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Iron in PDB 3tol: Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers

Protein crystallography data

The structure of Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers, PDB code: 3tol 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) 63.28 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.546, 69.506, 126.567, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 24.5

Other elements in 3tol:

The structure of Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Zinc (Zn) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers (pdb code 3tol). 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 1D, Zn- Mediated Coordination Polymers, PDB code: 3tol:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3tol

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Iron binding site 1 out of 4 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers


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 1D, Zn- Mediated Coordination Polymers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe150

b:22.3
occ:1.00
FE A:HEM150 0.0 22.3 1.0
NB A:HEM150 2.1 22.3 1.0
ND A:HEM150 2.1 23.1 1.0
NE2 A:HIS102 2.1 20.6 1.0
NA A:HEM150 2.1 23.6 1.0
NC A:HEM150 2.1 21.3 1.0
SD A:MET7 2.3 22.1 1.0
CD2 A:HIS102 3.0 19.2 1.0
C4B A:HEM150 3.1 22.1 1.0
C4D A:HEM150 3.1 25.2 1.0
C1D A:HEM150 3.1 24.7 1.0
C1C A:HEM150 3.1 21.1 1.0
C1A A:HEM150 3.1 25.0 1.0
CE1 A:HIS102 3.1 21.6 1.0
C1B A:HEM150 3.1 22.9 1.0
C4A A:HEM150 3.1 25.0 1.0
C4C A:HEM150 3.1 21.5 1.0
CHC A:HEM150 3.4 19.9 1.0
CHA A:HEM150 3.4 26.1 1.0
CE A:MET7 3.4 19.0 1.0
CHD A:HEM150 3.4 22.8 1.0
CG A:MET7 3.5 20.6 1.0
CHB A:HEM150 3.5 22.5 1.0
ND1 A:HIS102 4.2 23.2 1.0
CG A:HIS102 4.2 22.9 1.0
CB A:MET7 4.2 22.1 1.0
C3B A:HEM150 4.3 20.2 1.0
C3D A:HEM150 4.3 25.2 1.0
C2B A:HEM150 4.3 20.8 1.0
C2A A:HEM150 4.3 28.4 1.0
C3A A:HEM150 4.3 25.4 1.0
C2D A:HEM150 4.3 24.6 1.0
C2C A:HEM150 4.3 19.2 1.0
C3C A:HEM150 4.4 21.0 1.0

Iron binding site 2 out of 4 in 3tol

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Iron binding site 2 out of 4 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers


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 1D, Zn- Mediated Coordination Polymers within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe150

b:23.1
occ:1.00
FE C:HEM150 0.0 23.1 1.0
ND C:HEM150 1.9 20.2 1.0
NE2 C:HIS102 2.0 24.2 1.0
NB C:HEM150 2.0 19.8 1.0
NC C:HEM150 2.1 18.8 1.0
NA C:HEM150 2.1 21.5 1.0
SD C:MET7 2.4 26.0 1.0
C4D C:HEM150 2.9 26.0 1.0
C4B C:HEM150 2.9 22.7 1.0
CD2 C:HIS102 2.9 21.2 1.0
CE1 C:HIS102 3.0 25.1 1.0
C1C C:HEM150 3.0 19.0 1.0
C1A C:HEM150 3.1 23.7 1.0
C1D C:HEM150 3.1 23.0 1.0
C1B C:HEM150 3.1 23.4 1.0
C4C C:HEM150 3.2 17.6 1.0
C4A C:HEM150 3.2 22.9 1.0
CHC C:HEM150 3.3 19.3 1.0
CHA C:HEM150 3.3 22.8 1.0
CE C:MET7 3.4 23.9 1.0
CG C:MET7 3.5 26.2 1.0
CHD C:HEM150 3.5 19.9 1.0
CHB C:HEM150 3.6 22.4 1.0
ND1 C:HIS102 4.1 24.4 1.0
CG C:HIS102 4.1 25.2 1.0
C3D C:HEM150 4.2 25.9 1.0
C3B C:HEM150 4.2 21.8 1.0
CB C:MET7 4.2 27.3 1.0
C2D C:HEM150 4.2 22.9 1.0
C2B C:HEM150 4.3 22.1 1.0
C2C C:HEM150 4.3 17.6 1.0
C2A C:HEM150 4.3 25.1 1.0
C3C C:HEM150 4.4 18.2 1.0
C3A C:HEM150 4.4 25.1 1.0

Iron binding site 3 out of 4 in 3tol

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Iron binding site 3 out of 4 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers


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 1D, Zn- Mediated Coordination Polymers within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe150

b:24.1
occ:1.00
FE D:HEM150 0.0 24.1 1.0
NE2 D:HIS102 1.9 25.8 1.0
NB D:HEM150 2.1 23.4 1.0
ND D:HEM150 2.1 26.6 1.0
NC D:HEM150 2.1 23.4 1.0
NA D:HEM150 2.1 25.2 1.0
SD D:MET7 2.4 26.0 1.0
CE1 D:HIS102 2.9 27.6 1.0
CD2 D:HIS102 2.9 25.8 1.0
C4B D:HEM150 3.0 23.0 1.0
C1C D:HEM150 3.1 22.5 1.0
C4D D:HEM150 3.1 27.9 1.0
C1A D:HEM150 3.1 27.6 1.0
C1D D:HEM150 3.1 27.4 1.0
C4C D:HEM150 3.1 23.6 1.0
C1B D:HEM150 3.1 25.3 1.0
C4A D:HEM150 3.1 26.6 1.0
CHC D:HEM150 3.4 22.2 1.0
CHA D:HEM150 3.4 27.4 1.0
CG D:MET7 3.5 26.1 1.0
CE D:MET7 3.5 22.7 1.0
CHD D:HEM150 3.5 25.2 1.0
CHB D:HEM150 3.5 25.2 1.0
ND1 D:HIS102 4.0 28.4 1.0
CG D:HIS102 4.0 29.6 1.0
C3B D:HEM150 4.3 22.8 1.0
CB D:MET7 4.3 27.3 1.0
C2C D:HEM150 4.3 23.9 1.0
C3D D:HEM150 4.3 30.1 1.0
C2A D:HEM150 4.3 31.3 1.0
C2B D:HEM150 4.3 24.0 1.0
C2D D:HEM150 4.3 27.9 1.0
C3C D:HEM150 4.3 23.1 1.0
C3A D:HEM150 4.3 29.5 1.0

Iron binding site 4 out of 4 in 3tol

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Iron binding site 4 out of 4 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers


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 1D, Zn- Mediated Coordination Polymers within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe150

b:19.9
occ:1.00
FE B:HEM150 0.0 19.9 1.0
NE2 B:HIS102 1.9 19.0 1.0
ND B:HEM150 2.1 21.6 1.0
NB B:HEM150 2.1 19.5 1.0
NC B:HEM150 2.1 20.3 1.0
NA B:HEM150 2.1 22.8 1.0
SD B:MET7 2.2 20.3 1.0
CE1 B:HIS102 2.9 20.3 1.0
CD2 B:HIS102 2.9 18.4 1.0
C4B B:HEM150 3.1 18.7 1.0
C1C B:HEM150 3.1 21.6 1.0
C4D B:HEM150 3.1 24.5 1.0
C1D B:HEM150 3.1 22.4 1.0
C4C B:HEM150 3.1 21.6 1.0
C1B B:HEM150 3.1 21.8 1.0
C1A B:HEM150 3.1 24.9 1.0
C4A B:HEM150 3.2 24.1 1.0
CE B:MET7 3.3 19.4 1.0
CHC B:HEM150 3.4 19.3 1.0
CG B:MET7 3.4 19.6 1.0
CHA B:HEM150 3.4 25.3 1.0
CHD B:HEM150 3.5 21.1 1.0
CHB B:HEM150 3.5 22.6 1.0
ND1 B:HIS102 4.0 22.0 1.0
CG B:HIS102 4.1 21.6 1.0
CB B:MET7 4.3 19.9 1.0
C3B B:HEM150 4.3 18.7 1.0
C2C B:HEM150 4.3 19.1 1.0
C3D B:HEM150 4.3 24.4 1.0
C2D B:HEM150 4.3 23.9 1.0
C3C B:HEM150 4.3 21.0 1.0
C2B B:HEM150 4.3 20.1 1.0
C2A B:HEM150 4.4 27.3 1.0
C3A B:HEM150 4.4 25.7 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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