
1.0
|
S2
|
A:SF4301
|
4.0
|
13.8
|
1.0
|
HZ2
|
A:LYS131
|
4.0
|
17.9
|
1.0
|
NZ
|
A:LYS131
|
4.0
|
15.0
|
1.0
|
HB3
|
A:ASN106
|
4.1
|
16.5
|
1.0
|
OXT
|
A:SAM302
|
4.2
|
14.7
|
1.0
|
CE
|
A:SAM302
|
4.2
|
16.9
|
1.0
|
HE3
|
A:LYS131
|
4.3
|
16.2
|
1.0
|
HD22
|
A:ASN106
|
4.4
|
19.8
|
1.0
|
SG
|
A:CYS29
|
4.5
|
12.8
|
1.0
|
H3'
|
A:SAM302
|
4.5
|
15.3
|
1.0
|
H8
|
A:SAM302
|
4.6
|
16.2
|
1.0
|
HB2
|
A:SAM302
|
4.6
|
17.0
|
1.0
|
O
|
A:GLY78
|
4.6
|
13.4
|
1.0
|
HE3
|
A:SAM302
|
4.7
|
20.3
|
1.0
|
HO2'
|
A:SAM302
|
4.7
|
19.7
|
1.0
|
CE
|
A:LYS131
|
4.7
|
13.5
|
1.0
|
HZ3
|
A:LYS131
|
4.7
|
17.9
|
1.0
|
HB1
|
A:SAM302
|
4.7
|
17.0
|
1.0
|
HG1
|
A:SAM302
|
4.7
|
16.1
|
1.0
|
C2'
|
A:SAM302
|
4.8
|
13.4
|
1.0
|
SG
|
A:CYS33
|
4.8
|
12.9
|
1.0
|
HE2
|
A:LYS131
|
5.0
|
16.2
|
1.0
|
|
Iron binding site 3 out
of 4 in 8fsi
Go back to
Iron Binding Sites List in 8fsi
Iron binding site 3 out
of 4 in the The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:14.1
occ:1.00
|
FE3
|
A:SF4301
|
0.0
|
14.1
|
1.0
|
S1
|
A:SF4301
|
2.2
|
13.9
|
1.0
|
SG
|
A:CYS36
|
2.3
|
16.0
|
1.0
|
S4
|
A:SF4301
|
2.3
|
15.2
|
1.0
|
S2
|
A:SF4301
|
2.3
|
13.8
|
1.0
|
FE1
|
A:SF4301
|
2.7
|
13.0
|
1.0
|
FE4
|
A:SF4301
|
2.7
|
12.7
|
1.0
|
FE2
|
A:SF4301
|
2.9
|
14.5
|
1.0
|
HB2
|
A:CYS36
|
3.0
|
18.8
|
1.0
|
HE1
|
A:TRP42
|
3.2
|
22.1
|
1.0
|
CB
|
A:CYS36
|
3.3
|
15.7
|
1.0
|
HE2
|
A:SAM302
|
3.6
|
20.3
|
1.0
|
HA
|
A:CYS36
|
3.7
|
18.8
|
1.0
|
S3
|
A:SF4301
|
3.9
|
12.8
|
1.0
|
HB2
|
A:CYS33
|
3.9
|
17.6
|
1.0
|
NE1
|
A:TRP42
|
4.0
|
18.4
|
1.0
|
HB3
|
A:CYS36
|
4.0
|
18.8
|
1.0
|
CA
|
A:CYS36
|
4.1
|
15.7
|
1.0
|
H8
|
A:SAM302
|
4.2
|
16.2
|
1.0
|
HB2
|
A:ASN38
|
4.4
|
19.9
|
1.0
|
H
|
A:ASN38
|
4.4
|
19.0
|
1.0
|
CE
|
A:SAM302
|
4.4
|
16.9
|
1.0
|
HE3
|
A:SAM302
|
4.5
|
20.3
|
1.0
|
HD1
|
A:TRP42
|
4.6
|
19.3
|
1.0
|
SG
|
A:CYS33
|
4.6
|
12.9
|
1.0
|
CD1
|
A:TRP42
|
4.7
|
16.1
|
1.0
|
CB
|
A:CYS33
|
4.7
|
14.6
|
1.0
|
HG2
|
A:SAM302
|
4.8
|
16.1
|
1.0
|
H
|
A:CYS33
|
4.8
|
17.3
|
1.0
|
N
|
A:SAM302
|
4.8
|
14.3
|
1.0
|
O
|
A:SAM302
|
4.8
|
14.3
|
1.0
|
H
|
A:GLY78
|
4.8
|
17.1
|
1.0
|
H
|
A:HIS37
|
4.8
|
19.0
|
1.0
|
SD
|
A:SAM302
|
4.9
|
16.7
|
1.0
|
HZ2
|
A:TRP42
|
4.9
|
22.9
|
1.0
|
SG
|
A:CYS29
|
4.9
|
12.8
|
1.0
|
H2'
|
A:SAM302
|
4.9
|
16.0
|
1.0
|
C
|
A:CYS36
|
4.9
|
16.7
|
1.0
|
HG1
|
A:THR41
|
5.0
|
18.2
|
1.0
|
CE2
|
A:TRP42
|
5.0
|
15.8
|
1.0
|
|
Iron binding site 4 out
of 4 in 8fsi
Go back to
Iron Binding Sites List in 8fsi
Iron binding site 4 out
of 4 in the The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:12.7
occ:1.00
|
FE4
|
A:SF4301
|
0.0
|
12.7
|
1.0
|
S2
|
A:SF4301
|
2.2
|
13.8
|
1.0
|
SG
|
A:CYS29
|
2.3
|
12.8
|
1.0
|
S1
|
A:SF4301
|
2.3
|
13.9
|
1.0
|
S3
|
A:SF4301
|
2.3
|
12.8
|
1.0
|
FE3
|
A:SF4301
|
2.7
|
14.1
|
1.0
|
FE1
|
A:SF4301
|
2.7
|
13.0
|
1.0
|
FE2
|
A:SF4301
|
2.8
|
14.5
|
1.0
|
HB2
|
A:MET31
|
3.4
|
17.9
|
1.0
|
CB
|
A:CYS29
|
3.4
|
11.7
|
1.0
|
HB3
|
A:CYS29
|
3.4
|
14.1
|
1.0
|
HB2
|
A:CYS29
|
3.5
|
14.1
|
1.0
|
HN1
|
A:SAM302
|
3.7
|
17.2
|
1.0
|
HD22
|
A:ASN106
|
3.9
|
19.8
|
1.0
|
S4
|
A:SF4301
|
3.9
|
15.2
|
1.0
|
N
|
A:SAM302
|
3.9
|
14.3
|
1.0
|
H
|
A:MET31
|
4.0
|
16.5
|
1.0
|
HE1
|
A:TRP42
|
4.1
|
22.1
|
1.0
|
HN2
|
A:SAM302
|
4.1
|
17.2
|
1.0
|
CB
|
A:MET31
|
4.2
|
14.9
|
1.0
|
O
|
A:MET31
|
4.4
|
15.1
|
1.0
|
NE1
|
A:TRP42
|
4.4
|
18.4
|
1.0
|
HB3
|
A:MET31
|
4.5
|
17.9
|
1.0
|
HD1
|
A:TRP42
|
4.5
|
19.3
|
1.0
|
HB2
|
A:GLU79
|
4.6
|
15.7
|
1.0
|
C
|
A:MET31
|
4.6
|
13.7
|
1.0
|
ND2
|
A:ASN106
|
4.6
|
16.5
|
1.0
|
HA2
|
A:GLY78
|
4.6
|
18.8
|
1.0
|
H
|
A:CYS33
|
4.7
|
17.3
|
1.0
|
CD1
|
A:TRP42
|
4.7
|
16.1
|
1.0
|
SG
|
A:CYS36
|
4.7
|
16.0
|
1.0
|
N
|
A:MET31
|
4.7
|
13.8
|
1.0
|
O
|
A:SAM302
|
4.7
|
14.3
|
1.0
|
CA
|
A:MET31
|
4.7
|
13.5
|
1.0
|
CA
|
A:CYS29
|
4.7
|
13.0
|
1.0
|
HD21
|
A:ASN106
|
4.8
|
19.8
|
1.0
|
SG
|
A:CYS33
|
4.8
|
12.9
|
1.0
|
HA
|
A:CYS29
|
4.9
|
15.6
|
1.0
|
HG2
|
A:SAM302
|
5.0
|
16.1
|
1.0
|
|
Reference:
J.D.Moody,
S.Hill,
M.N.Lundahl,
A.J.Saxton,
A.Galambas,
W.E.Broderick,
C.M.Lawrence,
J.B.Broderick.
Computational Engineering of Previously Crystallized Pyruvate Formate-Lyase Activating Enzyme Reveals Insights Into Sam Binding and Reductive Cleavage. J.Biol.Chem. 04791 2023.
ISSN: ESSN 1083-351X
PubMed: 37156396
DOI: 10.1016/J.JBC.2023.104791
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