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Iron in PDB 4pxh: Structure of P450SKY (CYP163B3), A Cytochrome P450 From Skyllamycin Biosynthesis in Complex with A Peptidyl Carrier Protein Domain

Enzymatic activity of Structure of P450SKY (CYP163B3), A Cytochrome P450 From Skyllamycin Biosynthesis in Complex with A Peptidyl Carrier Protein Domain

All present enzymatic activity of Structure of P450SKY (CYP163B3), A Cytochrome P450 From Skyllamycin Biosynthesis in Complex with A Peptidyl Carrier Protein Domain:
1.14.14.1;

Protein crystallography data

The structure of Structure of P450SKY (CYP163B3), A Cytochrome P450 From Skyllamycin Biosynthesis in Complex with A Peptidyl Carrier Protein Domain, PDB code: 4pxh was solved by K.Haslinger, M.J.Cryle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.89 / 2.70
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 161.700, 161.700, 337.490, 90.00, 90.00, 120.00
R / Rfree (%) 21.4 / 24.6

Iron Binding Sites:

The binding sites of Iron atom in the Structure of P450SKY (CYP163B3), A Cytochrome P450 From Skyllamycin Biosynthesis in Complex with A Peptidyl Carrier Protein Domain (pdb code 4pxh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Structure of P450SKY (CYP163B3), A Cytochrome P450 From Skyllamycin Biosynthesis in Complex with A Peptidyl Carrier Protein Domain, PDB code: 4pxh:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 4pxh

Go back to Iron Binding Sites List in 4pxh
Iron binding site 1 out of 3 in the Structure of P450SKY (CYP163B3), A Cytochrome P450 From Skyllamycin Biosynthesis in Complex with A Peptidyl Carrier Protein Domain


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of P450SKY (CYP163B3), A Cytochrome P450 From Skyllamycin Biosynthesis in Complex with A Peptidyl Carrier Protein Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:32.9
occ:1.00
 FE A:HEM501 0.0 32.9 1.0
N3 B:KH4101 2.0 33.6 1.0
NA A:HEM501 2.0 33.2 1.0
NC A:HEM501 2.1 33.7 1.0
NB A:HEM501 2.1 33.7 1.0
ND A:HEM501 2.1 33.7 1.0
SG A:CYS357 2.3 33.3 1.0
C4 B:KH4101 3.0 33.8 1.0
C2 B:KH4101 3.0 34.0 1.0
C4C A:HEM501 3.1 34.1 1.0
C4A A:HEM501 3.1 33.0 1.0
C1C A:HEM501 3.1 33.8 1.0
C1B A:HEM501 3.1 33.3 1.0
C1A A:HEM501 3.1 33.2 1.0
C4B A:HEM501 3.1 33.6 1.0
C1D A:HEM501 3.1 33.5 1.0
C4D A:HEM501 3.1 33.5 1.0
CHD A:HEM501 3.4 33.9 1.0
CHB A:HEM501 3.4 33.1 1.0
CHC A:HEM501 3.4 33.9 1.0
CHA A:HEM501 3.4 33.5 1.0
CB A:CYS357 3.5 33.2 1.0
N4 B:KH4101 4.2 34.4 1.0
C5 B:KH4101 4.2 35.5 1.0
CA A:CYS357 4.3 33.5 1.0
C3C A:HEM501 4.3 34.2 1.0
C2C A:HEM501 4.3 34.1 1.0
C3A A:HEM501 4.3 33.2 1.0
C2B A:HEM501 4.3 33.3 1.0
C2A A:HEM501 4.3 33.2 1.0
C3B A:HEM501 4.3 33.8 1.0
C2D A:HEM501 4.3 33.4 1.0
C3D A:HEM501 4.4 33.6 1.0
O A:GLY247 4.8 38.3 1.0
N A:GLY359 4.8 34.7 1.0
N A:LEU358 4.8 34.6 1.0
C A:CYS357 4.9 34.1 1.0

Iron binding site 2 out of 3 in 4pxh

Go back to Iron Binding Sites List in 4pxh
Iron binding site 2 out of 3 in the Structure of P450SKY (CYP163B3), A Cytochrome P450 From Skyllamycin Biosynthesis in Complex with A Peptidyl Carrier Protein Domain


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of P450SKY (CYP163B3), A Cytochrome P450 From Skyllamycin Biosynthesis in Complex with A Peptidyl Carrier Protein Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:31.9
occ:1.00
 FE C:HEM501 0.0 31.9 1.0
N3 D:KH4101 2.0 34.1 1.0
NA C:HEM501 2.0 31.8 1.0
NC C:HEM501 2.1 32.9 1.0
NB C:HEM501 2.1 32.8 1.0
ND C:HEM501 2.1 32.5 1.0
SG C:CYS357 2.3 32.3 1.0
C4 D:KH4101 2.9 34.9 1.0
C2 D:KH4101 3.0 35.0 1.0
C4A C:HEM501 3.1 31.9 1.0
C1B C:HEM501 3.1 32.3 1.0
C1C C:HEM501 3.1 33.2 1.0
C1A C:HEM501 3.1 31.7 1.0
C4C C:HEM501 3.1 33.1 1.0
C4B C:HEM501 3.1 32.7 1.0
C4D C:HEM501 3.1 32.1 1.0
C1D C:HEM501 3.1 32.5 1.0
CHB C:HEM501 3.4 32.1 1.0
CHC C:HEM501 3.4 32.9 1.0
CHD C:HEM501 3.4 32.7 1.0
CHA C:HEM501 3.4 31.9 1.0
CB C:CYS357 3.5 32.7 1.0
C5 D:KH4101 4.1 36.2 1.0
N4 D:KH4101 4.2 35.2 1.0
CA C:CYS357 4.2 33.1 1.0
C3A C:HEM501 4.3 32.0 1.0
C2B C:HEM501 4.3 32.8 1.0
C2C C:HEM501 4.3 33.3 1.0
C2A C:HEM501 4.3 31.8 1.0
C3C C:HEM501 4.3 33.2 1.0
C3B C:HEM501 4.3 33.1 1.0
C3D C:HEM501 4.4 32.1 1.0
C2D C:HEM501 4.4 32.3 1.0
N C:LEU358 4.8 34.6 1.0
N C:GLY359 4.8 35.9 1.0
C C:CYS357 4.9 34.1 1.0
O C:GLY247 5.0 37.1 1.0

Iron binding site 3 out of 3 in 4pxh

Go back to Iron Binding Sites List in 4pxh
Iron binding site 3 out of 3 in the Structure of P450SKY (CYP163B3), A Cytochrome P450 From Skyllamycin Biosynthesis in Complex with A Peptidyl Carrier Protein Domain


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of P450SKY (CYP163B3), A Cytochrome P450 From Skyllamycin Biosynthesis in Complex with A Peptidyl Carrier Protein Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:36.7
occ:1.00
 FE E:HEM501 0.0 36.7 1.0
N3 F:KH4101 2.0 38.4 1.0
NA E:HEM501 2.0 37.1 1.0
NC E:HEM501 2.0 37.5 1.0
NB E:HEM501 2.1 37.7 1.0
ND E:HEM501 2.1 37.7 1.0
SG E:CYS357 2.4 37.9 1.0
C4 F:KH4101 2.9 38.9 1.0
C4A E:HEM501 3.1 36.9 1.0
C4C E:HEM501 3.1 37.8 1.0
C1B E:HEM501 3.1 37.4 1.0
C1A E:HEM501 3.1 37.3 1.0
C1C E:HEM501 3.1 37.6 1.0
C4B E:HEM501 3.1 37.6 1.0
C2 F:KH4101 3.1 39.2 1.0
C1D E:HEM501 3.1 37.7 1.0
C4D E:HEM501 3.1 37.3 1.0
CHB E:HEM501 3.4 37.3 1.0
CHC E:HEM501 3.4 37.7 1.0
CHD E:HEM501 3.4 37.6 1.0
CB E:CYS357 3.4 36.9 1.0
CHA E:HEM501 3.4 37.4 1.0
C5 F:KH4101 4.1 40.0 1.0
CA E:CYS357 4.1 36.8 1.0
N4 F:KH4101 4.2 38.9 1.0
C3A E:HEM501 4.3 37.2 1.0
C3C E:HEM501 4.3 38.0 1.0
C2A E:HEM501 4.3 37.3 1.0
C2C E:HEM501 4.3 37.7 1.0
C2B E:HEM501 4.3 37.3 1.0
C3B E:HEM501 4.3 37.6 1.0
C2D E:HEM501 4.4 37.6 1.0
C3D E:HEM501 4.4 37.4 1.0
C E:CYS357 4.8 38.1 1.0
N E:LEU358 4.8 38.7 1.0
N E:GLY359 4.9 41.0 1.0
O E:GLY247 4.9 43.8 1.0

Reference:

K.Haslinger, C.Brieke, S.Uhlmann, L.Sieverling, R.D.Sussmuth, M.J.Cryle. The Structure of A Transient Complex of A Nonribosomal Peptide Synthetase and A Cytochrome P450 Monooxygenase. Angew.Chem.Int.Ed.Engl. V. 53 8518 2014.
ISSN: ISSN 1433-7851
PubMed: 25044735
DOI: 10.1002/ANIE.201404977
Page generated: Mon Aug 5 08:31:56 2024

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