Zinc in PDB 6ds9: Elongated Version of A De Novo Designed Three Helix Bundle Structure (GRA3D)

The structure of Elongated Version of A De Novo Designed Three Helix Bundle Structure (GRA3D), PDB code: 6ds9 was solved by K.J.Koebke, L.R.Ruckthong, J.L.Meagher, J.A.Stuckey, V.L.Pecoraro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.23 / 1.34
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	46.396, 46.396, 109.303, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 18.6

The structure of Elongated Version of A De Novo Designed Three Helix Bundle Structure (GRA3D) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Elongated Version of A De Novo Designed Three Helix Bundle Structure (GRA3D) (pdb code 6ds9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Elongated Version of A De Novo Designed Three Helix Bundle Structure (GRA3D), PDB code: 6ds9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Elongated Version of A De Novo Designed Three Helix Bundle Structure (GRA3D)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Elongated Version of A De Novo Designed Three Helix Bundle Structure (GRA3D) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:9.9 occ:0.22 OE2 A:GLU6 2.0 14.3 1.0 O A:HOH233 2.2 23.8 0.3 CD A:GLU6 2.7 15.3 1.0 OE1 A:GLU6 2.7 18.7 1.0 HH11 A:ARG10 3.8 8.9 1.0 CG A:GLU6 4.1 14.0 1.0 NH1 A:ARG10 4.3 12.2 1.0 HA2 A:GLY2 4.4 42.5 1.0 HG3 A:GLU6 4.4 15.6 1.0 HH12 A:ARG10 4.4 10.4 1.0 HG2 A:GLU6 4.5 12.4 1.0 HD2 A:ARG10 4.5 10.2 1.0

Zinc binding site 2 out of 2 in the Elongated Version of A De Novo Designed Three Helix Bundle Structure (GRA3D)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Elongated Version of A De Novo Designed Three Helix Bundle Structure (GRA3D) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:31.6 occ:0.20 N A:SCN104 1.9 40.2 0.2 N A:SCN103 2.1 29.4 0.7 C A:SCN103 3.0 29.6 0.7 C A:SCN104 3.1 42.1 0.2 HB2 A:ALA27 3.3 19.7 1.0 HB1 A:ALA27 3.7 29.2 1.0 CB A:ALA27 3.9 24.1 1.0 HG2 A:ARG24 3.9 10.9 1.0 HB3 A:ALA27 4.2 26.5 1.0 HE A:ARG24 4.5 10.4 1.0 S A:SCN103 4.7 31.3 0.7 S A:SCN104 4.9 44.1 0.2 HA A:ARG24 5.0 4.6 1.0 CG A:ARG24 5.0 14.3 1.0

K.J.Koebke, L.Ruckthong, J.L.Meagher, E.Mathieu, J.Harland, A.Deb, N.Lehnert, C.Policar, C.Tard, J.E.Penner-Hahn, J.A.Stuckey, V.L.Pecoraro. Clarifying the Copper Coordination Environment in A De Novo Designed Red Copper Protein. Inorg Chem V. 57 12291 2018.
ISSN: ISSN 1520-510X
PubMed: 30226758
DOI: 10.1021/ACS.INORGCHEM.8B01989