Zinc in PDB 7x9x: Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn

All present enzymatic activity of Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn:
1.16.3.2;

The structure of Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn, PDB code: 7x9x was solved by Y.Liu, G.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.56 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.5, 66.62, 92.34, 90, 90, 90
R / Rfree (%)	19 / 25.1

The structure of Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Zinc atom in the Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn (pdb code 7x9x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn, PDB code: 7x9x:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:32.9 occ:0.74 OE2 B:GLU128 2.1 30.0 1.0 OE2 A:GLU128 2.1 34.5 1.0 OE2 A:GLU131 2.1 29.3 1.0 OE2 B:GLU131 2.1 37.6 1.0 OE1 A:GLU128 2.7 35.6 1.0 CD A:GLU128 2.7 35.4 1.0 CD B:GLU128 2.8 34.4 1.0 OE1 B:GLU128 2.9 34.7 1.0 CD A:GLU131 3.1 36.5 1.0 CD B:GLU131 3.1 37.1 1.0 OE1 A:GLU131 3.4 32.0 1.0 OE1 B:GLU131 3.4 28.2 1.0 O B:HOH307 3.8 36.8 1.0 O A:HOH309 3.9 32.2 1.0 HA B:GLU128 4.2 33.9 1.0 ZN B:ZN202 4.2 27.9 0.5 ZN A:ZN203 4.2 23.8 0.5 CG A:GLU128 4.3 32.1 1.0 CG B:GLU128 4.3 33.9 1.0 HA A:GLU128 4.3 32.0 1.0 HB3 B:GLU131 4.3 38.1 1.0 CG B:GLU131 4.4 34.2 1.0 CG A:GLU131 4.4 34.3 1.0 HB3 A:GLU131 4.5 31.9 1.0 HB2 B:GLU128 4.6 33.4 1.0 HG2 B:GLU131 4.6 41.1 1.0 HG2 A:GLU128 4.6 38.6 1.0 HG2 B:GLU128 4.7 40.7 1.0 HG2 A:GLU131 4.7 41.2 1.0 HG3 A:GLU128 4.8 38.6 1.0 HB2 A:GLU128 4.8 29.8 1.0 HG3 B:GLU128 4.8 40.7 1.0 CB B:GLU131 4.8 31.7 1.0 CB B:GLU128 4.8 27.8 1.0 HE22 A:GLN135 4.9 63.8 1.0 HB2 B:GLU131 4.9 38.1 1.0 CB A:GLU128 5.0 24.8 1.0 CB A:GLU131 5.0 26.5 1.0 CA B:GLU128 5.0 28.2 1.0

Zinc binding site 2 out of 5 in the Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:56.1 occ:0.64 OE1 B:GLU138 1.8 47.7 1.0 OE1 A:GLU40 2.2 54.6 1.0 ND1 A:HIS43 2.3 40.0 1.0 CD B:GLU138 2.5 52.8 1.0 OE2 B:GLU138 2.8 57.7 1.0 CE1 A:HIS43 3.1 44.2 1.0 HE1 A:HIS43 3.2 53.1 1.0 HB3 A:HIS43 3.2 40.8 1.0 CD A:GLU40 3.3 59.4 1.0 CG A:HIS43 3.4 37.0 1.0 HE1 A:TRP44 3.6 46.4 1.0 CB A:HIS43 3.7 34.0 1.0 HD1 A:TRP44 3.8 42.4 1.0 CG B:GLU138 3.9 55.4 1.0 OE2 A:GLU40 3.9 69.0 1.0 HG2 B:GLU138 4.0 66.5 1.0 HB2 A:HIS43 4.0 40.8 1.0 HA A:GLU40 4.0 48.1 1.0 NE1 A:TRP44 4.2 38.6 1.0 HG3 B:GLU138 4.2 66.5 1.0 CD1 A:TRP44 4.3 35.3 1.0 NE2 A:HIS43 4.3 45.1 1.0 CD2 A:HIS43 4.4 39.8 1.0 CG A:GLU40 4.5 44.5 1.0 HG3 A:GLU40 4.6 53.5 1.0 HB3 A:GLU40 4.6 44.2 1.0 HD21 B:LEU142 4.7 56.4 1.0 O A:GLU40 4.7 30.5 1.0 HZ3 A:LYS47 4.8 82.0 1.0 HA B:GLU138 4.8 50.4 1.0 CA A:GLU40 4.9 40.0 1.0 CB A:GLU40 4.9 36.8 1.0 HD2 A:LYS47 5.0 65.8 1.0

Zinc binding site 3 out of 5 in the Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:23.8 occ:0.50 OE1 A:GLU128 2.2 35.6 1.0 O A:HOH309 2.3 32.2 1.0 OE1 B:GLU131 2.3 28.2 1.0 OE2 A:GLU51 2.4 36.5 1.0 O A:HOH307 2.4 32.1 1.0 OE1 A:GLU51 2.5 33.9 1.0 OE2 A:GLU132 2.5 36.1 1.0 CD A:GLU51 2.8 29.8 1.0 HG2 A:GLU132 2.9 45.1 1.0 HG3 A:GLU132 3.3 45.1 1.0 CD A:GLU132 3.3 41.9 1.0 CG A:GLU132 3.3 37.5 1.0 CD A:GLU128 3.4 35.4 1.0 CD B:GLU131 3.4 37.1 1.0 HE22 A:GLN48 3.6 41.0 1.0 HG3 A:GLU128 3.9 38.6 1.0 OE2 B:GLU131 4.0 37.6 1.0 CG A:GLU128 4.1 32.1 1.0 OE2 A:GLU131 4.1 29.3 1.0 ZN A:ZN201 4.2 32.9 0.7 HG2 A:GLU128 4.2 38.6 1.0 HE2 A:HIS55 4.3 48.4 1.0 OE2 A:GLU128 4.3 34.5 1.0 CG A:GLU51 4.3 27.8 1.0 OE1 A:GLN48 4.4 24.5 1.0 NE2 A:GLN48 4.4 34.1 1.0 HE22 A:GLN135 4.5 63.8 1.0 HG3 B:GLU131 4.5 41.1 1.0 HE1 A:HIS55 4.5 48.8 1.0 OE1 A:GLU132 4.5 38.1 1.0 CG B:GLU131 4.6 34.2 1.0 HG3 A:GLU51 4.7 33.4 1.0 OE1 A:GLN135 4.7 43.7 1.0 HG2 A:GLU51 4.7 33.4 1.0 CD A:GLN48 4.8 27.5 1.0 CB A:GLU132 4.8 36.0 1.0 NE2 A:HIS55 4.9 40.3 1.0

Zinc binding site 4 out of 5 in the Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:47.1 occ:0.66 OE1 A:GLU138 2.0 56.2 1.0 OE1 B:GLU40 2.0 54.0 1.0 ND1 B:HIS43 2.4 44.9 1.0 CD A:GLU138 2.7 50.2 1.0 OE2 A:GLU138 2.7 55.3 1.0 CD B:GLU40 3.0 54.4 1.0 OE2 B:GLU40 3.2 55.3 1.0 CE1 B:HIS43 3.2 51.3 1.0 HB3 B:HIS43 3.3 44.8 1.0 HE1 B:HIS43 3.3 61.6 1.0 CG B:HIS43 3.4 40.2 1.0 CB B:HIS43 3.8 37.3 1.0 HE1 B:TRP44 3.8 54.3 1.0 HA B:GLU40 4.0 44.8 1.0 HD1 B:TRP44 4.0 39.3 1.0 HB2 B:HIS43 4.1 44.8 1.0 CG A:GLU138 4.1 42.9 1.0 HD21 A:LEU142 4.2 77.0 1.0 HG3 A:GLU138 4.3 51.5 1.0 NE2 B:HIS43 4.4 50.9 1.0 HD23 A:LEU142 4.4 77.0 1.0 CG B:GLU40 4.4 50.9 1.0 NE1 B:TRP44 4.4 45.2 1.0 CD1 B:TRP44 4.5 32.7 1.0 CD2 B:HIS43 4.5 42.9 1.0 HA A:GLU138 4.5 39.5 1.0 HB3 B:GLU40 4.5 51.2 1.0 HG2 A:GLU138 4.6 51.5 1.0 O B:GLU40 4.7 41.6 1.0 CD2 A:LEU142 4.7 64.2 1.0 CA B:GLU40 4.8 37.3 1.0 CB B:GLU40 4.8 42.6 1.0 HB2 A:ASP141 4.8 74.0 1.0 HG3 B:GLU40 4.8 61.1 1.0 HG A:LEU142 4.9 68.5 1.0 HG2 B:GLU40 5.0 61.1 1.0

Zinc binding site 5 out of 5 in the Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:27.9 occ:0.52 OE1 A:GLU131 2.2 32.0 1.0 OE1 B:GLU128 2.2 34.7 1.0 O B:HOH310 2.3 27.5 1.0 O B:HOH307 2.4 36.8 1.0 OE2 B:GLU132 2.4 44.6 1.0 OE1 B:GLU51 2.5 33.6 1.0 OE2 B:GLU51 2.5 42.0 1.0 CD B:GLU51 2.8 33.7 1.0 HG2 B:GLU132 3.0 45.9 1.0 CD B:GLU132 3.3 44.3 1.0 HG3 B:GLU132 3.4 45.9 1.0 CD A:GLU131 3.4 36.5 1.0 CG B:GLU132 3.4 38.2 1.0 CD B:GLU128 3.5 34.4 1.0 HE22 B:GLN135 3.6 51.1 1.0 HE22 B:GLN48 3.7 35.9 1.0 OE2 A:GLU131 4.0 29.3 1.0 OE2 B:GLU131 4.1 37.6 1.0 HG3 B:GLU128 4.2 40.7 1.0 ZN A:ZN201 4.2 32.9 0.7 OE2 B:GLU128 4.3 30.0 1.0 CG B:GLU128 4.3 33.9 1.0 HG3 A:GLU131 4.4 41.2 1.0 CG B:GLU51 4.4 34.3 1.0 HE2 B:HIS55 4.4 49.6 1.0 OE1 B:GLN48 4.4 31.4 1.0 NE2 B:GLN135 4.5 42.5 1.0 HG2 B:GLU128 4.5 40.7 1.0 OE1 B:GLU132 4.5 44.9 1.0 NE2 B:GLN48 4.5 29.9 1.0 CG A:GLU131 4.5 34.3 1.0 HE1 B:HIS55 4.5 45.7 1.0 HG3 B:GLU51 4.7 41.2 1.0 HG2 B:GLU51 4.8 41.2 1.0 OE1 B:GLN135 4.9 57.6 1.0 CB B:GLU132 4.9 35.0 1.0 CD B:GLN48 4.9 30.6 1.0 HB3 B:GLU51 5.0 30.8 1.0

Y.Liu, X.Chen, S.Yin, X.Chang, C.Lv, J.Zang, X.Leng, T.Zhang, G.Zhao. Directed Self-Assembly of Dimeric Building Blocks Into Networklike Protein Origami to Construct Hydrogels. Acs Nano V. 16 19472 2022.
ISSN: ESSN 1936-086X
PubMed: 36315654
DOI: 10.1021/ACSNANO.2C09391