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Iron in PDB 3m79: A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II)

Protein crystallography data

The structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II), PDB code: 3m79 was solved by J.D.Brodin, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.87 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.547, 78.068, 178.339, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 27.1

Other elements in 3m79:

The structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Iron Binding Sites:

The binding sites of Iron atom in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) (pdb code 3m79). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II), PDB code: 3m79:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3m79

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Iron binding site 1 out of 8 in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe150

b:14.1
occ:1.00
FE A:HEM150 0.0 14.1 1.0
NC A:HEM150 2.0 10.8 1.0
NA A:HEM150 2.0 11.7 1.0
ND A:HEM150 2.1 10.3 1.0
NB A:HEM150 2.1 10.8 1.0
NE2 A:HIS102 2.1 20.5 1.0
SD A:MET7 2.4 20.5 1.0
C1A A:HEM150 3.0 14.1 1.0
C4C A:HEM150 3.0 12.0 1.0
C1C A:HEM150 3.1 12.1 1.0
C4A A:HEM150 3.1 14.3 1.0
CD2 A:HIS102 3.1 19.7 1.0
C4D A:HEM150 3.1 13.3 1.0
C1D A:HEM150 3.1 11.7 1.0
C4B A:HEM150 3.1 12.4 1.0
C1B A:HEM150 3.1 12.3 1.0
CE1 A:HIS102 3.1 20.5 1.0
CG A:MET7 3.4 21.7 1.0
CHD A:HEM150 3.4 12.6 1.0
CHA A:HEM150 3.4 12.9 1.0
CHC A:HEM150 3.4 12.3 1.0
CHB A:HEM150 3.4 13.0 1.0
CE A:MET7 3.4 22.0 1.0
CB A:MET7 4.1 22.8 1.0
ND1 A:HIS102 4.2 22.2 1.0
CG A:HIS102 4.2 23.2 1.0
C2A A:HEM150 4.3 15.7 1.0
C3C A:HEM150 4.3 12.7 1.0
C2C A:HEM150 4.3 12.4 1.0
C3A A:HEM150 4.3 15.0 1.0
C2B A:HEM150 4.3 11.5 1.0
C3B A:HEM150 4.3 13.4 1.0
C3D A:HEM150 4.3 14.1 1.0
C2D A:HEM150 4.3 12.6 1.0
NH1 A:ARG106 4.7 31.3 1.0
CA A:MET7 4.9 23.8 1.0

Iron binding site 2 out of 8 in 3m79

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Iron binding site 2 out of 8 in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe150

b:16.9
occ:1.00
FE B:HEM150 0.0 16.9 1.0
NE2 B:HIS102 2.0 17.5 1.0
NB B:HEM150 2.0 16.5 1.0
NA B:HEM150 2.0 16.9 1.0
NC B:HEM150 2.1 16.9 1.0
ND B:HEM150 2.1 17.8 1.0
SD B:MET7 2.3 21.1 1.0
CD2 B:HIS102 3.0 19.1 1.0
CE1 B:HIS102 3.0 16.8 1.0
C4B B:HEM150 3.0 17.1 1.0
C1A B:HEM150 3.0 18.9 1.0
C1B B:HEM150 3.0 17.0 1.0
C4A B:HEM150 3.0 19.1 1.0
C1C B:HEM150 3.1 16.7 1.0
C4D B:HEM150 3.1 18.9 1.0
C4C B:HEM150 3.1 18.7 1.0
C1D B:HEM150 3.1 19.1 1.0
CHC B:HEM150 3.4 17.3 1.0
CHA B:HEM150 3.4 17.3 1.0
CHB B:HEM150 3.4 17.9 1.0
CE B:MET7 3.5 22.0 1.0
CHD B:HEM150 3.5 17.7 1.0
CG B:MET7 3.5 22.2 1.0
ND1 B:HIS102 4.1 19.6 1.0
CG B:HIS102 4.1 21.5 1.0
CB B:MET7 4.2 23.4 1.0
C3B B:HEM150 4.3 18.4 1.0
C2A B:HEM150 4.3 20.5 1.0
C2B B:HEM150 4.3 17.4 1.0
C3A B:HEM150 4.3 19.2 1.0
C2C B:HEM150 4.3 18.3 1.0
C3C B:HEM150 4.3 16.7 1.0
C3D B:HEM150 4.4 21.2 1.0
C2D B:HEM150 4.4 19.4 1.0

Iron binding site 3 out of 8 in 3m79

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Iron binding site 3 out of 8 in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe150

b:38.3
occ:1.00
FE C:HEM150 0.0 38.3 1.0
NE2 C:HIS102 2.0 28.0 1.0
ND C:HEM150 2.0 39.4 1.0
NA C:HEM150 2.1 40.5 1.0
NB C:HEM150 2.1 39.7 1.0
NC C:HEM150 2.1 39.1 1.0
SD C:MET7 2.3 30.8 1.0
CE1 C:HIS102 3.0 25.8 1.0
CD2 C:HIS102 3.0 25.9 1.0
C4D C:HEM150 3.0 40.6 1.0
C1A C:HEM150 3.0 41.2 1.0
C1D C:HEM150 3.1 40.5 1.0
C4B C:HEM150 3.1 38.7 1.0
C4A C:HEM150 3.1 41.4 1.0
C1B C:HEM150 3.1 40.0 1.0
C1C C:HEM150 3.1 38.4 1.0
C4C C:HEM150 3.1 38.4 1.0
CHA C:HEM150 3.4 40.9 1.0
CE C:MET7 3.4 27.8 1.0
CG C:MET7 3.4 26.4 1.0
CHD C:HEM150 3.4 39.5 1.0
CHC C:HEM150 3.5 38.5 1.0
CHB C:HEM150 3.5 40.2 1.0
ND1 C:HIS102 4.1 25.3 1.0
CB C:MET7 4.1 24.9 1.0
CG C:HIS102 4.1 25.2 1.0
C2A C:HEM150 4.3 42.3 1.0
C3A C:HEM150 4.3 41.7 1.0
C3D C:HEM150 4.3 41.1 1.0
C2B C:HEM150 4.3 38.7 1.0
C3B C:HEM150 4.3 38.5 1.0
C2D C:HEM150 4.3 40.9 1.0
C2C C:HEM150 4.3 38.4 1.0
C3C C:HEM150 4.3 37.9 1.0
CA C:MET7 5.0 24.2 1.0

Iron binding site 4 out of 8 in 3m79

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Iron binding site 4 out of 8 in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe150

b:20.9
occ:1.00
FE D:HEM150 0.0 20.9 1.0
NE2 D:HIS102 2.0 21.8 1.0
NB D:HEM150 2.0 21.9 1.0
ND D:HEM150 2.1 21.7 1.0
NC D:HEM150 2.1 20.8 1.0
NA D:HEM150 2.1 23.1 1.0
SD D:MET7 2.3 25.4 1.0
CE1 D:HIS102 3.0 22.2 1.0
CD2 D:HIS102 3.0 21.3 1.0
C4B D:HEM150 3.1 21.7 1.0
C1D D:HEM150 3.1 22.4 1.0
C1B D:HEM150 3.1 23.2 1.0
C1C D:HEM150 3.1 20.5 1.0
C4C D:HEM150 3.1 20.1 1.0
C4A D:HEM150 3.1 23.4 1.0
C4D D:HEM150 3.1 23.3 1.0
C1A D:HEM150 3.1 24.1 1.0
CE D:MET7 3.2 25.7 1.0
CHD D:HEM150 3.4 21.9 1.0
CHC D:HEM150 3.4 21.3 1.0
CG D:MET7 3.4 24.7 1.0
CHB D:HEM150 3.4 23.5 1.0
CHA D:HEM150 3.5 23.3 1.0
ND1 D:HIS102 4.1 22.1 1.0
CG D:HIS102 4.1 23.0 1.0
CB D:MET7 4.2 24.3 1.0
C3B D:HEM150 4.3 22.9 1.0
C2B D:HEM150 4.3 21.6 1.0
C2D D:HEM150 4.3 22.6 1.0
C2C D:HEM150 4.3 19.2 1.0
C3C D:HEM150 4.3 20.0 1.0
C3A D:HEM150 4.3 24.4 1.0
C3D D:HEM150 4.3 23.0 1.0
C2A D:HEM150 4.3 24.6 1.0
CA D:MET7 5.0 24.0 1.0

Iron binding site 5 out of 8 in 3m79

Go back to Iron Binding Sites List in 3m79
Iron binding site 5 out of 8 in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe150

b:12.2
occ:1.00
FE E:HEM150 0.0 12.2 1.0
NA E:HEM150 2.0 10.9 1.0
NE2 E:HIS102 2.0 18.8 1.0
NC E:HEM150 2.0 9.7 1.0
ND E:HEM150 2.1 9.7 1.0
NB E:HEM150 2.1 9.8 1.0
SD E:MET7 2.3 18.5 1.0
C1A E:HEM150 2.9 12.5 1.0
CD2 E:HIS102 3.0 21.2 1.0
CE1 E:HIS102 3.0 22.0 1.0
C4A E:HEM150 3.0 13.4 1.0
C4D E:HEM150 3.1 12.8 1.0
C4C E:HEM150 3.1 10.8 1.0
C1C E:HEM150 3.1 10.8 1.0
C1D E:HEM150 3.1 10.6 1.0
C4B E:HEM150 3.1 12.2 1.0
C1B E:HEM150 3.1 10.9 1.0
CHA E:HEM150 3.3 11.5 1.0
CHC E:HEM150 3.5 10.1 1.0
CHD E:HEM150 3.5 10.8 1.0
CHB E:HEM150 3.5 12.8 1.0
CG E:MET7 3.5 22.2 1.0
CE E:MET7 3.6 22.4 1.0
ND1 E:HIS102 4.1 22.4 1.0
CG E:HIS102 4.1 23.0 1.0
CB E:MET7 4.2 23.5 1.0
C2A E:HEM150 4.2 14.7 1.0
C3A E:HEM150 4.2 14.0 1.0
C3C E:HEM150 4.3 11.5 1.0
C2C E:HEM150 4.3 11.5 1.0
C3D E:HEM150 4.3 12.3 1.0
C2D E:HEM150 4.3 11.4 1.0
C2B E:HEM150 4.4 12.8 1.0
C3B E:HEM150 4.4 13.4 1.0
NH1 E:ARG106 4.8 22.7 1.0

Iron binding site 6 out of 8 in 3m79

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Iron binding site 6 out of 8 in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe150

b:17.1
occ:1.00
FE F:HEM150 0.0 17.1 1.0
NE2 F:HIS102 2.0 18.7 1.0
NA F:HEM150 2.0 17.7 1.0
ND F:HEM150 2.1 15.7 1.0
NB F:HEM150 2.1 15.4 1.0
NC F:HEM150 2.1 16.4 1.0
SD F:MET7 2.3 20.2 1.0
CE1 F:HIS102 2.9 18.7 1.0
C1A F:HEM150 3.0 17.8 1.0
CD2 F:HIS102 3.0 18.9 1.0
C4D F:HEM150 3.0 17.1 1.0
C1C F:HEM150 3.1 15.4 1.0
C4A F:HEM150 3.1 17.9 1.0
C4B F:HEM150 3.1 16.1 1.0
C1D F:HEM150 3.1 15.3 1.0
C4C F:HEM150 3.1 15.8 1.0
C1B F:HEM150 3.1 16.4 1.0
CHA F:HEM150 3.4 17.2 1.0
CHC F:HEM150 3.4 16.6 1.0
CG F:MET7 3.4 22.9 1.0
CE F:MET7 3.5 22.1 1.0
CHD F:HEM150 3.5 16.4 1.0
CHB F:HEM150 3.5 17.3 1.0
ND1 F:HIS102 4.0 20.4 1.0
CG F:HIS102 4.1 22.1 1.0
CB F:MET7 4.2 23.2 1.0
C2A F:HEM150 4.2 19.8 1.0
C3A F:HEM150 4.3 19.3 1.0
C2C F:HEM150 4.3 15.1 1.0
C3D F:HEM150 4.3 16.9 1.0
C2D F:HEM150 4.3 15.9 1.0
C3C F:HEM150 4.3 16.3 1.0
C3B F:HEM150 4.3 17.5 1.0
C2B F:HEM150 4.3 16.4 1.0
CA F:MET7 5.0 23.9 1.0

Iron binding site 7 out of 8 in 3m79

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Iron binding site 7 out of 8 in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe150

b:25.8
occ:1.00
FE G:HEM150 0.0 25.8 1.0
NE2 G:HIS102 2.0 23.4 1.0
ND G:HEM150 2.1 27.8 1.0
NC G:HEM150 2.1 27.5 1.0
NA G:HEM150 2.1 28.4 1.0
NB G:HEM150 2.1 27.0 1.0
SD G:MET7 2.3 25.9 1.0
CD2 G:HIS102 2.9 23.3 1.0
CE1 G:HIS102 3.0 22.9 1.0
C4C G:HEM150 3.1 27.2 1.0
C4D G:HEM150 3.1 29.0 1.0
C1D G:HEM150 3.1 28.1 1.0
C1A G:HEM150 3.1 28.6 1.0
C1C G:HEM150 3.1 26.9 1.0
C4A G:HEM150 3.1 28.1 1.0
C1B G:HEM150 3.1 27.0 1.0
C4B G:HEM150 3.1 26.3 1.0
CHA G:HEM150 3.4 28.4 1.0
CHD G:HEM150 3.4 27.6 1.0
CHB G:HEM150 3.5 27.6 1.0
CHC G:HEM150 3.5 26.5 1.0
CG G:MET7 3.5 23.9 1.0
CE G:MET7 3.5 23.7 1.0
CG G:HIS102 4.1 23.8 1.0
ND1 G:HIS102 4.1 22.3 1.0
CB G:MET7 4.2 24.1 1.0
C3C G:HEM150 4.3 27.3 1.0
C3D G:HEM150 4.3 28.9 1.0
C2D G:HEM150 4.3 28.3 1.0
C2C G:HEM150 4.3 27.4 1.0
C2A G:HEM150 4.3 29.3 1.0
C3A G:HEM150 4.3 28.8 1.0
C2B G:HEM150 4.3 27.4 1.0
C3B G:HEM150 4.3 26.9 1.0

Iron binding site 8 out of 8 in 3m79

Go back to Iron Binding Sites List in 3m79
Iron binding site 8 out of 8 in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe150

b:25.8
occ:1.00
FE H:HEM150 0.0 25.8 1.0
NE2 H:HIS102 2.0 23.7 1.0
NA H:HEM150 2.0 28.6 1.0
NB H:HEM150 2.1 26.9 1.0
ND H:HEM150 2.1 27.7 1.0
NC H:HEM150 2.1 26.9 1.0
SD H:MET7 2.3 25.7 1.0
CD2 H:HIS102 2.9 24.4 1.0
CE1 H:HIS102 3.0 23.6 1.0
C1A H:HEM150 3.0 30.2 1.0
C4A H:HEM150 3.0 29.6 1.0
C4B H:HEM150 3.1 26.6 1.0
C1B H:HEM150 3.1 28.0 1.0
C4D H:HEM150 3.1 28.0 1.0
C1C H:HEM150 3.1 26.2 1.0
C1D H:HEM150 3.1 27.9 1.0
C4C H:HEM150 3.1 27.1 1.0
CHA H:HEM150 3.4 28.8 1.0
CE H:MET7 3.4 25.4 1.0
CHB H:HEM150 3.4 28.9 1.0
CHC H:HEM150 3.4 26.9 1.0
CG H:MET7 3.5 24.2 1.0
CHD H:HEM150 3.5 27.1 1.0
ND1 H:HIS102 4.1 24.2 1.0
CG H:HIS102 4.1 24.8 1.0
CB H:MET7 4.2 24.5 1.0
C2A H:HEM150 4.2 31.1 1.0
C3A H:HEM150 4.2 30.0 1.0
C3B H:HEM150 4.3 27.4 1.0
C2B H:HEM150 4.3 27.6 1.0
C2C H:HEM150 4.3 26.1 1.0
C3D H:HEM150 4.3 28.9 1.0
C3C H:HEM150 4.4 25.4 1.0
C2D H:HEM150 4.4 27.2 1.0
NH2 H:ARG106 4.9 33.7 1.0

Reference:

J.D.Brodin, A.Medina-Morales, T.Ni, E.N.Salgado, X.I.Ambroggio, F.A.Tezcan. Evolution of Metal Selectivity in Templated Protein Interfaces. J.Am.Chem.Soc. V. 132 8610 2010.
ISSN: ISSN 0002-7863
PubMed: 20515031
DOI: 10.1021/JA910844N
Page generated: Sun Aug 4 14:43:54 2024

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