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Iron in PDB 1s6v: Structure of A Cytochrome C Peroxidase-Cytochrome C Site Specific Cross-Link

Enzymatic activity of Structure of A Cytochrome C Peroxidase-Cytochrome C Site Specific Cross-Link

All present enzymatic activity of Structure of A Cytochrome C Peroxidase-Cytochrome C Site Specific Cross-Link:
1.11.1.5;

Protein crystallography data

The structure of Structure of A Cytochrome C Peroxidase-Cytochrome C Site Specific Cross-Link, PDB code: 1s6v was solved by M.Guo, B.Bhaskar, H.Li, T.P.Barrows, T.L.Poulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.65 / 1.88
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.240, 107.920, 88.380, 90.00, 104.42, 90.00
R / Rfree (%) 19 / 24.3

Other elements in 1s6v:

The structure of Structure of A Cytochrome C Peroxidase-Cytochrome C Site Specific Cross-Link also contains other interesting chemical elements:

Iodine (I) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of A Cytochrome C Peroxidase-Cytochrome C Site Specific Cross-Link (pdb code 1s6v). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of A Cytochrome C Peroxidase-Cytochrome C Site Specific Cross-Link, PDB code: 1s6v:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1s6v

Go back to Iron Binding Sites List in 1s6v
Iron binding site 1 out of 4 in the Structure of A Cytochrome C Peroxidase-Cytochrome C Site Specific Cross-Link


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of A Cytochrome C Peroxidase-Cytochrome C Site Specific Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe296

b:15.1
occ:1.00
 FE A:HEM296 0.0 15.1 1.0
NC A:HEM296 2.0 13.7 1.0
ND A:HEM296 2.0 14.0 1.0
NB A:HEM296 2.0 15.9 1.0
NA A:HEM296 2.0 13.0 1.0
NE2 A:HIS175 2.1 13.8 1.0
C4C A:HEM296 3.0 16.2 1.0
C1C A:HEM296 3.0 15.7 1.0
C1A A:HEM296 3.0 14.2 1.0
C4D A:HEM296 3.0 15.7 1.0
C1D A:HEM296 3.0 13.5 1.0
CD2 A:HIS175 3.1 13.7 1.0
CE1 A:HIS175 3.1 15.2 1.0
C4B A:HEM296 3.1 15.1 1.0
C4A A:HEM296 3.1 15.4 1.0
C1B A:HEM296 3.1 15.9 1.0
O A:HOH1039 3.1 42.9 1.0
CHA A:HEM296 3.4 13.0 1.0
CHD A:HEM296 3.4 14.2 1.0
CHC A:HEM296 3.5 15.2 1.0
CHB A:HEM296 3.5 14.0 1.0
NE1 A:TRP51 4.1 15.7 1.0
ND1 A:HIS175 4.2 15.0 1.0
CG A:HIS175 4.2 15.5 1.0
C2C A:HEM296 4.2 12.7 1.0
C2A A:HEM296 4.2 12.6 1.0
C3D A:HEM296 4.3 14.6 1.0
C3C A:HEM296 4.3 15.6 1.0
O A:HOH870 4.3 29.2 1.0
C2D A:HEM296 4.3 16.6 1.0
C3A A:HEM296 4.3 14.9 1.0
C3B A:HEM296 4.3 16.4 1.0
C2B A:HEM296 4.4 13.2 1.0
CD1 A:TRP51 4.5 17.3 1.0
O A:HOH869 4.8 54.9 1.0
CH2 A:TRP191 4.9 18.0 1.0

Iron binding site 2 out of 4 in 1s6v

Go back to Iron Binding Sites List in 1s6v
Iron binding site 2 out of 4 in the Structure of A Cytochrome C Peroxidase-Cytochrome C Site Specific Cross-Link


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of A Cytochrome C Peroxidase-Cytochrome C Site Specific Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe104

b:19.1
occ:1.00
 FE B:HEM104 0.0 19.1 1.0
NB B:HEM104 2.0 18.7 1.0
ND B:HEM104 2.0 22.1 1.0
NA B:HEM104 2.0 21.3 1.0
NC B:HEM104 2.0 19.3 1.0
NE2 B:HIS18 2.0 20.6 1.0
SD B:MET80 2.2 18.8 1.0
CE1 B:HIS18 2.9 23.7 1.0
C4B B:HEM104 3.0 18.4 1.0
C1D B:HEM104 3.0 20.7 1.0
C1C B:HEM104 3.0 19.3 1.0
C1B B:HEM104 3.0 18.2 1.0
C4C B:HEM104 3.0 20.7 1.0
C4A B:HEM104 3.0 21.4 1.0
C4D B:HEM104 3.0 21.9 1.0
C1A B:HEM104 3.1 19.5 1.0
CD2 B:HIS18 3.1 22.6 1.0
CG B:MET80 3.3 17.6 1.0
CHD B:HEM104 3.4 21.7 1.0
CHC B:HEM104 3.4 18.0 1.0
CE B:MET80 3.4 15.0 1.0
CHB B:HEM104 3.4 20.7 1.0
CHA B:HEM104 3.4 21.8 1.0
ND1 B:HIS18 4.1 23.7 1.0
CB B:MET80 4.1 19.6 1.0
C3B B:HEM104 4.2 18.9 1.0
CG B:HIS18 4.2 23.1 1.0
C2B B:HEM104 4.2 17.6 1.0
C2D B:HEM104 4.2 22.6 1.0
C3A B:HEM104 4.3 19.0 1.0
C2C B:HEM104 4.3 19.0 1.0
C3D B:HEM104 4.3 21.1 1.0
C3C B:HEM104 4.3 19.8 1.0
C2A B:HEM104 4.3 21.0 1.0
OH B:TYR67 4.9 20.8 1.0

Iron binding site 3 out of 4 in 1s6v

Go back to Iron Binding Sites List in 1s6v
Iron binding site 3 out of 4 in the Structure of A Cytochrome C Peroxidase-Cytochrome C Site Specific Cross-Link


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of A Cytochrome C Peroxidase-Cytochrome C Site Specific Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe296

b:13.7
occ:1.00
 FE C:HEM296 0.0 13.7 1.0
ND C:HEM296 2.0 14.6 1.0
NB C:HEM296 2.0 13.4 1.0
NA C:HEM296 2.0 12.7 1.0
NC C:HEM296 2.0 12.8 1.0
NE2 C:HIS175 2.1 9.1 1.0
O C:HOH409 2.9 42.2 1.0
C4D C:HEM296 3.0 12.9 1.0
C4A C:HEM296 3.0 12.0 1.0
C1A C:HEM296 3.0 13.4 1.0
C1C C:HEM296 3.0 13.0 1.0
C1B C:HEM296 3.0 14.5 1.0
C1D C:HEM296 3.0 15.0 1.0
CE1 C:HIS175 3.1 11.8 1.0
C4B C:HEM296 3.1 14.7 1.0
CD2 C:HIS175 3.1 12.2 1.0
C4C C:HEM296 3.1 13.0 1.0
CHA C:HEM296 3.4 13.1 1.0
CHB C:HEM296 3.4 10.1 1.0
CHC C:HEM296 3.4 13.9 1.0
CHD C:HEM296 3.5 14.0 1.0
NE1 C:TRP51 4.0 13.7 1.0
O C:HOH442 4.2 25.7 1.0
ND1 C:HIS175 4.2 12.3 1.0
C3D C:HEM296 4.2 10.9 1.0
C2D C:HEM296 4.2 13.4 1.0
CG C:HIS175 4.3 10.1 1.0
C2A C:HEM296 4.3 13.0 1.0
C2B C:HEM296 4.3 14.3 1.0
C3A C:HEM296 4.3 15.5 1.0
C3B C:HEM296 4.3 13.4 1.0
C2C C:HEM296 4.4 11.4 1.0
CD1 C:TRP51 4.4 14.4 1.0
C3C C:HEM296 4.4 12.2 1.0
O C:HOH392 4.5 32.2 1.0
CH2 C:TRP191 5.0 15.7 1.0

Iron binding site 4 out of 4 in 1s6v

Go back to Iron Binding Sites List in 1s6v
Iron binding site 4 out of 4 in the Structure of A Cytochrome C Peroxidase-Cytochrome C Site Specific Cross-Link


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of A Cytochrome C Peroxidase-Cytochrome C Site Specific Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe104

b:24.7
occ:1.00
 FE D:HEM104 0.0 24.7 1.0
NB D:HEM104 2.0 24.8 1.0
ND D:HEM104 2.0 27.5 1.0
NA D:HEM104 2.0 24.7 1.0
NC D:HEM104 2.0 24.3 1.0
NE2 D:HIS18 2.0 25.2 1.0
SD D:MET80 2.1 21.1 1.0
CE1 D:HIS18 2.9 27.4 1.0
C4A D:HEM104 3.0 26.3 1.0
C1B D:HEM104 3.0 27.3 1.0
C4D D:HEM104 3.0 26.1 1.0
C1A D:HEM104 3.0 25.6 1.0
C4B D:HEM104 3.0 25.5 1.0
C1D D:HEM104 3.0 28.4 1.0
C1C D:HEM104 3.1 22.5 1.0
C4C D:HEM104 3.1 26.1 1.0
CD2 D:HIS18 3.1 25.2 1.0
CE D:MET80 3.4 25.8 1.0
CHA D:HEM104 3.4 27.3 1.0
CHB D:HEM104 3.4 23.4 1.0
CHC D:HEM104 3.4 21.6 1.0
CHD D:HEM104 3.4 25.1 1.0
CG D:MET80 3.4 24.3 1.0
ND1 D:HIS18 4.1 28.0 1.0
CG D:HIS18 4.2 26.6 1.0
C3D D:HEM104 4.2 29.2 1.0
C3A D:HEM104 4.2 24.5 1.0
C2B D:HEM104 4.3 25.2 1.0
C3B D:HEM104 4.3 25.2 1.0
C2D D:HEM104 4.3 27.5 1.0
C2A D:HEM104 4.3 26.4 1.0
C2C D:HEM104 4.3 24.4 1.0
CB D:MET80 4.3 25.2 1.0
C3C D:HEM104 4.3 23.4 1.0
OH D:TYR67 4.8 26.9 1.0

Reference:

M.Guo, B.Bhaskar, H.Li, T.P.Barrows, T.L.Poulos. Crystal Structure and Characterization of A Cytochrome C Peroxidase-Cytochrome C Site-Specific Cross-Link Proc.Natl.Acad.Sci.Usa V. 101 5940 2004.
ISSN: ISSN 0027-8424
PubMed: 15071191
DOI: 10.1073/PNAS.0306708101
Page generated: Sun Dec 13 14:31:16 2020

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