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Zinc in PDB 3m15: A Zn-Mediated Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1)

Protein crystallography data

The structure of A Zn-Mediated Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1), PDB code: 3m15 was solved by F.A.Tezcan, T.W.Ni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.90 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.879, 74.819, 81.358, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 31.3

Other elements in 3m15:

The structure of A Zn-Mediated Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1) also contains other interesting chemical elements:

Iron (Fe) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the A Zn-Mediated Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1) (pdb code 3m15). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the A Zn-Mediated Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1), PDB code: 3m15:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3m15

Go back to Zinc Binding Sites List in 3m15
Zinc binding site 1 out of 2 in the A Zn-Mediated Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Zn-Mediated Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn107

b:17.6
occ:1.00
NE2 A:HIS77 1.9 10.8 1.0
NE2 C:HIS59 2.0 10.9 1.0
NE2 A:HIS73 2.3 13.2 1.0
NE2 B:HIS59 2.4 19.4 1.0
CD2 A:HIS77 2.8 11.4 1.0
CE1 B:HIS59 2.9 17.1 1.0
CD2 C:HIS59 2.9 10.8 1.0
CE1 A:HIS77 3.0 10.6 1.0
CE1 C:HIS59 3.0 10.4 1.0
CD2 A:HIS73 3.0 13.0 1.0
CE1 A:HIS73 3.3 14.3 1.0
CD2 B:HIS59 3.6 19.3 1.0
CG A:HIS77 4.0 12.2 1.0
ND1 B:HIS59 4.0 18.1 1.0
ND1 A:HIS77 4.0 11.5 1.0
CG C:HIS59 4.1 11.7 1.0
ND1 C:HIS59 4.1 10.6 1.0
CG A:HIS73 4.2 12.8 1.0
ND1 A:HIS73 4.3 13.6 1.0
CG B:HIS59 4.4 18.3 1.0
CD2 B:HIS63 4.6 9.1 1.0
NE2 B:HIS63 5.0 11.8 1.0

Zinc binding site 2 out of 2 in 3m15

Go back to Zinc Binding Sites List in 3m15
Zinc binding site 2 out of 2 in the A Zn-Mediated Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Zn-Mediated Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn107

b:12.2
occ:1.00
NE2 B:HIS77 1.9 7.9 1.0
NE2 A:HIS59 2.0 10.6 1.0
NE2 C:HIS77 2.0 8.4 1.0
NE2 B:HIS73 2.1 7.2 1.0
CE1 B:HIS77 2.7 7.8 1.0
CE1 C:HIS77 2.9 8.0 1.0
CD2 A:HIS59 3.0 10.3 1.0
CE1 A:HIS59 3.0 9.7 1.0
CD2 B:HIS77 3.0 6.2 1.0
CD2 C:HIS77 3.0 9.2 1.0
CD2 B:HIS73 3.0 6.6 1.0
CE1 B:HIS73 3.1 8.1 1.0
ND1 B:HIS77 3.9 9.1 1.0
ND1 C:HIS77 4.0 9.5 1.0
CG B:HIS77 4.0 7.5 1.0
ND1 A:HIS59 4.1 9.7 1.0
CG A:HIS59 4.1 9.6 1.0
CG C:HIS77 4.1 10.1 1.0
ND1 B:HIS73 4.2 7.7 1.0
CG B:HIS73 4.2 5.2 1.0

Reference:

T.W.Ni, F.A.Tezcan. Structural Characterization of A Microperoxidase Inside A Metal-Directed Protein Cage. Angew.Chem.Int.Ed.Engl. V. 49 7014 2010.
ISSN: ISSN 1433-7851
PubMed: 20721993
DOI: 10.1002/ANIE.201001487
Page generated: Wed Dec 16 04:33:37 2020

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