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Iron in PDB 6ldg: Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I AB5

Protein crystallography data

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I AB5, PDB code: 6ldg was solved by W.J.Song, J.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.38 / 1.98
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 53.723, 53.723, 250.757, 90, 90, 120
R / Rfree (%) 16.8 / 22.1

Other elements in 6ldg:

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I AB5 also contains other interesting chemical elements:

Zinc (Zn) 7 atoms
Magnesium (Mg) 2 atoms
Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I AB5 (pdb code 6ldg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I AB5, PDB code: 6ldg:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6ldg

Go back to Iron Binding Sites List in 6ldg
Iron binding site 1 out of 2 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I 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 Cb 562 Variant, C96I AB5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:10.3
occ:1.00
FE A:HEC201 0.0 10.3 1.0
ND A:HEC201 1.9 10.3 1.0
NE2 A:HIS102 2.0 10.3 1.0
NA A:HEC201 2.0 10.7 1.0
NC A:HEC201 2.0 9.3 1.0
NB A:HEC201 2.1 9.1 1.0
SD A:MET7 2.3 10.4 1.0
C4D A:HEC201 2.9 11.4 1.0
C1D A:HEC201 3.0 10.8 1.0
CD2 A:HIS102 3.0 10.7 1.0
CE1 A:HIS102 3.0 10.5 1.0
C4B A:HEC201 3.0 9.7 1.0
C1C A:HEC201 3.0 9.6 1.0
C1A A:HEC201 3.1 11.2 1.0
C4C A:HEC201 3.1 9.9 1.0
C1B A:HEC201 3.1 9.5 1.0
C4A A:HEC201 3.1 10.8 1.0
CE A:MET7 3.3 11.3 1.0
CHC A:HEC201 3.4 9.3 1.0
CG A:MET7 3.4 10.8 1.0
CHA A:HEC201 3.4 11.5 1.0
CHD A:HEC201 3.4 9.9 1.0
CHB A:HEC201 3.5 9.9 1.0
ND1 A:HIS102 4.1 10.0 1.0
CG A:HIS102 4.1 11.1 1.0
C3D A:HEC201 4.2 12.6 1.0
C2D A:HEC201 4.2 11.6 1.0
CB A:MET7 4.3 11.4 1.0
C2C A:HEC201 4.3 9.0 1.0
C2A A:HEC201 4.3 12.7 1.0
C3C A:HEC201 4.3 9.3 1.0
C2B A:HEC201 4.3 9.6 1.0
C3A A:HEC201 4.3 11.4 1.0
C3B A:HEC201 4.3 9.5 1.0
NH2 A:ARG106 4.7 18.9 1.0

Iron binding site 2 out of 2 in 6ldg

Go back to Iron Binding Sites List in 6ldg
Iron binding site 2 out of 2 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I 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 Cb 562 Variant, C96I AB5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:11.6
occ:1.00
FE C:HEC201 0.0 11.6 1.0
ND C:HEC201 1.9 11.3 1.0
NE2 C:HIS102 2.0 9.4 1.0
NA C:HEC201 2.0 12.4 1.0
NB C:HEC201 2.1 10.8 1.0
NC C:HEC201 2.1 10.9 1.0
SD C:MET7 2.3 13.3 1.0
C4D C:HEC201 2.9 13.4 1.0
CE1 C:HIS102 3.0 10.8 1.0
C1A C:HEC201 3.0 13.1 1.0
C1D C:HEC201 3.0 11.9 1.0
C4B C:HEC201 3.0 12.0 1.0
CD2 C:HIS102 3.0 10.8 1.0
C4A C:HEC201 3.1 13.1 1.0
C1C C:HEC201 3.1 11.0 1.0
C4C C:HEC201 3.1 11.3 1.0
C1B C:HEC201 3.1 11.4 1.0
CE C:MET7 3.3 14.1 1.0
CHC C:HEC201 3.3 11.2 1.0
CHA C:HEC201 3.4 13.5 1.0
CG C:MET7 3.4 14.1 1.0
CHD C:HEC201 3.5 11.5 1.0
CHB C:HEC201 3.5 11.7 1.0
ND1 C:HIS102 4.1 11.2 1.0
CB C:MET7 4.1 14.4 1.0
CG C:HIS102 4.1 10.7 1.0
C2A C:HEC201 4.2 15.5 1.0
C3D C:HEC201 4.2 14.5 1.0
C3A C:HEC201 4.2 14.1 1.0
C2D C:HEC201 4.2 12.8 1.0
C2B C:HEC201 4.3 11.8 1.0
C2C C:HEC201 4.3 10.4 1.0
C3B C:HEC201 4.3 11.8 1.0
C3C C:HEC201 4.3 10.9 1.0
CA C:MET7 5.0 15.5 1.0

Reference:

J.Yu, J.Yang, C.Seok, W.J.Song. Symmetry-Related Residues As Promising Hotspots For the Evolution of De Novo Oligomeric Enzymes Chem Sci 2021.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC06823C
Page generated: Wed Aug 7 00:54:00 2024

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