Calcium in PDB 6wxp: De Novo Tim Barrel-Ferredoxin Fold Fusion Homodimer with 4-Glutamate Centre Tfd-Ee

The structure of De Novo Tim Barrel-Ferredoxin Fold Fusion Homodimer with 4-Glutamate Centre Tfd-Ee, PDB code: 6wxp was solved by S.J.Caldwell, C.Zeymer, I.C.Haydon, P.Huang, D.Hilvert, D.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.44 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.910, 101.160, 117.730, 90.00, 95.50, 90.00
R / Rfree (%)	22.7 / 28.1

The binding sites of Calcium atom in the De Novo Tim Barrel-Ferredoxin Fold Fusion Homodimer with 4-Glutamate Centre Tfd-Ee (pdb code 6wxp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the De Novo Tim Barrel-Ferredoxin Fold Fusion Homodimer with 4-Glutamate Centre Tfd-Ee, PDB code: 6wxp:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the De Novo Tim Barrel-Ferredoxin Fold Fusion Homodimer with 4-Glutamate Centre Tfd-Ee


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of De Novo Tim Barrel-Ferredoxin Fold Fusion Homodimer with 4-Glutamate Centre Tfd-Ee within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:75.4 occ:1.00 OE1 B:GLU31 2.4 68.3 1.0 OE1 A:GLU154 2.4 63.6 1.0 OE1 A:GLU31 2.5 78.6 1.0 OE1 B:GLU154 2.5 66.3 1.0 OE2 B:GLU31 2.7 64.8 1.0 CD B:GLU31 2.9 68.2 1.0 OE2 A:GLU31 2.9 76.1 1.0 CD A:GLU31 3.1 70.6 1.0 OE2 A:GLU154 3.1 76.9 1.0 CD A:GLU154 3.1 66.3 1.0 CD B:GLU154 3.3 70.5 1.0 OE2 B:GLU154 3.3 81.9 1.0 CG B:GLU31 4.4 51.0 1.0 CG A:GLU31 4.5 52.8 1.0 CG A:GLU154 4.6 55.6 1.0 CG B:GLU154 4.8 58.6 1.0 ND2 B:ASN52 4.8 81.5 1.0

Calcium binding site 2 out of 3 in the De Novo Tim Barrel-Ferredoxin Fold Fusion Homodimer with 4-Glutamate Centre Tfd-Ee


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of De Novo Tim Barrel-Ferredoxin Fold Fusion Homodimer with 4-Glutamate Centre Tfd-Ee within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:89.1 occ:1.00 OE1 D:GLU31 2.4 90.6 1.0 OE1 C:GLU31 2.4 75.9 1.0 OE1 C:GLU154 2.4 87.7 1.0 OE1 D:GLU154 2.6 59.8 1.0 OE2 D:GLU154 2.9 77.0 1.0 OE2 C:GLU31 2.9 67.2 1.0 OE2 D:GLU31 3.0 81.8 1.0 CD C:GLU31 3.0 65.0 1.0 CD D:GLU31 3.0 77.8 1.0 CD D:GLU154 3.1 63.9 1.0 CD C:GLU154 3.3 96.4 1.0 OE2 C:GLU154 3.5 0.2 1.0 CG C:GLU31 4.5 64.9 1.0 CG D:GLU31 4.5 65.3 1.0 CG D:GLU154 4.6 55.2 1.0 CG C:GLU154 4.8 0.1 1.0 ND2 D:ASN52 4.9 56.4 1.0 CG2 C:ILE50 4.9 53.4 1.0

Calcium binding site 3 out of 3 in the De Novo Tim Barrel-Ferredoxin Fold Fusion Homodimer with 4-Glutamate Centre Tfd-Ee


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of De Novo Tim Barrel-Ferredoxin Fold Fusion Homodimer with 4-Glutamate Centre Tfd-Ee within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:0.2 occ:1.00 OE2 F:GLU31 2.4 0.5 1.0 OE2 E:GLU31 2.5 0.8 1.0 OE1 F:GLU31 2.5 0.4 1.0 OE1 F:GLU154 2.6 0.9 1.0 OE1 E:GLU31 2.7 0.3 1.0 CD F:GLU31 2.8 0.4 1.0 OE1 E:GLU154 2.9 0.8 1.0 CD E:GLU31 2.9 0.1 1.0 OE2 E:GLU154 2.9 0.9 1.0 OE2 F:GLU154 3.0 98.3 1.0 CD F:GLU154 3.2 0.9 1.0 CD E:GLU154 3.3 98.5 1.0 CG F:GLU31 4.3 97.5 1.0 CG E:GLU31 4.4 0.6 1.0 ND2 F:ASN6 4.4 0.8 1.0 ND2 F:ASN52 4.5 0.0 1.0 CG F:GLU154 4.6 0.5 1.0 ND2 E:ASN52 4.8 0.5 1.0 CG E:GLU154 4.8 97.5 1.0 ND2 E:ASN6 4.8 1.0 1.0

S.J.Caldwell, I.C.Haydon, N.Piperidou, P.S.Huang, M.J.Bick, H.S.Sjostrom, D.Hilvert, D.Baker, C.Zeymer. Tight and Specific Lanthanide Binding in A De Novo Tim Barrel with A Large Internal Cavity Designed By Symmetric Domain Fusion. Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
PubMed: 33203677
DOI: 10.1073/PNAS.2008535117