Calcium in PDB 9fbk: Diheme Cytochrome C KUSTD1711 From Kuenenia Stuttgartiensis, Without Glycerol Cryoprotectant

The structure of Diheme Cytochrome C KUSTD1711 From Kuenenia Stuttgartiensis, Without Glycerol Cryoprotectant, PDB code: 9fbk was solved by D.Hauser, T.R.M.Barends, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.43 / 1.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.6, 92.1, 55.27, 90, 90, 90
R / Rfree (%)	19.4 / 23.2

The structure of Diheme Cytochrome C KUSTD1711 From Kuenenia Stuttgartiensis, Without Glycerol Cryoprotectant also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Calcium atom in the Diheme Cytochrome C KUSTD1711 From Kuenenia Stuttgartiensis, Without Glycerol Cryoprotectant (pdb code 9fbk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Diheme Cytochrome C KUSTD1711 From Kuenenia Stuttgartiensis, Without Glycerol Cryoprotectant, PDB code: 9fbk:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Diheme Cytochrome C KUSTD1711 From Kuenenia Stuttgartiensis, Without Glycerol Cryoprotectant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Diheme Cytochrome C KUSTD1711 From Kuenenia Stuttgartiensis, Without Glycerol Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:20.0 occ:1.00 O A:VAL231 2.2 26.0 1.0 O A:PRO228 2.3 18.6 1.0 O A:HOH654 2.4 17.0 1.0 O1D A:HEC406 2.4 20.4 1.0 O A:HOH621 2.5 19.9 1.0 O2D A:HEC406 2.5 22.2 1.0 O A:HOH582 2.5 19.2 1.0 CGD A:HEC406 2.8 27.1 1.0 C A:PRO228 3.4 20.4 1.0 C A:VAL231 3.4 18.4 1.0 CA A:PRO228 3.8 16.8 1.0 CA A:VAL231 4.2 20.1 1.0 N A:VAL231 4.2 23.7 1.0 N A:ILE232 4.3 20.6 1.0 CBD A:HEC406 4.3 23.7 1.0 CB A:VAL231 4.4 17.5 1.0 CA A:ILE232 4.4 18.7 1.0 N A:SER229 4.5 15.9 1.0 CHA A:HEC406 4.5 18.6 1.0 CB A:PRO228 4.5 19.8 1.0 O A:HOH604 4.6 21.6 1.0 OG A:SER224 4.7 21.5 1.0 O A:SER224 4.7 16.2 1.0 CA A:SER224 4.7 16.6 1.0 O A:GLU227 4.8 18.2 1.0 OG A:SER290 4.8 20.3 1.0 CG1 A:VAL231 4.8 22.4 1.0 CA A:SER229 4.9 23.2 1.0 CD1 A:ILE232 4.9 29.6 1.0 CB A:SER290 5.0 24.2 1.0 N A:VAL233 5.0 22.1 1.0 CB A:SER224 5.0 17.0 1.0 CAA A:HEC406 5.0 19.0 1.0

Calcium binding site 2 out of 5 in the Diheme Cytochrome C KUSTD1711 From Kuenenia Stuttgartiensis, Without Glycerol Cryoprotectant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Diheme Cytochrome C KUSTD1711 From Kuenenia Stuttgartiensis, Without Glycerol Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:21.6 occ:1.00 O A:TYR107 2.2 29.0 1.0 O A:HOH624 2.4 21.0 1.0 O A:PRO104 2.5 21.9 1.0 O1D A:HEC407 2.5 23.0 1.0 O2D A:HEC407 2.5 24.1 1.0 O A:HOH633 2.5 24.1 1.0 O A:HOH627 2.5 18.8 1.0 CGD A:HEC407 2.8 20.1 1.0 C A:PRO104 3.5 22.2 1.0 C A:TYR107 3.5 23.5 1.0 CA A:PRO104 3.8 19.2 1.0 N A:TYR107 4.3 22.2 1.0 CBD A:HEC407 4.4 21.4 1.0 N A:VAL108 4.4 22.6 1.0 CA A:VAL108 4.4 21.1 1.0 CA A:TYR107 4.4 20.4 1.0 CB A:PRO104 4.6 20.2 1.0 O A:HOH562 4.6 23.5 1.0 N A:GLU105 4.6 21.6 1.0 O A:SER100 4.7 21.1 1.0 CHA A:HEC407 4.7 21.1 1.0 O A:ASP103 4.7 20.1 1.0 CA A:SER100 4.7 20.7 1.0 CB A:TYR107 4.7 25.3 1.0 OG A:SER100 4.8 22.1 1.0 CB A:SER100 4.9 22.8 1.0 N A:VAL109 4.9 24.4 1.0 CD2 A:TYR107 4.9 20.5 1.0

Calcium binding site 3 out of 5 in the Diheme Cytochrome C KUSTD1711 From Kuenenia Stuttgartiensis, Without Glycerol Cryoprotectant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Diheme Cytochrome C KUSTD1711 From Kuenenia Stuttgartiensis, Without Glycerol Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:26.9 occ:1.00 OE2 A:GLU272 2.5 31.8 1.0 OE1 A:GLU272 2.6 24.7 1.0 CD A:GLU272 2.9 34.0 1.0 CG A:GLU272 4.4 26.6 1.0 O A:HOH518 4.9 28.1 1.0

Calcium binding site 4 out of 5 in the Diheme Cytochrome C KUSTD1711 From Kuenenia Stuttgartiensis, Without Glycerol Cryoprotectant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Diheme Cytochrome C KUSTD1711 From Kuenenia Stuttgartiensis, Without Glycerol Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:31.6 occ:1.00 O A:HOH585 2.2 26.3 1.0 O A:HOH714 2.4 26.2 1.0 O A:HOH810 2.4 29.3 1.0 O A:GLU266 2.4 21.5 1.0 C A:GLU266 3.6 24.6 1.0 N A:GLU266 4.0 23.9 1.0 O A:HOH584 4.2 19.6 0.5 O A:ASN250 4.3 24.5 1.0 CA A:GLU266 4.3 22.2 1.0 OE1 A:GLU266 4.4 23.2 1.0 O A:HOH774 4.5 27.7 1.0 O A:HOH816 4.5 29.9 1.0 N A:GLU267 4.6 23.8 1.0 O A:HOH708 4.6 32.2 1.0 CB A:GLU266 4.7 22.2 1.0 CA A:GLU267 4.8 25.8 1.0 OE1 A:GLU267 4.9 49.1 1.0

Calcium binding site 5 out of 5 in the Diheme Cytochrome C KUSTD1711 From Kuenenia Stuttgartiensis, Without Glycerol Cryoprotectant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Diheme Cytochrome C KUSTD1711 From Kuenenia Stuttgartiensis, Without Glycerol Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:37.7 occ:0.68 O A:HOH767 2.3 60.1 1.0 O A:HOH717 2.4 56.4 1.0 OE1 A:GLU259 2.5 65.0 1.0 OD1 A:ASP279 2.6 60.0 1.0 OE2 A:GLU259 2.9 71.9 1.0 CD A:GLU259 3.1 69.4 1.0 CG A:ASP279 3.5 60.8 1.0 OD2 A:ASP279 3.7 65.8 1.0 O A:HOH657 4.2 40.3 1.0 O A:GLU258 4.5 49.0 1.0 CG A:GLU259 4.6 64.0 1.0 CB A:ASP279 4.9 49.8 1.0

M.Akram, D.Hauser, A.Dietl, G.M.Ullmann, T.R.M.Barends. Redox Potential Tuning By Calcium Ions in A Novel C-Type Cytochrome From An Anammox Organism J.Biol.Chem. 2024.
ISSN: ESSN 1083-351X