Iron 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:

Zinc

(Zn)

5 atoms

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron where determined in the Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn, PDB code: 7x9x:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe204 b:38.8 occ:1.00 ND1 A:HIS55 2.1 35.7 1.0 OE1 A:GLU19 2.1 42.7 1.0 OE1 A:GLU52 2.2 30.5 1.0 CE1 A:HIS55 2.9 40.7 1.0 HE1 A:HIS55 3.0 48.8 1.0 FE A:FE205 3.1 42.3 1.0 CD A:GLU19 3.1 40.4 1.0 CD A:GLU52 3.2 27.0 1.0 CG A:HIS55 3.2 26.3 1.0 OE2 A:GLU19 3.4 41.9 1.0 HB2 A:HIS55 3.5 34.0 1.0 HB3 A:HIS55 3.6 34.0 1.0 OE1 A:GLN129 3.6 40.4 1.0 OE2 A:GLU52 3.6 33.8 1.0 CB A:HIS55 3.7 28.3 1.0 HA A:GLU52 3.7 30.1 1.0 HG11 A:VAL99 3.8 38.0 1.0 NE2 A:HIS55 4.1 40.3 1.0 HB3 A:GLU19 4.3 31.5 1.0 CD2 A:HIS55 4.3 28.9 1.0 CG A:GLU19 4.4 36.0 1.0 HB3 A:GLU52 4.4 34.9 1.0 CG A:GLU52 4.5 31.9 1.0 CA A:GLU52 4.6 25.0 1.0 OE1 A:GLU132 4.6 38.1 1.0 CG1 A:VAL99 4.7 31.6 1.0 HA A:GLU19 4.7 29.9 1.0 HD2 A:PHE125 4.7 38.6 1.0 CD A:GLN129 4.7 34.0 1.0 CB A:GLU52 4.7 29.0 1.0 HG3 A:GLU19 4.8 43.3 1.0 CB A:GLU19 4.8 26.2 1.0 HG12 A:VAL99 4.8 38.0 1.0 HE2 A:HIS55 4.8 48.4 1.0 HE2 A:PHE125 4.9 44.0 1.0 HG13 A:VAL99 4.9 38.0 1.0 HB2 A:SER22 5.0 33.9 1.0

Iron binding site 2 out of 4 in the Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe205 b:42.3 occ:1.00 OE1 A:GLU132 2.2 38.1 1.0 OE2 A:GLU52 2.2 33.8 1.0 OE2 A:GLU96 2.3 33.1 1.0 OE1 A:GLU96 2.7 31.4 1.0 CD A:GLU96 2.8 43.4 1.0 CD A:GLU52 3.0 27.0 1.0 FE A:FE204 3.1 38.8 1.0 OE1 A:GLU52 3.1 30.5 1.0 OE1 A:GLN129 3.2 40.4 1.0 CD A:GLU132 3.3 41.9 1.0 HE1 A:HIS55 3.4 48.8 1.0 HE21 A:GLN48 3.5 41.0 1.0 HE22 A:GLN129 3.6 41.0 1.0 OE2 A:GLU132 3.7 36.1 1.0 HE22 A:GLN48 3.9 41.0 1.0 HH A:TYR26 4.0 50.8 1.0 NE2 A:GLN48 4.0 34.1 1.0 HE2 A:TYR26 4.0 36.1 1.0 CE1 A:HIS55 4.1 40.7 1.0 CD A:GLN129 4.1 34.0 1.0 HG11 A:VAL99 4.2 38.0 1.0 NE2 A:GLN129 4.2 34.1 1.0 ND1 A:HIS55 4.3 35.7 1.0 CG A:GLU96 4.3 38.2 1.0 HB3 A:GLU132 4.3 43.3 1.0 CG A:GLU52 4.4 31.9 1.0 HB2 A:GLU132 4.5 43.3 1.0 CG A:GLU132 4.5 37.5 1.0 HG3 A:GLU96 4.5 45.9 1.0 OH A:TYR26 4.6 42.3 1.0 CB A:GLU132 4.7 36.0 1.0 HG3 A:GLU52 4.7 38.3 1.0 HG2 A:GLU96 4.7 45.9 1.0 HG2 A:GLU52 4.7 38.3 1.0 OE1 A:GLU19 4.8 42.7 1.0 CE2 A:TYR26 4.8 30.0 1.0 HG21 A:VAL99 4.9 42.5 1.0 HA A:GLU96 4.9 31.2 1.0 HB3 A:SER22 4.9 33.9 1.0 CG1 A:VAL99 5.0 31.6 1.0

Iron binding site 3 out of 4 in the Thermotoga Maritima Ferritin Variant-Tm-E(G40E) with Zn


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 B:Fe203 b:36.4 occ:1.00 OE1 B:GLU19 2.0 38.0 1.0 ND1 B:HIS55 2.1 34.1 1.0 OE1 B:GLU52 2.1 29.3 1.0 O B:HOH301 2.3 28.5 1.0 O B:HOH305 2.4 35.5 1.0 CE1 B:HIS55 2.9 38.1 1.0 HE1 B:HIS55 3.0 45.7 1.0 CD B:GLU19 3.0 34.1 1.0 HE22 B:GLN129 3.1 41.9 1.0 CD B:GLU52 3.2 28.2 1.0 CG B:HIS55 3.2 32.3 1.0 FE B:FE204 3.3 42.0 1.0 OE2 B:GLU19 3.3 32.9 1.0 HE21 B:GLN129 3.5 41.9 1.0 HB2 B:HIS55 3.5 30.5 1.0 OE2 B:GLU52 3.6 37.5 1.0 HB3 B:HIS55 3.6 30.5 1.0 NE2 B:GLN129 3.6 34.9 1.0 CB B:HIS55 3.7 25.4 1.0 HA B:GLU52 3.7 31.3 1.0 HG11 B:VAL99 3.9 40.2 1.0 NE2 B:HIS55 4.1 41.3 1.0 CD2 B:HIS55 4.2 34.4 1.0 HB3 B:GLU19 4.3 31.0 1.0 HB3 B:GLU52 4.4 37.3 1.0 CG B:GLU19 4.4 35.1 1.0 CG B:GLU52 4.5 29.6 1.0 CA B:GLU52 4.6 26.1 1.0 HE2 B:PHE125 4.6 38.2 1.0 HA B:GLU19 4.6 26.9 1.0 OE1 B:GLU132 4.7 44.9 1.0 CB B:GLU52 4.7 31.0 1.0 CG1 B:VAL99 4.8 33.5 1.0 HG3 B:GLU19 4.8 42.2 1.0 HD2 B:PHE125 4.8 43.4 1.0 HE2 B:HIS55 4.8 49.6 1.0 CB B:GLU19 4.8 25.8 1.0 CD B:GLN129 4.9 39.2 1.0 HG12 B:VAL99 5.0 40.2 1.0

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


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe204 b:42.0 occ:1.00 O B:HOH301 1.7 28.5 1.0 OE2 B:GLU52 2.0 37.5 1.0 OE1 B:GLU132 2.1 44.9 1.0 OE2 B:GLU96 2.3 30.6 1.0 OE1 B:GLU96 2.7 34.9 1.0 CD B:GLU96 2.8 31.6 1.0 HE22 B:GLN129 2.9 41.9 1.0 CD B:GLU52 2.9 28.2 1.0 OE1 B:GLU52 3.2 29.3 1.0 HE21 B:GLN48 3.2 35.9 1.0 FE B:FE203 3.3 36.4 1.0 CD B:GLU132 3.3 44.3 1.0 HE1 B:HIS55 3.5 45.7 1.0 HE22 B:GLN48 3.7 35.9 1.0 NE2 B:GLN129 3.7 34.9 1.0 HE2 B:TYR26 3.7 34.7 1.0 NE2 B:GLN48 3.7 29.9 1.0 OE2 B:GLU132 3.8 44.6 1.0 HH B:TYR26 3.8 45.9 1.0 HE21 B:GLN129 4.2 41.9 1.0 CE1 B:HIS55 4.2 38.1 1.0 HB3 B:GLU132 4.2 42.0 1.0 HG11 B:VAL99 4.3 40.2 1.0 CG B:GLU96 4.3 33.1 1.0 CG B:GLU52 4.3 29.6 1.0 ND1 B:HIS55 4.4 34.1 1.0 OE1 B:GLN129 4.5 32.8 1.0 CG B:GLU132 4.5 38.2 1.0 HB2 B:GLU132 4.5 42.0 1.0 CD B:GLN129 4.5 39.2 1.0 CE2 B:TYR26 4.5 28.9 1.0 HG2 B:GLU52 4.5 35.6 1.0 OH B:TYR26 4.5 38.2 1.0 HG3 B:GLU96 4.6 39.8 1.0 HG3 B:GLU52 4.6 35.6 1.0 CB B:GLU132 4.6 35.0 1.0 HG21 B:VAL99 4.7 38.2 1.0 HG2 B:GLU96 4.7 39.8 1.0 HB3 B:SER22 4.8 32.8 1.0 O B:HOH305 4.9 35.5 1.0 OE1 B:GLU19 4.9 38.0 1.0 HA B:GLU96 4.9 33.9 1.0 CD B:GLN48 4.9 30.6 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