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Iron in PDB 5d3u: Crystal Structure of the 5-Selective H176F Mutant of Cytochrome Txte

Protein crystallography data

The structure of Crystal Structure of the 5-Selective H176F Mutant of Cytochrome Txte, PDB code: 5d3u was solved by J.K.B.Cahn, S.C.Dodani, F.H.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.33 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.795, 99.351, 105.499, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 25.1

Other elements in 5d3u:

The structure of Crystal Structure of the 5-Selective H176F Mutant of Cytochrome Txte also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the 5-Selective H176F Mutant of Cytochrome Txte (pdb code 5d3u). 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 5-Selective H176F Mutant of Cytochrome Txte, PDB code: 5d3u:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 5d3u

Go back to Iron Binding Sites List in 5d3u
Iron binding site 1 out of 2 in the Crystal Structure of the 5-Selective H176F Mutant of Cytochrome Txte


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 5-Selective H176F Mutant of Cytochrome Txte within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:7.0
occ:1.00
FE A:HEM501 0.0 7.0 1.0
ND A:HEM501 2.0 7.5 1.0
NA A:HEM501 2.1 6.5 1.0
NB A:HEM501 2.1 6.5 1.0
NC A:HEM501 2.1 7.5 1.0
SG A:CYS357 2.4 7.0 1.0
C4B A:HEM501 3.0 6.3 1.0
C4D A:HEM501 3.0 5.7 1.0
C1D A:HEM501 3.0 7.9 1.0
C1A A:HEM501 3.1 5.5 1.0
C4C A:HEM501 3.1 7.7 1.0
C1B A:HEM501 3.1 5.7 1.0
C1C A:HEM501 3.1 7.4 1.0
C4A A:HEM501 3.1 5.4 1.0
CB A:CYS357 3.4 6.3 1.0
CHC A:HEM501 3.4 8.0 1.0
CHD A:HEM501 3.4 7.9 1.0
CHB A:HEM501 3.4 5.7 1.0
CHA A:HEM501 3.5 5.7 1.0
CA A:CYS357 4.0 5.3 1.0
C3A A:HEM501 4.3 5.2 1.0
C2D A:HEM501 4.3 7.3 1.0
C3B A:HEM501 4.3 6.8 1.0
C2A A:HEM501 4.3 5.6 1.0
C3C A:HEM501 4.3 7.1 1.0
C2B A:HEM501 4.3 6.4 1.0
C3D A:HEM501 4.3 5.8 1.0
C2C A:HEM501 4.3 7.7 1.0
NE1 A:TRP502 4.4 9.6 1.0
O A:HOH641 4.5 12.4 1.0
N A:LEU358 4.8 7.0 1.0
C A:CYS357 4.8 6.1 1.0

Iron binding site 2 out of 2 in 5d3u

Go back to Iron Binding Sites List in 5d3u
Iron binding site 2 out of 2 in the Crystal Structure of the 5-Selective H176F Mutant of Cytochrome Txte


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 5-Selective H176F Mutant of Cytochrome Txte within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:7.2
occ:1.00
FE B:HEM501 0.0 7.2 1.0
ND B:HEM501 2.0 6.8 1.0
NC B:HEM501 2.1 6.9 1.0
NB B:HEM501 2.1 7.0 1.0
NA B:HEM501 2.1 7.2 1.0
SG B:CYS357 2.4 7.3 1.0
O B:HOH622 2.5 30.1 1.0
C4B B:HEM501 3.0 7.2 1.0
C4D B:HEM501 3.0 5.5 1.0
C1C B:HEM501 3.0 7.1 1.0
C4C B:HEM501 3.0 7.0 1.0
C1A B:HEM501 3.1 5.7 1.0
C1D B:HEM501 3.1 6.8 1.0
C1B B:HEM501 3.1 6.5 1.0
C4A B:HEM501 3.1 5.6 1.0
CHC B:HEM501 3.4 7.6 1.0
CB B:CYS357 3.4 5.9 1.0
CHD B:HEM501 3.4 6.4 1.0
CHA B:HEM501 3.5 5.3 1.0
CHB B:HEM501 3.5 5.7 1.0
CA B:CYS357 4.0 5.3 1.0
C3B B:HEM501 4.3 7.5 1.0
C2D B:HEM501 4.3 5.8 1.0
C2C B:HEM501 4.3 7.3 1.0
C3C B:HEM501 4.3 6.0 1.0
C3A B:HEM501 4.3 5.2 1.0
C2A B:HEM501 4.3 5.1 1.0
C3D B:HEM501 4.3 6.2 1.0
C2B B:HEM501 4.3 6.6 1.0
NE1 B:TRP502 4.4 8.2 1.0
O B:HOH640 4.5 10.6 1.0
N B:LEU358 4.7 7.2 1.0
C B:CYS357 4.8 5.5 1.0

Reference:

S.C.Dodani, G.Kiss, J.K.Cahn, Y.Su, V.S.Pande, F.H.Arnold. Discovery of A Regioselectivity Switch in Nitrating P450S Guided By Molecular Dynamics Simulations and Markov Models. Nat.Chem. V. 8 419 2016.
ISSN: ESSN 1755-4349
PubMed: 27102675
DOI: 10.1038/NCHEM.2474
Page generated: Mon Aug 5 21:45:02 2024

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