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Iron in PDB 4u9d: Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3

Protein crystallography data

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3, PDB code: 4u9d was solved by F.A.Tezcan, W.J.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.48 / 2.50
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 54.830, 54.830, 237.820, 90.00, 90.00, 120.00
R / Rfree (%) 23.8 / 29.6

Other elements in 4u9d:

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3 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-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3 (pdb code 4u9d). 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-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3, PDB code: 4u9d:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4u9d

Go back to Iron Binding Sites List in 4u9d
Iron binding site 1 out of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3


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-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:61.2
occ:1.00
FE A:HEM201 0.0 61.2 1.0
ND A:HEM201 1.9 65.1 1.0
NA A:HEM201 2.0 64.4 1.0
NC A:HEM201 2.1 62.0 1.0
NB A:HEM201 2.1 61.4 1.0
NE2 A:HIS102 2.1 52.9 1.0
SD A:MET7 2.3 57.7 1.0
C4D A:HEM201 2.9 65.5 1.0
C1D A:HEM201 2.9 64.5 1.0
C1A A:HEM201 3.0 65.3 1.0
C4A A:HEM201 3.0 64.2 1.0
CE1 A:HIS102 3.1 53.6 1.0
C4B A:HEM201 3.1 60.7 1.0
C1B A:HEM201 3.1 61.2 1.0
C4C A:HEM201 3.1 62.0 1.0
C1C A:HEM201 3.1 60.7 1.0
CD2 A:HIS102 3.1 53.9 1.0
CHA A:HEM201 3.4 65.5 1.0
CE A:MET7 3.4 58.7 1.0
CHD A:HEM201 3.4 63.6 1.0
CHB A:HEM201 3.5 62.8 1.0
CHC A:HEM201 3.5 60.1 1.0
CG A:MET7 3.5 59.2 1.0
C3D A:HEM201 4.2 66.3 1.0
ND1 A:HIS102 4.2 54.2 1.0
C2D A:HEM201 4.2 65.5 1.0
C2A A:HEM201 4.2 67.4 1.0
C3A A:HEM201 4.2 65.6 1.0
CB A:MET7 4.2 58.4 1.0
CG A:HIS102 4.3 54.9 1.0
C2C A:HEM201 4.3 61.1 1.0
C3C A:HEM201 4.3 60.9 1.0
C2B A:HEM201 4.3 60.2 1.0
C3B A:HEM201 4.3 60.0 1.0

Iron binding site 2 out of 4 in 4u9d

Go back to Iron Binding Sites List in 4u9d
Iron binding site 2 out of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3


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-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:72.0
occ:1.00
FE B:HEM201 0.0 72.0 1.0
ND B:HEM201 1.9 72.4 1.0
NA B:HEM201 2.0 76.0 1.0
NC B:HEM201 2.1 71.1 1.0
NB B:HEM201 2.1 71.7 1.0
NE2 B:HIS102 2.2 64.3 1.0
SD B:MET7 2.5 68.8 1.0
C4D B:HEM201 2.9 73.9 1.0
C1D B:HEM201 2.9 71.8 1.0
C1A B:HEM201 3.0 77.0 1.0
CD2 B:HIS102 3.0 64.5 1.0
C4A B:HEM201 3.0 76.4 1.0
C4B B:HEM201 3.1 70.9 1.0
C1B B:HEM201 3.1 72.8 1.0
C4C B:HEM201 3.1 70.2 1.0
C1C B:HEM201 3.1 70.1 1.0
CE1 B:HIS102 3.3 65.0 1.0
CHA B:HEM201 3.4 75.3 1.0
CHD B:HEM201 3.4 71.1 1.0
CE B:MET7 3.4 69.6 1.0
CHB B:HEM201 3.4 74.6 1.0
CHC B:HEM201 3.5 70.1 1.0
CG B:MET7 3.6 70.4 1.0
C3D B:HEM201 4.2 72.8 1.0
C2D B:HEM201 4.2 71.1 1.0
C2A B:HEM201 4.2 80.0 1.0
C3A B:HEM201 4.2 78.6 1.0
CG B:HIS102 4.2 65.0 1.0
C3C B:HEM201 4.3 69.5 1.0
C2C B:HEM201 4.3 69.6 1.0
C2B B:HEM201 4.3 71.8 1.0
CB B:MET7 4.3 70.3 1.0
C3B B:HEM201 4.3 70.8 1.0
ND1 B:HIS102 4.3 65.3 1.0

Iron binding site 3 out of 4 in 4u9d

Go back to Iron Binding Sites List in 4u9d
Iron binding site 3 out of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3


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-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:62.9
occ:1.00
FE C:HEM201 0.0 62.9 1.0
ND C:HEM201 1.9 64.7 1.0
NA C:HEM201 2.0 65.8 1.0
NC C:HEM201 2.1 62.0 1.0
NB C:HEM201 2.1 63.5 1.0
NE2 C:HIS102 2.3 58.8 1.0
SD C:MET7 2.4 66.1 1.0
C4D C:HEM201 2.9 66.0 1.0
C1D C:HEM201 2.9 64.3 1.0
C1A C:HEM201 3.0 67.6 1.0
C4A C:HEM201 3.0 67.0 1.0
C4B C:HEM201 3.1 62.3 1.0
C1B C:HEM201 3.1 64.2 1.0
C4C C:HEM201 3.1 61.7 1.0
C1C C:HEM201 3.1 61.6 1.0
CD2 C:HIS102 3.2 59.3 1.0
CE1 C:HIS102 3.3 59.3 1.0
CE C:MET7 3.4 66.1 1.0
CHA C:HEM201 3.4 66.7 1.0
CHD C:HEM201 3.4 62.8 1.0
CHB C:HEM201 3.4 65.6 1.0
CHC C:HEM201 3.5 62.0 1.0
CG C:MET7 3.6 66.2 1.0
C3D C:HEM201 4.2 67.2 1.0
C2D C:HEM201 4.2 65.5 1.0
C2A C:HEM201 4.2 70.0 1.0
C3A C:HEM201 4.2 68.9 1.0
C2B C:HEM201 4.3 63.1 1.0
C2C C:HEM201 4.3 61.4 1.0
CB C:MET7 4.3 66.2 1.0
C3C C:HEM201 4.3 61.0 1.0
C3B C:HEM201 4.3 62.3 1.0
CG C:HIS102 4.4 60.6 1.0
ND1 C:HIS102 4.4 60.0 1.0

Iron binding site 4 out of 4 in 4u9d

Go back to Iron Binding Sites List in 4u9d
Iron binding site 4 out of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3


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-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:0.0
occ:1.00
FE D:HEM201 0.0 0.0 1.0
ND D:HEM201 1.9 0.0 1.0
NA D:HEM201 2.0 0.0 1.0
NC D:HEM201 2.1 0.0 1.0
NB D:HEM201 2.1 0.0 1.0
NE2 D:HIS102 2.4 90.9 1.0
SD D:MET7 2.6 0.0 1.0
C4D D:HEM201 2.9 0.0 1.0
C1D D:HEM201 2.9 0.0 1.0
C1A D:HEM201 3.0 0.0 1.0
C4A D:HEM201 3.0 0.0 1.0
C4B D:HEM201 3.1 0.0 1.0
C1B D:HEM201 3.1 0.0 1.0
C4C D:HEM201 3.1 0.0 1.0
C1C D:HEM201 3.1 0.0 1.0
CD2 D:HIS102 3.3 92.3 1.0
CHA D:HEM201 3.4 0.0 1.0
CHD D:HEM201 3.4 0.0 1.0
CE1 D:HIS102 3.4 91.1 1.0
CHB D:HEM201 3.4 0.0 1.0
CHC D:HEM201 3.5 0.0 1.0
CE D:MET7 3.6 0.0 1.0
CG D:MET7 3.8 0.0 1.0
C3D D:HEM201 4.2 0.0 1.0
C2D D:HEM201 4.2 0.0 1.0
C2A D:HEM201 4.2 0.0 1.0
C3A D:HEM201 4.2 0.0 1.0
C3C D:HEM201 4.3 0.0 1.0
C2C D:HEM201 4.3 0.0 1.0
C2B D:HEM201 4.3 0.0 1.0
C3B D:HEM201 4.3 0.0 1.0
CB D:MET7 4.4 0.0 1.0
CG D:HIS102 4.5 93.6 1.0
ND1 D:HIS102 4.5 91.4 1.0

Reference:

W.J.Song, F.A.Tezcan. A Designed Supramolecular Protein Assembly with in Vivo Enzymatic Activity. Science V. 346 1525 2014.
ISSN: ESSN 1095-9203
PubMed: 25525249
DOI: 10.1126/SCIENCE.1259680
Page generated: Sun Dec 13 15:47:53 2020

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