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Iron in PDB 4jb4: Expression, Purification, Characterization, and Solution uc(Nmr) Study of Highly Deuterated Yeast Cytochrome C Peroxidase with Enhanced Solubility

Enzymatic activity of Expression, Purification, Characterization, and Solution uc(Nmr) Study of Highly Deuterated Yeast Cytochrome C Peroxidase with Enhanced Solubility

All present enzymatic activity of Expression, Purification, Characterization, and Solution uc(Nmr) Study of Highly Deuterated Yeast Cytochrome C Peroxidase with Enhanced Solubility:
1.11.1.5;

Protein crystallography data

The structure of Expression, Purification, Characterization, and Solution uc(Nmr) Study of Highly Deuterated Yeast Cytochrome C Peroxidase with Enhanced Solubility, PDB code: 4jb4 was solved by A.C.Wohlkonig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.57 / 2.39
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.052, 87.920, 87.526, 90.00, 105.14, 90.00
R / Rfree (%) 21.2 / 27.9

Other elements in 4jb4:

The structure of Expression, Purification, Characterization, and Solution uc(Nmr) Study of Highly Deuterated Yeast Cytochrome C Peroxidase with Enhanced Solubility also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Expression, Purification, Characterization, and Solution uc(Nmr) Study of Highly Deuterated Yeast Cytochrome C Peroxidase with Enhanced Solubility (pdb code 4jb4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Expression, Purification, Characterization, and Solution uc(Nmr) Study of Highly Deuterated Yeast Cytochrome C Peroxidase with Enhanced Solubility, PDB code: 4jb4:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 4jb4

Go back to Iron Binding Sites List in 4jb4
Iron binding site 1 out of 2 in the Expression, Purification, Characterization, and Solution uc(Nmr) Study of Highly Deuterated Yeast Cytochrome C Peroxidase with Enhanced Solubility


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Expression, Purification, Characterization, and Solution uc(Nmr) Study of Highly Deuterated Yeast Cytochrome C Peroxidase with Enhanced Solubility within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:16.6
occ:1.00
 FE A:HEM401 0.0 16.6 1.0
NB A:HEM401 1.9 15.2 1.0
ND A:HEM401 2.0 16.0 1.0
NC A:HEM401 2.0 17.0 1.0
NE2 A:HIS175 2.1 5.1 1.0
NA A:HEM401 2.1 16.8 1.0
F A:F402 2.3 14.2 1.0
C4B A:HEM401 2.9 13.3 1.0
C4D A:HEM401 2.9 19.4 1.0
C1A A:HEM401 3.0 14.4 1.0
C1C A:HEM401 3.0 15.3 1.0
C1B A:HEM401 3.0 16.3 1.0
CE1 A:HIS175 3.1 12.4 1.0
CD2 A:HIS175 3.1 11.0 1.0
C1D A:HEM401 3.1 19.3 1.0
C4C A:HEM401 3.1 18.3 1.0
C4A A:HEM401 3.2 17.1 1.0
CHA A:HEM401 3.3 18.4 1.0
CHC A:HEM401 3.3 12.9 1.0
CHD A:HEM401 3.5 16.4 1.0
CHB A:HEM401 3.5 15.9 1.0
NE1 A:TRP51 4.0 14.7 1.0
NE A:ARG48 4.1 6.1 0.4
C3B A:HEM401 4.2 8.2 1.0
ND1 A:HIS175 4.2 12.3 1.0
C2B A:HEM401 4.2 9.7 1.0
CG A:HIS175 4.2 13.4 1.0
C3D A:HEM401 4.2 17.4 1.0
C2C A:HEM401 4.3 16.6 1.0
C2A A:HEM401 4.3 18.3 1.0
C3C A:HEM401 4.3 17.6 1.0
C2D A:HEM401 4.3 18.6 1.0
C3A A:HEM401 4.4 16.5 1.0
CD1 A:TRP51 4.6 17.2 1.0
NH2 A:ARG48 4.7 2.0 0.4
CZ A:ARG48 4.9 2.0 0.4
CD A:ARG48 4.9 8.0 0.4
CE2 A:TRP51 5.0 14.7 1.0

Iron binding site 2 out of 2 in 4jb4

Go back to Iron Binding Sites List in 4jb4
Iron binding site 2 out of 2 in the Expression, Purification, Characterization, and Solution uc(Nmr) Study of Highly Deuterated Yeast Cytochrome C Peroxidase with Enhanced Solubility


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Expression, Purification, Characterization, and Solution uc(Nmr) Study of Highly Deuterated Yeast Cytochrome C Peroxidase with Enhanced Solubility within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:15.5
occ:1.00
 FE C:HEM401 0.0 15.5 1.0
NB C:HEM401 2.0 9.9 1.0
ND C:HEM401 2.0 13.4 1.0
NA C:HEM401 2.0 13.4 1.0
NC C:HEM401 2.1 10.9 1.0
NE2 C:HIS175 2.3 9.1 1.0
F C:F402 2.4 17.8 1.0
C1B C:HEM401 3.0 12.3 1.0
C1D C:HEM401 3.0 16.7 1.0
C4A C:HEM401 3.0 13.7 1.0
C4D C:HEM401 3.0 15.8 1.0
C1A C:HEM401 3.1 15.8 1.0
C4B C:HEM401 3.1 12.0 1.0
C4C C:HEM401 3.1 14.8 1.0
CE1 C:HIS175 3.2 15.0 1.0
C1C C:HEM401 3.2 8.2 1.0
CD2 C:HIS175 3.3 14.9 1.0
CHB C:HEM401 3.3 13.1 1.0
CHD C:HEM401 3.3 14.1 1.0
CHA C:HEM401 3.4 14.8 1.0
CHC C:HEM401 3.6 7.5 1.0
NE1 C:TRP51 3.9 18.8 1.0
NE C:ARG48 4.1 4.8 0.4
C2B C:HEM401 4.2 7.5 1.0
O C:HOH504 4.2 20.6 1.0
C2D C:HEM401 4.2 14.7 1.0
C3A C:HEM401 4.2 17.1 1.0
C3B C:HEM401 4.3 10.0 1.0
C2A C:HEM401 4.3 19.5 1.0
C3D C:HEM401 4.3 15.8 1.0
ND1 C:HIS175 4.3 15.6 1.0
C3C C:HEM401 4.4 11.2 1.0
C2C C:HEM401 4.4 9.5 1.0
CG C:HIS175 4.4 18.8 1.0
CD1 C:TRP51 4.4 16.6 1.0
NH2 C:ARG48 4.6 2.0 0.4
CG C:ARG48 4.6 12.6 0.4
CZ C:ARG48 4.8 2.0 0.4
CD C:ARG48 4.9 5.8 0.4

Reference:

A.N.Volkov, A.Wohlkonig, S.H.Soror, N.A.Van Nuland. Expression, Purification, Characterization, and Solution Nuclear Magnetic Resonance Study of Highly Deuterated Yeast Cytochrome C Peroxidase with Enhanced Solubility. Biochemistry V. 52 2165 2013.
ISSN: ISSN 0006-2960
PubMed: 23517193
DOI: 10.1021/BI400220W
Page generated: Sun Dec 13 15:38:13 2020

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