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Iron in PDB 3tom: Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets

Protein crystallography data

The structure of Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets, PDB code: 3tom was solved by J.B.Brodin, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.80 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 95.690, 37.843, 138.489, 90.00, 112.61, 90.00
R / Rfree (%) 21 / 28.6

Other elements in 3tom:

The structure of Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets (pdb code 3tom). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets, PDB code: 3tom:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3tom

Go back to Iron Binding Sites List in 3tom
Iron binding site 1 out of 4 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets


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 An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets 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 23.2 1.0
NC A:HEM150 2.0 20.8 1.0
NB A:HEM150 2.0 18.0 1.0
ND A:HEM150 2.1 20.8 1.0
NA A:HEM150 2.1 23.0 1.0
SD A:MET7 2.4 21.4 1.0
CE1 A:HIS102 2.9 26.1 1.0
C1C A:HEM150 3.0 22.4 1.0
CD2 A:HIS102 3.0 25.9 1.0
C4B A:HEM150 3.0 20.3 1.0
C4C A:HEM150 3.1 21.7 1.0
C1D A:HEM150 3.1 22.2 1.0
C1B A:HEM150 3.1 19.3 1.0
C4D A:HEM150 3.1 21.7 1.0
C4A A:HEM150 3.1 22.8 1.0
C1A A:HEM150 3.1 24.1 1.0
CG A:MET7 3.3 21.4 1.0
CHC A:HEM150 3.4 21.5 1.0
CHD A:HEM150 3.4 21.9 1.0
CE A:MET7 3.4 20.1 1.0
CHA A:HEM150 3.5 21.5 1.0
CHB A:HEM150 3.5 21.5 1.0
ND1 A:HIS102 4.0 30.0 1.0
CB A:MET7 4.1 22.3 1.0
CG A:HIS102 4.1 28.8 1.0
C2C A:HEM150 4.2 23.5 1.0
C3B A:HEM150 4.3 18.8 1.0
C2B A:HEM150 4.3 17.7 1.0
C3C A:HEM150 4.3 21.3 1.0
C2D A:HEM150 4.3 22.3 1.0
C3D A:HEM150 4.3 23.0 1.0
C3A A:HEM150 4.4 26.5 1.0
C2A A:HEM150 4.4 27.7 1.0
NH1 A:ARG106 4.8 37.8 1.0
CA A:MET7 5.0 22.2 1.0

Iron binding site 2 out of 4 in 3tom

Go back to Iron Binding Sites List in 3tom
Iron binding site 2 out of 4 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets


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 An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe150

b:27.9
occ:1.00
FE B:HEM150 0.0 27.9 1.0
NC B:HEM150 2.0 24.8 1.0
NB B:HEM150 2.0 26.8 1.0
NE2 B:HIS102 2.0 29.9 1.0
ND B:HEM150 2.1 28.9 1.0
NA B:HEM150 2.1 31.4 1.0
SD B:MET7 2.4 28.6 1.0
C4B B:HEM150 3.0 24.7 1.0
CE1 B:HIS102 3.0 33.1 1.0
CD2 B:HIS102 3.0 32.5 1.0
C1C B:HEM150 3.0 24.1 1.0
C4C B:HEM150 3.0 24.3 1.0
C1B B:HEM150 3.1 26.0 1.0
C1D B:HEM150 3.1 27.2 1.0
C4A B:HEM150 3.1 32.0 1.0
C4D B:HEM150 3.1 31.8 1.0
C1A B:HEM150 3.1 34.4 1.0
CHC B:HEM150 3.4 24.0 1.0
CHD B:HEM150 3.4 24.5 1.0
CHB B:HEM150 3.4 30.1 1.0
CHA B:HEM150 3.5 34.1 1.0
CE B:MET7 3.5 26.4 1.0
CG B:MET7 3.6 30.5 1.0
ND1 B:HIS102 4.1 36.3 1.0
CG B:HIS102 4.2 35.5 1.0
C3B B:HEM150 4.2 22.5 1.0
C3C B:HEM150 4.2 23.1 1.0
C2C B:HEM150 4.3 23.1 1.0
C2B B:HEM150 4.3 23.5 1.0
CB B:MET7 4.3 31.8 1.0
C3A B:HEM150 4.3 36.4 1.0
C2D B:HEM150 4.4 28.6 1.0
C3D B:HEM150 4.4 30.9 1.0
C2A B:HEM150 4.4 38.5 1.0

Iron binding site 3 out of 4 in 3tom

Go back to Iron Binding Sites List in 3tom
Iron binding site 3 out of 4 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets


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 An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe150

b:30.7
occ:1.00
FE C:HEM150 0.0 30.7 1.0
NE2 C:HIS102 1.9 35.1 1.0
NA C:HEM150 2.0 34.0 1.0
ND C:HEM150 2.1 30.8 1.0
NB C:HEM150 2.1 31.0 1.0
NC C:HEM150 2.1 30.6 1.0
SD C:MET7 2.4 31.8 1.0
CE1 C:HIS102 2.9 37.2 1.0
CD2 C:HIS102 3.0 36.2 1.0
C1A C:HEM150 3.0 35.1 1.0
C4A C:HEM150 3.0 36.3 1.0
C4D C:HEM150 3.1 31.4 1.0
C4B C:HEM150 3.1 30.7 1.0
C1D C:HEM150 3.1 31.2 1.0
C1C C:HEM150 3.1 30.9 1.0
C1B C:HEM150 3.1 32.2 1.0
C4C C:HEM150 3.1 29.8 1.0
CHA C:HEM150 3.4 33.7 1.0
CG C:MET7 3.4 30.4 1.0
CHB C:HEM150 3.4 35.4 1.0
CHC C:HEM150 3.4 30.4 1.0
CE C:MET7 3.5 28.6 1.0
CHD C:HEM150 3.5 29.7 1.0
ND1 C:HIS102 4.0 39.8 1.0
CB C:MET7 4.1 31.3 1.0
CG C:HIS102 4.1 38.8 1.0
C2A C:HEM150 4.2 37.8 1.0
C3A C:HEM150 4.3 37.9 1.0
C2B C:HEM150 4.3 31.6 1.0
C3B C:HEM150 4.3 30.2 1.0
C3D C:HEM150 4.3 32.1 1.0
C2C C:HEM150 4.3 30.2 1.0
C2D C:HEM150 4.3 31.6 1.0
C3C C:HEM150 4.3 29.7 1.0
CA C:MET7 5.0 30.6 1.0

Iron binding site 4 out of 4 in 3tom

Go back to Iron Binding Sites List in 3tom
Iron binding site 4 out of 4 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets


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 An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe150

b:29.7
occ:1.00
FE D:HEM150 0.0 29.7 1.0
NE2 D:HIS102 2.0 34.8 1.0
NC D:HEM150 2.0 29.4 1.0
NA D:HEM150 2.1 33.8 1.0
NB D:HEM150 2.1 31.6 1.0
ND D:HEM150 2.1 30.2 1.0
SD D:MET7 2.3 32.9 1.0
CE1 D:HIS102 2.9 37.4 1.0
C4C D:HEM150 3.0 28.7 1.0
C4A D:HEM150 3.1 35.2 1.0
C1C D:HEM150 3.1 29.6 1.0
C1B D:HEM150 3.1 32.1 1.0
CD2 D:HIS102 3.1 35.8 1.0
C1D D:HEM150 3.1 27.3 1.0
C1A D:HEM150 3.1 35.7 1.0
C4B D:HEM150 3.1 31.3 1.0
C4D D:HEM150 3.2 31.6 1.0
CG D:MET7 3.4 31.1 1.0
CHB D:HEM150 3.4 34.3 1.0
CHD D:HEM150 3.4 27.4 1.0
CHC D:HEM150 3.5 29.8 1.0
CE D:MET7 3.5 28.7 1.0
CHA D:HEM150 3.5 32.4 1.0
ND1 D:HIS102 4.0 40.2 1.0
CB D:MET7 4.1 32.9 1.0
CG D:HIS102 4.2 39.9 1.0
C3C D:HEM150 4.3 29.4 1.0
C2C D:HEM150 4.3 29.1 1.0
C3A D:HEM150 4.3 39.3 1.0
C2B D:HEM150 4.3 32.3 1.0
C2A D:HEM150 4.3 39.8 1.0
C3B D:HEM150 4.4 31.1 1.0
C2D D:HEM150 4.4 26.9 1.0
C3D D:HEM150 4.4 29.1 1.0
CA D:MET7 4.9 32.7 1.0

Reference:

J.D.Brodin, X.I.Ambroggio, C.Tang, K.N.Parent, T.S.Baker, F.A.Tezcan. Metal-Directed, Chemically Tunable Assembly of One-, Two- and Three-Dimensional Crystalline Protein Arrays. Nat Chem V. 4 375 2012.
PubMed: 22522257
DOI: 10.1038/NCHEM.1290
Page generated: Sun Dec 13 15:22:24 2020

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