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Iron in PDB 3hni: Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1

Protein crystallography data

The structure of Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1, PDB code: 3hni was solved by E.N.Salgado, R.A.Lewis, J.Brodin, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.74 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.208, 87.935, 152.174, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 27.8

Other elements in 3hni:

The structure of Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 (pdb code 3hni). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1, PDB code: 3hni:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3hni

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Iron binding site 1 out of 8 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1


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 Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe150

b:22.6
occ:1.00
FE A:HEM150 0.0 22.6 1.0
NE2 A:HIS102 2.0 31.8 1.0
NC A:HEM150 2.0 21.9 1.0
NB A:HEM150 2.0 22.0 1.0
NA A:HEM150 2.1 22.9 1.0
ND A:HEM150 2.1 23.3 1.0
SD A:MET7 2.3 28.8 1.0
CE1 A:HIS102 2.9 32.8 1.0
CD2 A:HIS102 3.0 29.8 1.0
C1B A:HEM150 3.0 22.4 1.0
C4C A:HEM150 3.0 22.1 1.0
C4A A:HEM150 3.1 21.6 1.0
C1C A:HEM150 3.1 22.8 1.0
C1D A:HEM150 3.1 23.1 1.0
C4B A:HEM150 3.1 22.7 1.0
C4D A:HEM150 3.1 24.4 1.0
C1A A:HEM150 3.1 24.5 1.0
CHB A:HEM150 3.4 23.3 1.0
CHD A:HEM150 3.4 23.0 1.0
CHC A:HEM150 3.5 22.2 1.0
CHA A:HEM150 3.5 23.8 1.0
CG A:MET7 3.5 28.2 1.0
CE A:MET7 3.6 26.1 1.0
ND1 A:HIS102 4.1 32.9 1.0
CG A:HIS102 4.1 32.3 1.0
CB A:MET7 4.3 29.0 1.0
C3C A:HEM150 4.3 22.6 1.0
C2B A:HEM150 4.3 23.6 1.0
C2C A:HEM150 4.3 22.6 1.0
C3A A:HEM150 4.3 22.7 1.0
C2D A:HEM150 4.3 23.4 1.0
C3B A:HEM150 4.3 23.3 1.0
C2A A:HEM150 4.3 23.9 1.0
C3D A:HEM150 4.3 25.4 1.0

Iron binding site 2 out of 8 in 3hni

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Iron binding site 2 out of 8 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1


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 Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe150

b:24.3
occ:1.00
FE B:HEM150 0.0 24.3 1.0
NE2 B:HIS102 2.0 30.5 1.0
ND B:HEM150 2.0 25.6 1.0
NC B:HEM150 2.0 24.1 1.0
NB B:HEM150 2.1 23.1 1.0
NA B:HEM150 2.1 26.3 1.0
SD B:MET7 2.3 28.3 1.0
CE1 B:HIS102 3.0 32.3 1.0
CD2 B:HIS102 3.0 32.5 1.0
C1D B:HEM150 3.0 25.9 1.0
C4D B:HEM150 3.0 26.4 1.0
C4C B:HEM150 3.0 24.7 1.0
C4B B:HEM150 3.1 21.1 1.0
C1C B:HEM150 3.1 22.3 1.0
C1A B:HEM150 3.1 27.3 1.0
C1B B:HEM150 3.1 22.6 1.0
C4A B:HEM150 3.1 27.1 1.0
CHD B:HEM150 3.4 24.6 1.0
CHA B:HEM150 3.4 26.2 1.0
CG B:MET7 3.4 30.1 1.0
CHC B:HEM150 3.4 21.8 1.0
CE B:MET7 3.5 28.3 1.0
CHB B:HEM150 3.5 25.1 1.0
ND1 B:HIS102 4.1 34.0 1.0
CG B:HIS102 4.1 33.4 1.0
CB B:MET7 4.2 30.1 1.0
C2D B:HEM150 4.3 27.0 1.0
C3D B:HEM150 4.3 27.8 1.0
C3C B:HEM150 4.3 24.1 1.0
C3B B:HEM150 4.3 21.9 1.0
C2C B:HEM150 4.3 23.3 1.0
C2B B:HEM150 4.3 21.7 1.0
C2A B:HEM150 4.3 29.3 1.0
C3A B:HEM150 4.3 28.6 1.0
CA B:MET7 5.0 30.2 1.0

Iron binding site 3 out of 8 in 3hni

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Iron binding site 3 out of 8 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe150

b:31.0
occ:1.00
FE C:HEM150 0.0 31.0 1.0
NB C:HEM150 2.0 29.4 1.0
NE2 C:HIS102 2.0 32.1 1.0
ND C:HEM150 2.1 30.4 1.0
NA C:HEM150 2.1 30.8 1.0
NC C:HEM150 2.1 30.7 1.0
SD C:MET7 2.4 26.1 1.0
CE1 C:HIS102 2.9 32.9 1.0
C1B C:HEM150 3.0 31.3 1.0
C4B C:HEM150 3.0 29.8 1.0
CD2 C:HIS102 3.1 31.8 1.0
C4A C:HEM150 3.1 30.7 1.0
C1D C:HEM150 3.1 31.5 1.0
C4D C:HEM150 3.1 32.4 1.0
C1A C:HEM150 3.1 31.8 1.0
C1C C:HEM150 3.1 29.1 1.0
C4C C:HEM150 3.1 30.7 1.0
CHB C:HEM150 3.4 32.0 1.0
CE C:MET7 3.4 26.2 1.0
CHC C:HEM150 3.4 30.5 1.0
CHA C:HEM150 3.5 31.8 1.0
CHD C:HEM150 3.5 31.2 1.0
CG C:MET7 3.5 28.0 1.0
ND1 C:HIS102 4.1 32.4 1.0
CG C:HIS102 4.1 32.6 1.0
C2B C:HEM150 4.2 29.8 1.0
C3B C:HEM150 4.2 29.8 1.0
CB C:MET7 4.3 28.7 1.0
C3A C:HEM150 4.3 30.4 1.0
C2D C:HEM150 4.3 32.6 1.0
C2A C:HEM150 4.3 32.6 1.0
C3D C:HEM150 4.3 34.1 1.0
C2C C:HEM150 4.4 29.9 1.0
C3C C:HEM150 4.4 28.7 1.0

Iron binding site 4 out of 8 in 3hni

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Iron binding site 4 out of 8 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe150

b:26.2
occ:1.00
FE D:HEM150 0.0 26.2 1.0
NE2 D:HIS102 2.0 31.1 1.0
NC D:HEM150 2.0 25.3 1.0
NB D:HEM150 2.1 26.1 1.0
NA D:HEM150 2.1 28.3 1.0
ND D:HEM150 2.1 27.0 1.0
SD D:MET7 2.4 28.7 1.0
CD2 D:HIS102 2.9 29.9 1.0
C1C D:HEM150 3.0 24.7 1.0
C4B D:HEM150 3.0 25.6 1.0
C4C D:HEM150 3.0 25.0 1.0
CE1 D:HIS102 3.1 32.0 1.0
C1A D:HEM150 3.1 28.2 1.0
C1D D:HEM150 3.1 26.8 1.0
C4D D:HEM150 3.1 27.2 1.0
C1B D:HEM150 3.1 26.3 1.0
C4A D:HEM150 3.1 28.0 1.0
CHC D:HEM150 3.4 25.0 1.0
CHD D:HEM150 3.4 27.3 1.0
CHA D:HEM150 3.4 27.0 1.0
CE D:MET7 3.5 26.2 1.0
CHB D:HEM150 3.5 27.2 1.0
CG D:MET7 3.5 29.3 1.0
CG D:HIS102 4.1 30.6 1.0
ND1 D:HIS102 4.1 31.0 1.0
CB D:MET7 4.2 29.5 1.0
C2C D:HEM150 4.2 25.0 1.0
C3C D:HEM150 4.3 24.2 1.0
C3B D:HEM150 4.3 25.5 1.0
C2A D:HEM150 4.3 29.6 1.0
C2B D:HEM150 4.3 23.5 1.0
C2D D:HEM150 4.3 27.4 1.0
C3A D:HEM150 4.3 28.7 1.0
C3D D:HEM150 4.3 28.7 1.0

Iron binding site 5 out of 8 in 3hni

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Iron binding site 5 out of 8 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe150

b:23.2
occ:1.00
FE E:HEM150 0.0 23.2 1.0
NE2 E:HIS102 2.0 30.2 1.0
ND E:HEM150 2.0 25.0 1.0
NA E:HEM150 2.0 24.2 1.0
NC E:HEM150 2.1 23.9 1.0
NB E:HEM150 2.1 24.2 1.0
SD E:MET7 2.3 29.6 1.0
CD2 E:HIS102 3.0 31.2 1.0
C1D E:HEM150 3.0 26.2 1.0
CE1 E:HIS102 3.0 30.6 1.0
C4A E:HEM150 3.0 24.8 1.0
C4D E:HEM150 3.0 26.9 1.0
C4C E:HEM150 3.1 23.5 1.0
C1A E:HEM150 3.1 25.2 1.0
C1B E:HEM150 3.1 23.0 1.0
C4B E:HEM150 3.1 23.6 1.0
C1C E:HEM150 3.1 23.9 1.0
CHD E:HEM150 3.4 24.6 1.0
CHA E:HEM150 3.4 25.7 1.0
CHB E:HEM150 3.4 24.7 1.0
CE E:MET7 3.5 28.9 1.0
CHC E:HEM150 3.5 23.8 1.0
CG E:MET7 3.5 29.1 1.0
ND1 E:HIS102 4.1 31.2 1.0
CG E:HIS102 4.1 31.5 1.0
CB E:MET7 4.2 29.7 1.0
C2D E:HEM150 4.2 27.3 1.0
C3D E:HEM150 4.3 28.2 1.0
C3A E:HEM150 4.3 25.5 1.0
C2A E:HEM150 4.3 26.6 1.0
C2B E:HEM150 4.3 23.2 1.0
C3B E:HEM150 4.3 23.6 1.0
C3C E:HEM150 4.3 24.8 1.0
C2C E:HEM150 4.3 22.9 1.0
NH1 E:ARG106 4.7 46.8 1.0
CA E:MET7 5.0 30.1 1.0

Iron binding site 6 out of 8 in 3hni

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Iron binding site 6 out of 8 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe150

b:26.9
occ:1.00
FE F:HEM150 0.0 26.9 1.0
NE2 F:HIS102 2.0 29.4 1.0
NC F:HEM150 2.0 25.1 1.0
ND F:HEM150 2.1 27.2 1.0
NA F:HEM150 2.1 27.0 1.0
NB F:HEM150 2.1 24.9 1.0
SD F:MET7 2.3 30.3 1.0
CE1 F:HIS102 3.0 31.0 1.0
CD2 F:HIS102 3.0 29.8 1.0
C4D F:HEM150 3.0 26.9 1.0
C1A F:HEM150 3.0 27.6 1.0
C1C F:HEM150 3.0 22.9 1.0
C4B F:HEM150 3.1 23.9 1.0
C4C F:HEM150 3.1 25.5 1.0
C1D F:HEM150 3.1 27.1 1.0
C4A F:HEM150 3.2 26.9 1.0
C1B F:HEM150 3.2 24.9 1.0
CHA F:HEM150 3.3 26.1 1.0
CE F:MET7 3.4 29.5 1.0
CHC F:HEM150 3.4 24.0 1.0
CG F:MET7 3.4 29.7 1.0
CHD F:HEM150 3.5 26.1 1.0
CHB F:HEM150 3.6 26.0 1.0
ND1 F:HIS102 4.1 29.7 1.0
CG F:HIS102 4.1 30.2 1.0
CB F:MET7 4.2 30.0 1.0
C2C F:HEM150 4.3 22.4 1.0
C3D F:HEM150 4.3 28.0 1.0
C3C F:HEM150 4.3 23.7 1.0
C2A F:HEM150 4.3 28.7 1.0
C2D F:HEM150 4.3 27.4 1.0
C3B F:HEM150 4.3 24.6 1.0
C3A F:HEM150 4.4 27.7 1.0
C2B F:HEM150 4.4 23.0 1.0
CA F:MET7 5.0 30.1 1.0

Iron binding site 7 out of 8 in 3hni

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Iron binding site 7 out of 8 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe150

b:28.0
occ:1.00
FE G:HEM150 0.0 28.0 1.0
NE2 G:HIS102 2.0 29.9 1.0
NA G:HEM150 2.1 28.4 1.0
NB G:HEM150 2.1 26.4 1.0
ND G:HEM150 2.1 28.0 1.0
NC G:HEM150 2.1 27.4 1.0
SD G:MET7 2.4 25.9 1.0
CD2 G:HIS102 3.0 30.6 1.0
CE1 G:HIS102 3.0 31.5 1.0
C4D G:HEM150 3.1 28.4 1.0
C1A G:HEM150 3.1 27.7 1.0
C1B G:HEM150 3.1 26.3 1.0
C4A G:HEM150 3.1 27.9 1.0
C1D G:HEM150 3.1 28.5 1.0
C4B G:HEM150 3.1 26.2 1.0
C4C G:HEM150 3.1 26.9 1.0
C1C G:HEM150 3.1 25.6 1.0
CHA G:HEM150 3.4 27.7 1.0
CHB G:HEM150 3.4 27.6 1.0
CHD G:HEM150 3.4 28.2 1.0
CHC G:HEM150 3.5 26.5 1.0
CG G:MET7 3.5 28.6 1.0
CE G:MET7 3.5 25.9 1.0
ND1 G:HIS102 4.1 31.1 1.0
CG G:HIS102 4.2 31.6 1.0
CB G:MET7 4.2 29.2 1.0
C2B G:HEM150 4.3 26.3 1.0
C2A G:HEM150 4.3 28.6 1.0
C3A G:HEM150 4.3 26.9 1.0
C3B G:HEM150 4.3 26.1 1.0
C3D G:HEM150 4.3 30.9 1.0
C2D G:HEM150 4.3 29.5 1.0
C3C G:HEM150 4.3 25.7 1.0
C2C G:HEM150 4.3 26.3 1.0
CD G:ARG106 4.9 37.9 1.0
CA G:MET7 5.0 30.0 1.0

Iron binding site 8 out of 8 in 3hni

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Iron binding site 8 out of 8 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe150

b:24.5
occ:1.00
FE H:HEM150 0.0 24.5 1.0
NE2 H:HIS102 2.0 31.2 1.0
NC H:HEM150 2.0 22.6 1.0
NB H:HEM150 2.1 23.8 1.0
ND H:HEM150 2.1 24.7 1.0
NA H:HEM150 2.1 26.4 1.0
SD H:MET7 2.4 25.1 1.0
CD2 H:HIS102 3.0 32.0 1.0
CE1 H:HIS102 3.0 32.7 1.0
C1C H:HEM150 3.0 22.2 1.0
C4C H:HEM150 3.1 23.7 1.0
C4D H:HEM150 3.1 26.0 1.0
C4B H:HEM150 3.1 23.0 1.0
C1A H:HEM150 3.1 27.6 1.0
C1D H:HEM150 3.1 24.1 1.0
C1B H:HEM150 3.1 24.7 1.0
C4A H:HEM150 3.1 27.1 1.0
CE H:MET7 3.4 28.8 1.0
CHA H:HEM150 3.4 26.1 1.0
CHC H:HEM150 3.4 22.4 1.0
CHD H:HEM150 3.4 24.3 1.0
CHB H:HEM150 3.5 26.6 1.0
CG H:MET7 3.5 29.3 1.0
ND1 H:HIS102 4.1 32.4 1.0
CG H:HIS102 4.1 32.0 1.0
C2C H:HEM150 4.3 23.0 1.0
C3C H:HEM150 4.3 23.2 1.0
C3B H:HEM150 4.3 22.6 1.0
CB H:MET7 4.3 29.8 1.0
C2B H:HEM150 4.3 21.6 1.0
C3D H:HEM150 4.3 27.2 1.0
C2A H:HEM150 4.3 30.1 1.0
C2D H:HEM150 4.3 25.4 1.0
C3A H:HEM150 4.3 28.3 1.0

Reference:

E.N.Salgado, X.I.Ambroggio, J.D.Brodin, R.A.Lewis, B.Kuhlman, F.A.Tezcan. Metal Templated Design of Protein Interfaces. Proc.Natl.Acad.Sci.Usa V. 107 1827 2010.
ISSN: ISSN 0027-8424
PubMed: 20080561
DOI: 10.1073/PNAS.0906852107
Page generated: Sun Aug 4 11:31:36 2024

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