Calcium in PDB 1b4n: Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate

The structure of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate, PDB code: 1b4n was solved by Y.L.Hu, S.Faham, R.Roy, M.W.W.Adams, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.400, 170.500, 180.700, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 24.4

The structure of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate also contains other interesting chemical elements:

Tungsten	(W)	4 atoms
Magnesium	(Mg)	4 atoms
Iron	(Fe)	16 atoms

The binding sites of Calcium atom in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate (pdb code 1b4n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate, PDB code: 1b4n:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca620 b:61.3 occ:1.00 O8 A:PTE623 2.1 36.4 1.0 O A:HOH661 2.4 43.9 1.0 O A:GLY179 2.4 38.6 1.0 O A:HOH660 2.5 43.7 1.0 OD2 A:ASP306 2.7 43.3 1.0 OE1 A:GLU304 2.8 43.6 1.0 C A:GLY179 3.4 29.3 1.0 C8 A:PTE623 3.5 24.4 1.0 CG A:ASP306 4.0 35.6 1.0 CD A:GLU304 4.0 37.4 1.0 CA A:GLY179 4.0 30.9 1.0 O A:GLU304 4.0 26.2 1.0 ND2 A:ASN309 4.1 8.7 1.0 N9 A:PTE623 4.2 24.2 1.0 O7P A:PTE623 4.3 20.6 1.0 N A:ARG180 4.4 27.2 1.0 C7 A:PTE623 4.5 24.3 1.0 OD2 A:ASP333 4.6 21.0 1.0 CB A:GLU304 4.6 26.2 1.0 CB A:ASP306 4.6 29.5 1.0 CA A:ARG180 4.7 23.4 1.0 N6 A:PTE623 4.7 24.6 1.0 CG A:GLU304 4.7 32.7 1.0 C A:GLU304 4.9 24.1 1.0 OE2 A:GLU304 4.9 36.6 1.0 OD1 A:ASP306 4.9 32.4 1.0 OD1 A:ASP333 4.9 22.6 1.0

Calcium binding site 2 out of 4 in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca620 b:64.6 occ:1.00 O8 B:PTE623 2.2 34.7 1.0 O B:GLY179 2.4 36.7 1.0 O B:HOH669 2.4 43.4 1.0 O B:HOH668 2.5 41.9 1.0 OD2 B:ASP306 2.6 38.9 1.0 OE1 B:GLU304 2.7 40.4 1.0 C B:GLY179 3.3 27.3 1.0 C8 B:PTE623 3.5 20.3 1.0 CA B:GLY179 3.8 29.3 1.0 CG B:ASP306 3.9 30.4 1.0 CD B:GLU304 3.9 31.2 1.0 O B:GLU304 4.2 21.6 1.0 N B:ARG180 4.2 24.7 1.0 N9 B:PTE623 4.3 18.2 1.0 ND2 B:ASN309 4.3 15.4 1.0 CB B:GLU304 4.4 20.6 1.0 O7P B:PTE623 4.5 19.3 1.0 CA B:ARG180 4.5 19.0 1.0 C7 B:PTE623 4.6 18.8 1.0 OD2 B:ASP333 4.6 25.0 1.0 CG B:GLU304 4.7 27.5 1.0 CB B:ASP306 4.7 25.9 1.0 CZ B:ARG180 4.7 24.4 1.0 OD1 B:ASP306 4.7 28.2 1.0 NE B:ARG180 4.8 24.6 1.0 OE2 B:GLU304 4.8 32.4 1.0 N6 B:PTE623 4.8 19.4 1.0 C B:GLU304 4.9 19.6 1.0 NH1 B:ARG180 5.0 25.8 1.0

Calcium binding site 3 out of 4 in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca620 b:61.8 occ:1.00 O8 C:PTE623 2.2 38.1 1.0 O C:HOH672 2.4 42.0 1.0 O C:HOH671 2.5 43.1 1.0 O C:GLY179 2.5 37.9 1.0 OD2 C:ASP306 2.6 41.6 1.0 OE1 C:GLU304 2.8 39.9 1.0 C C:GLY179 3.5 28.8 1.0 C8 C:PTE623 3.6 22.3 1.0 CG C:ASP306 3.8 31.0 1.0 ND2 C:ASN309 4.0 25.8 1.0 CD C:GLU304 4.1 29.6 1.0 O C:GLU304 4.1 25.2 1.0 CA C:GLY179 4.1 30.7 1.0 N9 C:PTE623 4.3 22.2 1.0 O7P C:PTE623 4.4 17.7 1.0 CB C:GLU304 4.5 25.5 1.0 N C:ARG180 4.5 24.9 1.0 OD1 C:ASP306 4.6 31.0 1.0 C7 C:PTE623 4.6 21.5 1.0 CB C:ASP306 4.7 25.3 1.0 OD2 C:ASP333 4.7 19.6 1.0 CA C:ARG180 4.7 20.8 1.0 C C:GLU304 4.8 23.9 1.0 CG C:GLU304 4.8 27.2 1.0 N6 C:PTE623 4.9 22.6 1.0 NH2 C:ARG180 4.9 19.9 1.0 OE2 C:GLU304 5.0 29.9 1.0 NE C:ARG180 5.0 18.0 1.0 CZ C:ARG180 5.0 14.3 1.0

Calcium binding site 4 out of 4 in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca620 b:62.3 occ:1.00 O8 D:PTE623 2.2 39.9 1.0 O D:HOH673 2.4 45.3 1.0 O D:HOH674 2.4 44.6 1.0 O D:GLY179 2.5 40.7 1.0 OD2 D:ASP306 2.6 41.9 1.0 OE1 D:GLU304 2.8 47.5 1.0 C D:GLY179 3.4 30.4 1.0 C8 D:PTE623 3.5 26.9 1.0 CG D:ASP306 3.9 30.5 1.0 CA D:GLY179 4.0 33.2 1.0 CD D:GLU304 4.0 40.8 1.0 ND2 D:ASN309 4.1 18.7 1.0 O D:GLU304 4.1 23.8 1.0 N9 D:PTE623 4.3 26.4 1.0 CB D:GLU304 4.3 27.9 1.0 N D:ARG180 4.4 28.1 1.0 OD2 D:ASP333 4.5 18.9 1.0 C7 D:PTE623 4.5 26.8 1.0 N6 D:PTE623 4.7 26.5 1.0 CG D:GLU304 4.7 35.0 1.0 O7P D:PTE623 4.7 17.2 1.0 CA D:ARG180 4.7 25.8 1.0 C D:GLU304 4.7 23.4 1.0 OD1 D:ASP306 4.7 28.2 1.0 CB D:ASP306 4.8 26.2 1.0 OD1 D:ASP333 4.9 10.4 1.0 OE2 D:GLU304 5.0 42.5 1.0

Y.Hu, S.Faham, R.Roy, M.W.Adams, D.C.Rees. Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus: the 1.85 A Resolution Crystal Structure and Its Mechanistic Implications. J.Mol.Biol. V. 286 899 1999.
ISSN: ISSN 0022-2836
PubMed: 10024458
DOI: 10.1006/JMBI.1998.2488