Calcium in PDB 7dy8: Thermotoga Maritima Ferritin Mutant-Flal

All present enzymatic activity of Thermotoga Maritima Ferritin Mutant-Flal:
1.16.3.2;

The structure of Thermotoga Maritima Ferritin Mutant-Flal, PDB code: 7dy8 was solved by X.Zhang, G.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.05 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.418, 85.981, 107.09, 90, 90, 90
R / Rfree (%)	21.2 / 26.5

The structure of Thermotoga Maritima Ferritin Mutant-Flal also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Calcium atom in the Thermotoga Maritima Ferritin Mutant-Flal (pdb code 7dy8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Thermotoga Maritima Ferritin Mutant-Flal, PDB code: 7dy8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Thermotoga Maritima Ferritin Mutant-Flal


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermotoga Maritima Ferritin Mutant-Flal within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca203 b:43.2 occ:1.00 O H:HOH310 2.3 37.2 1.0 OE2 H:GLU51 2.4 40.7 1.0 O H:HOH303 2.4 38.4 1.0 OE1 H:GLU51 2.6 41.7 1.0 OE1 H:GLU132 2.6 35.4 1.0 CD H:GLU51 2.8 37.8 1.0 CD H:GLU132 3.8 45.2 1.0 CB H:GLU132 3.8 54.8 1.0 OE1 H:GLU131 4.1 55.6 1.0 CG H:GLU51 4.3 36.5 1.0 OE1 H:GLN48 4.3 39.2 1.0 NE2 H:GLN48 4.3 40.3 1.0 CG H:GLU132 4.4 49.8 1.0 NH2 H:ARG163 4.4 36.6 1.0 OE1 H:GLN135 4.6 53.2 1.0 CD H:GLN48 4.8 35.8 1.0 OE2 H:GLU132 4.8 46.3 1.0 NE2 H:HIS55 4.9 48.0 1.0

Calcium binding site 2 out of 5 in the Thermotoga Maritima Ferritin Mutant-Flal


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermotoga Maritima Ferritin Mutant-Flal within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:39.7 occ:1.00 O A:HOH316 2.3 46.8 1.0 OE1 A:GLU51 2.4 26.4 1.0 O A:HOH314 2.4 41.4 1.0 OE2 A:GLU51 2.5 41.3 1.0 O A:HOH312 2.6 35.1 1.0 OE2 A:GLU128 2.6 43.1 1.0 CD A:GLU51 2.8 34.0 1.0 OE2 A:GLU132 2.8 42.1 1.0 CD A:GLU132 3.7 39.2 1.0 CD A:GLU128 3.7 46.6 1.0 CG A:GLU132 3.8 30.2 1.0 CG A:GLU128 4.3 36.8 1.0 NH2 A:ARG163 4.3 33.4 1.0 CG A:GLU51 4.3 32.1 1.0 OE1 A:GLN48 4.5 31.2 1.0 OE1 A:GLU131 4.6 56.5 1.0 NE2 A:GLN48 4.7 29.7 1.0 OE1 A:GLU128 4.8 44.6 1.0 OE1 A:GLU132 4.9 35.5 1.0 OE1 A:GLN135 4.9 51.8 1.0

Calcium binding site 3 out of 5 in the Thermotoga Maritima Ferritin Mutant-Flal


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermotoga Maritima Ferritin Mutant-Flal within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:46.9 occ:1.00 O A:HOH315 2.4 43.7 1.0 OE2 A:GLU108 2.4 40.1 1.0 OD1 A:ASN105 2.6 43.2 1.0 OE1 A:GLU108 2.6 41.3 1.0 CD A:GLU108 2.8 41.1 1.0 CG A:ASN105 3.7 41.8 1.0 NE2 A:GLN101 3.8 40.9 1.0 CG A:GLU108 4.4 34.4 1.0 ND2 A:ASN105 4.4 40.4 1.0 CA A:ASN105 4.6 41.0 1.0 CB A:ASN105 4.7 42.9 1.0 N A:ASN105 4.8 36.8 1.0

Calcium binding site 4 out of 5 in the Thermotoga Maritima Ferritin Mutant-Flal


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermotoga Maritima Ferritin Mutant-Flal within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:70.3 occ:1.00 OE2 A:GLU71 2.6 43.6 1.0 OE1 A:GLU71 2.7 50.2 1.0 CD A:GLU71 3.0 46.3 1.0 NZ H:LYS77 4.2 47.8 1.0 CG A:GLU71 4.5 39.2 1.0 OE2 A:GLU73 4.5 40.9 1.0

Calcium binding site 5 out of 5 in the Thermotoga Maritima Ferritin Mutant-Flal


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Thermotoga Maritima Ferritin Mutant-Flal within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:56.4 occ:1.00 FE A:FE201 2.7 39.2 0.8 OG A:SER22 3.0 37.2 1.0 OE1 A:GLU52 3.2 34.7 1.0 FE A:FE202 3.3 42.8 0.7 OE2 A:GLU19 3.5 35.9 1.0 CB A:SER22 3.5 32.1 1.0 CG2 A:VAL99 3.5 35.3 1.0 CD A:GLU52 3.5 38.5 1.0 CG1 A:VAL99 3.5 36.1 1.0 OE2 A:GLU52 3.6 34.6 1.0 OE1 A:GLU96 3.8 35.1 1.0 OE1 A:GLN129 3.8 32.4 1.0 CB A:VAL99 3.9 39.4 1.0 OE2 A:GLU96 4.1 31.2 1.0 NE2 A:HIS95 4.1 38.1 1.0 O A:HOH310 4.1 36.9 1.0 CD A:GLU96 4.3 35.0 1.0 CD A:GLU19 4.3 38.2 1.0 CD A:GLN129 4.5 35.4 1.0 OE1 A:GLU19 4.6 49.0 1.0 CG A:GLU52 4.7 24.7 1.0 NE2 A:GLN129 4.8 35.5 1.0 CD2 A:HIS95 4.8 31.7 1.0 CE1 A:HIS95 4.9 35.7 1.0

X.Zhang, Y.Liu, B.Zheng, J.Zang, C.Lv, T.Zhang, H.Wang, G.Zhao. Protein Interface Redesign Facilitates the Transformation of Nanocage Building Blocks to 1D and 2D Nanomaterials. Nat Commun V. 12 4849 2021.
ISSN: ESSN 2041-1723
PubMed: 34381032
DOI: 10.1038/S41467-021-25199-X