Copper in PDB 5cj3: Crystal Structure of the Zorbamycin Binding Protein (Zbma) From Streptomyces Flavoviridis with Zorbamycin

The structure of Crystal Structure of the Zorbamycin Binding Protein (Zbma) From Streptomyces Flavoviridis with Zorbamycin, PDB code: 5cj3 was solved by C.Chang, L.Bigelow, S.Clancy, G.Babnigg, A.Joachimiak, Midwest Center Forstructural Genomics (Mcsg), J.D.Rudolf, M.Ma, C.-Y.Chang, J.R.Lohman, D.Yang, B.Shen, Enzyme Discovery For Natural Product Biosynthesis, Enzyme Discovery For Natural Product Biosynthesis (Natpro), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.52 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.737, 78.989, 79.542, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.3

The structure of Crystal Structure of the Zorbamycin Binding Protein (Zbma) From Streptomyces Flavoviridis with Zorbamycin also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Copper atom in the Crystal Structure of the Zorbamycin Binding Protein (Zbma) From Streptomyces Flavoviridis with Zorbamycin (pdb code 5cj3). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Crystal Structure of the Zorbamycin Binding Protein (Zbma) From Streptomyces Flavoviridis with Zorbamycin, PDB code: 5cj3:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the Crystal Structure of the Zorbamycin Binding Protein (Zbma) From Streptomyces Flavoviridis with Zorbamycin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of the Zorbamycin Binding Protein (Zbma) From Streptomyces Flavoviridis with Zorbamycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu202 b:18.0 occ:1.00 NJ A:52G201 1.9 16.3 0.5 NJ A:52G201 1.9 14.3 0.6 NG A:52G201 2.0 7.5 0.5 NG A:52G201 2.0 6.9 0.6 NH A:52G201 2.2 11.9 0.6 NH A:52G201 2.2 11.9 0.5 NB A:52G201 2.2 23.3 0.6 NB A:52G201 2.3 23.6 0.5 NC A:52G201 2.3 13.8 0.5 NC A:52G201 2.3 12.7 0.6 C10 A:52G201 2.8 10.6 0.5 C10 A:52G201 2.8 10.7 0.6 C27 A:52G201 2.9 18.1 0.6 C27 A:52G201 2.9 17.6 0.5 C7 A:52G201 2.9 9.6 0.5 C7 A:52G201 2.9 9.9 0.6 C12 A:52G201 2.9 11.9 0.5 C12 A:52G201 2.9 12.0 0.6 C29 A:52G201 3.0 20.1 0.5 C2 A:52G201 3.0 28.5 0.6 C29 A:52G201 3.0 20.1 0.6 C3 A:52G201 3.0 18.9 0.6 C6 A:52G201 3.0 10.8 0.6 C2 A:52G201 3.0 27.8 0.5 C6 A:52G201 3.0 10.8 0.5 C3 A:52G201 3.1 19.7 0.5 CL A:CL203 3.1 33.4 1.0 C13 A:52G201 3.2 11.8 0.6 C13 A:52G201 3.2 11.9 0.5 C14 A:52G201 3.3 12.1 0.6 C14 A:52G201 3.3 12.8 0.5 OH1 A:52G201 3.4 15.0 0.6 OH1 A:52G201 3.4 14.9 0.5 C1 A:52G201 3.5 35.5 0.6 C1 A:52G201 3.5 35.4 0.5 O1 A:52G201 3.8 39.4 0.6 NK A:52G201 3.9 13.1 0.5 NK A:52G201 3.9 13.3 0.6 O1 A:52G201 4.0 38.5 0.5 C28 A:52G201 4.0 20.1 0.5 C28 A:52G201 4.0 20.2 0.6 C30 A:52G201 4.0 16.7 0.6 NI A:52G201 4.1 20.7 0.5 C30 A:52G201 4.1 16.5 0.5 NI A:52G201 4.1 20.9 0.6 NA A:52G201 4.1 35.1 0.5 C9 A:52G201 4.1 8.4 0.5 NE A:52G201 4.1 7.7 0.5 NE A:52G201 4.1 7.3 0.6 C9 A:52G201 4.1 8.6 0.6 O12 A:52G201 4.1 10.9 0.5 O12 A:52G201 4.1 10.6 0.6 NA A:52G201 4.2 34.2 0.6 C5 A:52G201 4.4 10.6 0.5 C5 A:52G201 4.5 11.9 0.6 C8 A:52G201 4.6 9.2 0.5 C8 A:52G201 4.6 9.3 0.6 O A:HOH313 4.7 18.7 1.0 O58 A:52G201 4.7 21.1 0.6 O58 A:52G201 4.7 21.6 0.5 C63 A:52G201 4.8 19.4 0.6 C63 A:52G201 4.8 19.1 0.5 C34 A:52G201 5.0 26.2 0.5

Copper binding site 2 out of 2 in the Crystal Structure of the Zorbamycin Binding Protein (Zbma) From Streptomyces Flavoviridis with Zorbamycin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of the Zorbamycin Binding Protein (Zbma) From Streptomyces Flavoviridis with Zorbamycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu202 b:19.3 occ:1.00 NG B:52G201 2.0 8.0 0.5 NG B:52G201 2.0 7.6 0.5 NJ B:52G201 2.0 11.9 0.5 NJ B:52G201 2.0 14.6 0.5 NH B:52G201 2.1 14.3 0.5 NH B:52G201 2.1 14.8 0.5 NC B:52G201 2.3 14.6 0.5 NC B:52G201 2.4 15.8 0.5 NB B:52G201 2.4 19.8 0.5 NB B:52G201 2.6 24.1 0.5 C10 B:52G201 2.8 9.4 0.5 C10 B:52G201 2.8 9.8 0.5 C12 B:52G201 2.9 10.2 0.5 C27 B:52G201 2.9 15.2 0.5 C7 B:52G201 2.9 10.6 0.5 C27 B:52G201 2.9 15.8 0.5 C7 B:52G201 2.9 10.5 0.5 C12 B:52G201 2.9 11.0 0.5 C6 B:52G201 3.0 12.1 0.5 C6 B:52G201 3.1 12.2 0.5 C29 B:52G201 3.1 18.2 0.5 CL B:CL203 3.1 34.8 1.0 C29 B:52G201 3.1 20.1 0.5 C2 B:52G201 3.2 19.4 0.5 C3 B:52G201 3.2 17.4 0.5 C13 B:52G201 3.2 16.0 0.5 C13 B:52G201 3.2 16.2 0.5 C14 B:52G201 3.3 17.4 0.5 C14 B:52G201 3.3 18.0 0.5 OH1 B:52G201 3.4 21.2 0.5 C3 B:52G201 3.4 18.2 0.5 OH1 B:52G201 3.4 20.5 0.5 C2 B:52G201 3.5 18.6 0.5 C1 B:52G201 3.5 26.8 0.5 C1 B:52G201 3.7 27.5 0.5 NA B:52G201 3.8 22.4 0.5 NK B:52G201 3.9 17.6 0.5 O1 B:52G201 3.9 32.1 0.5 NK B:52G201 4.0 17.2 0.5 C28 B:52G201 4.0 21.4 0.5 C30 B:52G201 4.1 19.8 0.5 C28 B:52G201 4.1 21.4 0.5 C30 B:52G201 4.1 20.3 0.5 O1 B:52G201 4.1 33.4 0.5 C9 B:52G201 4.1 10.4 0.5 O12 B:52G201 4.1 13.8 0.5 NI B:52G201 4.1 23.0 0.5 C9 B:52G201 4.1 10.1 0.5 O12 B:52G201 4.1 13.1 0.5 NE B:52G201 4.1 9.6 0.5 NE B:52G201 4.1 8.9 0.5 NI B:52G201 4.2 23.2 0.5 NA B:52G201 4.3 24.2 0.5 C5 B:52G201 4.4 13.2 0.5 C5 B:52G201 4.5 12.9 0.5 O58 B:52G201 4.5 27.3 0.5 O B:HOH329 4.6 16.4 1.0 C8 B:52G201 4.6 8.3 0.5 C8 B:52G201 4.6 8.9 0.5 C63 B:52G201 4.8 23.6 0.5 C63 B:52G201 4.8 23.6 0.5 O58 B:52G201 4.9 19.2 0.5

J.D.Rudolf, L.Bigelow, C.Chang, M.E.Cuff, J.R.Lohman, C.Y.Chang, M.Ma, D.Yang, S.Clancy, G.Babnigg, A.Joachimiak, G.N.Phillips, B.Shen. Crystal Structure of the Zorbamycin-Binding Protein Zbma, the Primary Self-Resistance Element in Streptomyces Flavoviridis ATCC21892. Biochemistry V. 54 6842 2015.
ISSN: ISSN 0006-2960
PubMed: 26512730
DOI: 10.1021/ACS.BIOCHEM.5B01008