Iron in PDB 5ndc: Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography

All present enzymatic activity of Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography:
1.9.3.1;

The structure of Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography, PDB code: 5ndc was solved by R.Andersson, C.Safari, R.Dods, E.Nango, R.Tanaka, T.Nakane, K.Tono, Y.Joti, P.Bath, E.Dunevall, E.Bosman, O.Nureki, S.Iwata, R.Neutze, G.Branden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.40 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.850, 100.320, 96.620, 90.00, 126.76, 90.00
R / Rfree (%)	16.2 / 19.7

The structure of Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography also contains other interesting chemical elements:

Copper

(Cu)

3 atoms

The binding sites of Iron atom in the Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography (pdb code 5ndc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography, PDB code: 5ndc:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:33.4 occ:1.00 FE A:HEM602 0.0 33.4 1.0 ND A:HEM602 1.9 34.5 1.0 NA A:HEM602 2.0 33.0 1.0 NE2 A:HIS386 2.1 36.1 1.0 NE2 A:HIS72 2.1 37.2 1.0 NC A:HEM602 2.1 33.8 1.0 NB A:HEM602 2.1 33.7 1.0 C1D A:HEM602 2.9 35.0 1.0 C4D A:HEM602 3.0 34.0 1.0 CE1 A:HIS72 3.0 37.2 1.0 CE1 A:HIS386 3.0 36.3 1.0 C4A A:HEM602 3.0 32.9 1.0 C1A A:HEM602 3.0 34.6 1.0 C4B A:HEM602 3.0 34.1 1.0 C1B A:HEM602 3.1 32.5 1.0 C4C A:HEM602 3.1 34.3 1.0 CD2 A:HIS386 3.1 35.3 1.0 C1C A:HEM602 3.1 34.3 1.0 CD2 A:HIS72 3.1 36.3 1.0 CHD A:HEM602 3.4 33.9 1.0 CHB A:HEM602 3.4 32.9 1.0 CHA A:HEM602 3.4 34.3 1.0 CHC A:HEM602 3.5 33.0 1.0 ND1 A:HIS386 4.1 36.0 1.0 ND1 A:HIS72 4.2 36.2 1.0 C3A A:HEM602 4.2 33.3 1.0 C2A A:HEM602 4.2 32.8 1.0 C2D A:HEM602 4.2 34.6 1.0 CG A:HIS386 4.2 35.3 1.0 C3D A:HEM602 4.2 32.3 1.0 CG A:HIS72 4.2 36.1 1.0 C2B A:HEM602 4.3 33.0 1.0 C3B A:HEM602 4.3 33.4 1.0 C3C A:HEM602 4.3 34.9 1.0 C2C A:HEM602 4.3 33.8 1.0 OE1 A:GLN42 4.7 40.3 1.0

Iron binding site 2 out of 2 in the Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:36.1 occ:1.00 FE A:HAS603 0.0 36.1 1.0 ND A:HAS603 2.1 35.9 1.0 NA A:HAS603 2.1 33.3 1.0 NC A:HAS603 2.1 34.9 1.0 NB A:HAS603 2.1 34.6 1.0 NE2 A:HIS384 2.1 40.9 1.0 O A:HOH752 2.9 18.6 1.0 C1D A:HAS603 3.0 36.0 1.0 C4D A:HAS603 3.1 33.9 1.0 CE1 A:HIS384 3.1 44.5 1.0 C1A A:HAS603 3.1 32.7 1.0 C4A A:HAS603 3.1 32.2 1.0 C1C A:HAS603 3.1 34.1 1.0 C4C A:HAS603 3.1 34.0 1.0 C4B A:HAS603 3.1 33.5 1.0 C1B A:HAS603 3.1 34.4 1.0 CD2 A:HIS384 3.2 42.3 1.0 CHC A:HAS603 3.4 34.2 1.0 CHA A:HAS603 3.4 33.5 1.0 CHB A:HAS603 3.4 35.8 1.0 CHD A:HAS603 3.5 34.0 1.0 ND1 A:HIS384 4.2 42.4 1.0 C2D A:HAS603 4.3 35.1 1.0 CG A:HIS384 4.3 41.9 1.0 C3D A:HAS603 4.4 34.5 1.0 C3C A:HAS603 4.4 33.5 1.0 C2A A:HAS603 4.4 30.6 1.0 C3A A:HAS603 4.4 31.0 1.0 C2C A:HAS603 4.4 33.1 1.0 C3B A:HAS603 4.4 34.8 1.0 C2B A:HAS603 4.4 35.1 1.0 CU A:CU601 4.8 35.5 1.0

R.Andersson, C.Safari, R.Dods, E.Nango, R.Tanaka, A.Yamashita, T.Nakane, K.Tono, Y.Joti, P.Bath, E.Dunevall, R.Bosman, O.Nureki, S.Iwata, R.Neutze, G.Branden. Serial Femtosecond Crystallography Structure of Cytochrome C Oxidase at Room Temperature. Sci Rep V. 7 4518 2017.
ISSN: ESSN 2045-2322
PubMed: 28674417
DOI: 10.1038/S41598-017-04817-Z