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Iron in PDB 3hnj: Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2

Protein crystallography data

The structure of Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2, PDB code: 3hnj 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) 30.70 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.448, 65.316, 70.773, 90.00, 104.70, 90.00
R / Rfree (%) 22.4 / 27.2

Other elements in 3hnj:

The structure of Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2 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-2 (pdb code 3hnj). 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 the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2, PDB code: 3hnj:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3hnj

Go back to Iron Binding Sites List in 3hnj
Iron binding site 1 out of 4 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2


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-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe150

b:16.1
occ:1.00
FE A:HEM150 0.0 16.1 1.0
NA A:HEM150 2.0 16.8 1.0
NB A:HEM150 2.0 16.2 1.0
NE2 A:HIS102 2.1 17.3 1.0
NC A:HEM150 2.1 15.2 1.0
ND A:HEM150 2.1 16.8 1.0
SD A:MET7 2.3 21.6 1.0
C4A A:HEM150 3.0 16.5 1.0
C1B A:HEM150 3.0 16.4 1.0
C1A A:HEM150 3.1 17.1 1.0
CD2 A:HIS102 3.1 19.8 1.0
C4B A:HEM150 3.1 14.7 1.0
CE1 A:HIS102 3.1 19.2 1.0
C1C A:HEM150 3.1 14.6 1.0
C4D A:HEM150 3.1 17.8 1.0
C4C A:HEM150 3.1 15.8 1.0
C1D A:HEM150 3.2 18.5 1.0
CHB A:HEM150 3.3 16.4 1.0
CE A:MET7 3.5 21.0 1.0
CHA A:HEM150 3.5 17.0 1.0
CG A:MET7 3.5 21.4 1.0
CHC A:HEM150 3.5 15.9 1.0
CHD A:HEM150 3.5 16.4 1.0
ND1 A:HIS102 4.2 19.1 1.0
C3A A:HEM150 4.2 16.7 1.0
CB A:MET7 4.2 22.1 1.0
CG A:HIS102 4.2 21.1 1.0
C2B A:HEM150 4.2 15.4 1.0
C2A A:HEM150 4.2 17.4 1.0
C3B A:HEM150 4.3 15.5 1.0
C2C A:HEM150 4.3 15.1 1.0
C3C A:HEM150 4.4 14.2 1.0
C3D A:HEM150 4.4 17.6 1.0
C2D A:HEM150 4.4 18.1 1.0
CA A:MET7 5.0 22.5 1.0

Iron binding site 2 out of 4 in 3hnj

Go back to Iron Binding Sites List in 3hnj
Iron binding site 2 out of 4 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2


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-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe150

b:21.4
occ:1.00
FE B:HEM150 0.0 21.4 1.0
NE2 B:HIS102 2.0 20.5 1.0
NA B:HEM150 2.0 22.9 1.0
NC B:HEM150 2.1 21.9 1.0
ND B:HEM150 2.1 22.1 1.0
NB B:HEM150 2.1 21.9 1.0
SD B:MET7 2.4 22.1 1.0
CE1 B:HIS102 2.9 21.4 1.0
CD2 B:HIS102 3.0 22.1 1.0
C1A B:HEM150 3.0 22.2 1.0
C4D B:HEM150 3.1 22.6 1.0
C4A B:HEM150 3.1 22.6 1.0
C4C B:HEM150 3.1 21.0 1.0
C4B B:HEM150 3.1 21.1 1.0
C1C B:HEM150 3.1 21.1 1.0
C1B B:HEM150 3.1 22.4 1.0
C1D B:HEM150 3.1 22.3 1.0
CHA B:HEM150 3.4 22.5 1.0
CE B:MET7 3.4 23.6 1.0
CHC B:HEM150 3.4 21.6 1.0
CHB B:HEM150 3.5 23.1 1.0
CHD B:HEM150 3.5 22.0 1.0
CG B:MET7 3.5 23.1 1.0
ND1 B:HIS102 4.1 21.4 1.0
CG B:HIS102 4.1 22.4 1.0
CB B:MET7 4.2 22.4 1.0
C2A B:HEM150 4.3 23.4 1.0
C3A B:HEM150 4.3 22.0 1.0
C2B B:HEM150 4.3 21.6 1.0
C3C B:HEM150 4.3 21.1 1.0
C3D B:HEM150 4.3 23.6 1.0
C3B B:HEM150 4.3 21.9 1.0
C2C B:HEM150 4.3 20.6 1.0
C2D B:HEM150 4.4 22.4 1.0

Iron binding site 3 out of 4 in 3hnj

Go back to Iron Binding Sites List in 3hnj
Iron binding site 3 out of 4 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2


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-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe150

b:21.0
occ:1.00
FE C:HEM150 0.0 21.0 1.0
NA C:HEM150 2.0 20.6 1.0
NE2 C:HIS102 2.0 21.9 1.0
NC C:HEM150 2.1 19.7 1.0
NB C:HEM150 2.1 20.0 1.0
ND C:HEM150 2.1 19.9 1.0
SD C:MET7 2.4 20.8 1.0
C1A C:HEM150 2.9 21.4 1.0
CD2 C:HIS102 3.0 21.6 1.0
CE1 C:HIS102 3.0 20.8 1.0
C4D C:HEM150 3.0 20.8 1.0
C4A C:HEM150 3.0 21.6 1.0
C1C C:HEM150 3.1 19.2 1.0
C4B C:HEM150 3.1 18.6 1.0
C1B C:HEM150 3.1 20.6 1.0
C4C C:HEM150 3.1 20.1 1.0
C1D C:HEM150 3.2 20.9 1.0
CHA C:HEM150 3.3 20.6 1.0
CHC C:HEM150 3.4 20.1 1.0
CE C:MET7 3.4 21.1 1.0
CHB C:HEM150 3.5 22.5 1.0
CG C:MET7 3.5 21.8 1.0
CHD C:HEM150 3.6 20.7 1.0
ND1 C:HIS102 4.1 21.4 1.0
CG C:HIS102 4.2 21.4 1.0
CB C:MET7 4.2 22.2 1.0
C2A C:HEM150 4.2 22.5 1.0
C3A C:HEM150 4.2 22.5 1.0
C2C C:HEM150 4.3 19.6 1.0
C3B C:HEM150 4.3 20.4 1.0
C3D C:HEM150 4.3 21.5 1.0
C2B C:HEM150 4.3 19.9 1.0
C3C C:HEM150 4.3 19.6 1.0
C2D C:HEM150 4.4 20.2 1.0
CA C:MET7 5.0 22.4 1.0

Iron binding site 4 out of 4 in 3hnj

Go back to Iron Binding Sites List in 3hnj
Iron binding site 4 out of 4 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2


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-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe150

b:25.1
occ:1.00
FE D:HEM150 0.0 25.1 1.0
NE2 D:HIS102 2.0 22.2 1.0
ND D:HEM150 2.0 25.4 1.0
NA D:HEM150 2.0 26.3 1.0
NC D:HEM150 2.1 24.9 1.0
NB D:HEM150 2.1 26.2 1.0
SD D:MET7 2.4 27.1 1.0
CD2 D:HIS102 2.9 21.7 1.0
CE1 D:HIS102 3.0 20.8 1.0
C1D D:HEM150 3.0 24.4 1.0
C1A D:HEM150 3.1 25.7 1.0
C4D D:HEM150 3.1 25.1 1.0
C4C D:HEM150 3.1 24.7 1.0
C4A D:HEM150 3.1 26.2 1.0
C1C D:HEM150 3.1 24.6 1.0
C4B D:HEM150 3.1 25.4 1.0
C1B D:HEM150 3.1 26.6 1.0
CHD D:HEM150 3.4 24.5 1.0
CHA D:HEM150 3.4 24.9 1.0
CE D:MET7 3.5 25.2 1.0
CHC D:HEM150 3.5 25.6 1.0
CHB D:HEM150 3.5 26.3 1.0
CG D:MET7 3.6 23.8 1.0
CG D:HIS102 4.0 21.9 1.0
ND1 D:HIS102 4.1 20.1 1.0
C2D D:HEM150 4.3 23.6 1.0
C2A D:HEM150 4.3 26.1 1.0
C3C D:HEM150 4.3 24.6 1.0
C3D D:HEM150 4.3 24.2 1.0
C3A D:HEM150 4.3 25.5 1.0
C2C D:HEM150 4.3 25.6 1.0
C2B D:HEM150 4.3 26.4 1.0
C3B D:HEM150 4.4 26.2 1.0
CB D:MET7 4.4 22.8 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 11:42:54 2024

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