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Iron in PDB 5xzj: Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5

Protein crystallography data

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5, PDB code: 5xzj was solved by W.J.Song, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.89 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.747, 63.481, 127.785, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.7

Other elements in 5xzj:

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 14 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, C96T/AB5 (pdb code 5xzj). 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, C96T/AB5, PDB code: 5xzj:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5xzj

Go back to Iron Binding Sites List in 5xzj
Iron binding site 1 out of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5


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, C96T/AB5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:27.2
occ:1.00
FE A:HEC201 0.0 27.2 1.0
ND A:HEC201 1.9 27.8 1.0
NA A:HEC201 2.0 28.3 1.0
NB A:HEC201 2.1 25.6 1.0
NE2 A:HIS102 2.1 29.7 1.0
NC A:HEC201 2.1 26.2 1.0
SD A:MET7 2.3 27.8 1.0
C4D A:HEC201 3.0 30.8 1.0
C1D A:HEC201 3.0 29.7 1.0
C1A A:HEC201 3.0 29.5 1.0
CE1 A:HIS102 3.1 31.3 1.0
C4B A:HEC201 3.1 26.2 1.0
C4A A:HEC201 3.1 27.8 1.0
C1B A:HEC201 3.1 27.0 1.0
C4C A:HEC201 3.1 27.3 1.0
C1C A:HEC201 3.1 26.3 1.0
CD2 A:HIS102 3.1 29.2 1.0
CE A:MET7 3.4 29.2 1.0
CHA A:HEC201 3.4 30.9 1.0
CG A:MET7 3.5 26.3 1.0
CHB A:HEC201 3.5 28.4 1.0
CHC A:HEC201 3.5 25.4 1.0
CHD A:HEC201 3.5 26.9 1.0
ND1 A:HIS102 4.2 29.7 1.0
CB A:MET7 4.2 26.8 1.0
C3D A:HEC201 4.3 31.8 1.0
C2D A:HEC201 4.3 30.0 1.0
C2A A:HEC201 4.3 33.8 1.0
CG A:HIS102 4.3 28.9 1.0
C3A A:HEC201 4.3 29.3 1.0
C2B A:HEC201 4.3 26.6 1.0
C2C A:HEC201 4.3 25.2 1.0
C3C A:HEC201 4.4 25.4 1.0
C3B A:HEC201 4.4 24.8 1.0
NH2 A:ARG106 4.8 68.1 1.0

Iron binding site 2 out of 4 in 5xzj

Go back to Iron Binding Sites List in 5xzj
Iron binding site 2 out of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5


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, C96T/AB5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:25.9
occ:1.00
FE B:HEC201 0.0 25.9 1.0
ND B:HEC201 1.9 27.1 1.0
NA B:HEC201 2.0 30.0 1.0
NE2 B:HIS102 2.0 25.9 1.0
NC B:HEC201 2.1 26.1 1.0
NB B:HEC201 2.1 26.3 1.0
SD B:MET7 2.3 26.6 1.0
C1D B:HEC201 3.0 26.5 1.0
C4D B:HEC201 3.0 28.1 1.0
CE1 B:HIS102 3.0 26.4 1.0
C1A B:HEC201 3.0 29.1 1.0
C4A B:HEC201 3.1 29.6 1.0
CD2 B:HIS102 3.1 29.0 1.0
C4B B:HEC201 3.1 26.5 1.0
C4C B:HEC201 3.1 25.6 1.0
C1B B:HEC201 3.1 27.8 1.0
C1C B:HEC201 3.1 26.7 1.0
CE B:MET7 3.4 26.9 1.0
CHA B:HEC201 3.4 28.8 1.0
CHD B:HEC201 3.4 25.0 1.0
CHB B:HEC201 3.5 27.7 1.0
CHC B:HEC201 3.5 25.0 1.0
CG B:MET7 3.5 27.2 1.0
ND1 B:HIS102 4.1 26.6 1.0
CG B:HIS102 4.2 26.6 1.0
C2D B:HEC201 4.2 28.3 1.0
C3A B:HEC201 4.2 32.7 1.0
C2A B:HEC201 4.3 34.8 1.0
C3D B:HEC201 4.3 29.5 1.0
CB B:MET7 4.3 26.6 1.0
C2C B:HEC201 4.4 24.3 1.0
C3C B:HEC201 4.4 24.5 1.0
C2B B:HEC201 4.4 27.4 1.0
C3B B:HEC201 4.4 24.9 1.0

Iron binding site 3 out of 4 in 5xzj

Go back to Iron Binding Sites List in 5xzj
Iron binding site 3 out of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5


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, C96T/AB5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:30.0
occ:1.00
FE C:HEC201 0.0 30.0 1.0
ND C:HEC201 1.9 30.8 1.0
NA C:HEC201 2.0 33.6 1.0
NE2 C:HIS102 2.1 30.4 1.0
NC C:HEC201 2.1 27.8 1.0
NB C:HEC201 2.1 31.1 1.0
SD C:MET7 2.3 31.8 1.0
C4D C:HEC201 3.0 34.2 1.0
C1D C:HEC201 3.0 31.5 1.0
C1A C:HEC201 3.0 35.2 1.0
CE1 C:HIS102 3.0 30.5 1.0
C4B C:HEC201 3.1 30.7 1.0
C4A C:HEC201 3.1 34.5 1.0
C1B C:HEC201 3.1 31.7 1.0
C1C C:HEC201 3.1 29.0 1.0
CD2 C:HIS102 3.1 28.8 1.0
C4C C:HEC201 3.1 29.6 1.0
CHA C:HEC201 3.4 33.4 1.0
CHC C:HEC201 3.4 29.1 1.0
CHD C:HEC201 3.5 30.4 1.0
CE C:MET7 3.5 31.7 1.0
CHB C:HEC201 3.5 32.2 1.0
CG C:MET7 3.5 33.7 1.0
ND1 C:HIS102 4.2 28.4 1.0
CG C:HIS102 4.2 28.1 1.0
C2A C:HEC201 4.3 38.0 1.0
C2D C:HEC201 4.3 32.9 1.0
C3D C:HEC201 4.3 34.1 1.0
C3A C:HEC201 4.3 36.5 1.0
CB C:MET7 4.3 32.4 1.0
C2B C:HEC201 4.3 31.7 1.0
C2C C:HEC201 4.3 27.9 1.0
C3B C:HEC201 4.4 29.6 1.0
C3C C:HEC201 4.4 27.4 1.0

Iron binding site 4 out of 4 in 5xzj

Go back to Iron Binding Sites List in 5xzj
Iron binding site 4 out of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5


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, C96T/AB5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:38.3
occ:1.00
FE D:HEC201 0.0 38.3 1.0
ND D:HEC201 1.9 37.8 1.0
NA D:HEC201 2.0 40.2 1.0
NB D:HEC201 2.1 35.8 1.0
NC D:HEC201 2.1 37.8 1.0
NE2 D:HIS102 2.1 28.1 1.0
SD D:MET7 2.4 39.4 1.0
C4D D:HEC201 2.9 39.5 1.0
C1D D:HEC201 3.0 38.5 1.0
C1A D:HEC201 3.0 41.8 1.0
CD2 D:HIS102 3.0 30.6 1.0
C4B D:HEC201 3.1 35.6 1.0
C4A D:HEC201 3.1 41.5 1.0
C1B D:HEC201 3.1 38.0 1.0
C1C D:HEC201 3.1 36.0 1.0
C4C D:HEC201 3.1 37.9 1.0
CE1 D:HIS102 3.1 30.3 1.0
CHA D:HEC201 3.4 40.0 1.0
CE D:MET7 3.4 39.6 1.0
CHC D:HEC201 3.4 34.8 1.0
CHD D:HEC201 3.4 38.6 1.0
CHB D:HEC201 3.5 40.2 1.0
CG D:MET7 3.5 41.8 1.0
C2D D:HEC201 4.2 38.7 1.0
CG D:HIS102 4.2 31.8 1.0
C3D D:HEC201 4.2 40.1 1.0
ND1 D:HIS102 4.2 29.8 1.0
C2A D:HEC201 4.2 46.3 1.0
C3A D:HEC201 4.3 44.8 1.0
C2C D:HEC201 4.3 37.7 1.0
CB D:MET7 4.3 38.3 1.0
C2B D:HEC201 4.3 35.6 1.0
C3C D:HEC201 4.3 37.6 1.0
C3B D:HEC201 4.3 34.4 1.0

Reference:

W.J.Song, J.Yu, F.A.Tezcan. Importance of Scaffold Flexibility/Rigidity in the Design and Directed Evolution of Artificial Metallo-Beta-Lactamases. J. Am. Chem. Soc. V. 139 16772 2017.
ISSN: ESSN 1520-5126
PubMed: 28992705
DOI: 10.1021/JACS.7B08981
Page generated: Tue Aug 6 12:36:34 2024

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