Iron in PDB 4mdz: Metallo-Enzyme From P. Marina

The structure of Metallo-Enzyme From P. Marina, PDB code: 4mdz was solved by D.Bellini, M.A.Walsh, Oxford Protein Production Facility (Oppf), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.54 / 2.68
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	70.190, 183.010, 233.460, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.8

The binding sites of Iron atom in the Metallo-Enzyme From P. Marina (pdb code 4mdz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Metallo-Enzyme From P. Marina, PDB code: 4mdz:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Metallo-Enzyme From P. Marina


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Metallo-Enzyme From P. Marina within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:21.1 occ:0.50 O4 A:SIN404 1.9 57.4 0.8 O A:HOH501 2.0 40.9 1.0 NE2 A:HIS277 2.1 44.9 1.0 OD1 A:ASP222 2.2 46.3 1.0 NE2 A:HIS276 2.2 53.2 1.0 NE2 A:HIS250 2.3 43.8 1.0 CD2 A:HIS277 3.1 43.8 1.0 C4 A:SIN404 3.1 70.4 0.8 CE1 A:HIS276 3.1 54.5 1.0 CE1 A:HIS277 3.1 42.4 1.0 CG A:ASP222 3.1 47.2 1.0 CE1 A:HIS250 3.2 46.6 1.0 CD2 A:HIS250 3.2 46.2 1.0 CD2 A:HIS276 3.3 52.6 1.0 OD2 A:ASP222 3.4 52.4 1.0 FE A:FE402 3.5 50.8 0.5 O3 A:SIN404 3.7 76.9 0.8 ND1 A:HIS277 4.2 42.8 1.0 CG A:HIS277 4.3 43.8 1.0 C3 A:SIN404 4.3 72.1 0.8 CD2 A:HIS221 4.3 40.9 1.0 ND1 A:HIS276 4.3 54.5 1.0 ND1 A:HIS250 4.4 45.9 1.0 CG A:HIS250 4.4 45.9 1.0 CG A:HIS276 4.4 49.6 1.0 CB A:ASP222 4.5 40.6 1.0 O1 A:SIN405 4.6 64.8 0.5 CE A:LYS225 4.8 52.6 1.0 NE2 A:HIS221 4.9 45.7 1.0 CA A:ASP222 4.9 40.3 1.0

Iron binding site 2 out of 4 in the Metallo-Enzyme From P. Marina


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Metallo-Enzyme From P. Marina within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:50.8 occ:0.50 OD2 A:ASP222 2.1 52.4 1.0 O3 A:SIN404 2.1 76.9 0.8 O A:HOH501 2.2 40.9 1.0 FE A:FE403 2.8 51.1 0.5 C4 A:SIN404 2.9 70.4 0.8 O1 A:SIN405 2.9 64.8 0.5 O4 A:SIN404 3.0 57.4 0.8 O2 A:SIN405 3.1 54.7 0.5 CG A:ASP222 3.1 47.2 1.0 OE1 A:GLU185 3.2 87.5 1.0 C1 A:SIN405 3.4 60.4 0.5 OE2 A:GLU185 3.4 93.9 1.0 FE A:FE401 3.5 21.1 0.5 NZ A:LYS225 3.5 53.5 1.0 OD1 A:ASP222 3.6 46.3 1.0 CD A:GLU185 3.7 90.0 1.0 O A:HOH508 4.0 60.4 1.0 NE2 A:HIS221 4.1 45.7 1.0 CE A:LYS225 4.3 52.6 1.0 O A:HOH509 4.3 97.2 1.0 C3 A:SIN404 4.4 72.1 0.8 CB A:ASP222 4.4 40.6 1.0 OD2 A:ASP305 4.4 54.0 1.0 CD2 A:HIS221 4.5 40.9 1.0 O A:HOH503 4.6 73.8 1.0 NE2 A:HIS277 4.8 44.9 1.0 CE1 A:HIS277 4.9 42.4 1.0 OD1 A:ASP305 4.9 60.2 1.0 C2 A:SIN405 4.9 58.8 0.5 NE2 A:HIS276 4.9 53.2 1.0

Iron binding site 3 out of 4 in the Metallo-Enzyme From P. Marina


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Metallo-Enzyme From P. Marina within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:51.1 occ:0.50 OD1 A:ASP305 2.6 60.2 1.0 O A:HOH508 2.7 60.4 1.0 NE2 A:HIS189 2.7 44.5 1.0 OE1 A:GLU185 2.7 87.5 1.0 FE A:FE402 2.8 50.8 0.5 NE2 A:HIS221 3.0 45.7 1.0 O2 A:SIN405 3.0 54.7 0.5 OE2 A:GLU185 3.3 93.9 1.0 O A:HOH510 3.3 71.9 1.0 C1 A:SIN405 3.3 60.4 0.5 CD A:GLU185 3.4 90.0 1.0 CE1 A:HIS189 3.4 44.6 1.0 CG A:ASP305 3.4 53.5 1.0 O1 A:SIN405 3.5 64.8 0.5 OD2 A:ASP305 3.5 54.0 1.0 OD2 A:ASP222 3.7 52.4 1.0 CE1 A:HIS221 3.7 41.6 1.0 O A:HOH501 3.7 40.9 1.0 CD2 A:HIS189 3.7 44.2 1.0 CD2 A:HIS221 4.2 40.9 1.0 C2 A:SIN405 4.3 58.8 0.5 ND1 A:HIS189 4.6 44.3 1.0 CG A:ASP222 4.6 47.2 1.0 CG A:HIS189 4.8 42.3 1.0 CG A:GLU185 4.8 81.7 1.0 O3 A:SIN404 4.8 76.9 0.8 CB A:ASP305 4.8 45.3 1.0 ND1 A:HIS221 5.0 42.1 1.0

Iron binding site 4 out of 4 in the Metallo-Enzyme From P. Marina


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Metallo-Enzyme From P. Marina within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:55.4 occ:1.00 NE2 B:HIS277 2.1 53.4 1.0 OD2 B:ASP222 2.1 50.0 1.0 O B:HOH546 2.3 43.7 1.0 NE2 B:HIS250 2.4 61.9 1.0 NE2 B:HIS276 2.4 53.1 1.0 CD2 B:HIS277 3.1 51.4 1.0 CE1 B:HIS277 3.1 48.2 1.0 CG B:ASP222 3.2 48.6 1.0 CD2 B:HIS276 3.3 54.6 1.0 CE1 B:HIS250 3.3 60.8 1.0 CD2 B:HIS250 3.4 57.8 1.0 CE1 B:HIS276 3.4 51.0 1.0 O B:HOH545 3.5 42.8 1.0 OD1 B:ASP222 3.6 49.7 1.0 CD2 B:HIS221 4.1 49.6 1.0 ND1 B:HIS277 4.2 45.7 1.0 O B:HOH511 4.2 99.0 1.0 CG B:HIS277 4.2 47.9 1.0 OD2 B:ASP305 4.4 57.0 1.0 CG B:HIS276 4.5 51.1 1.0 ND1 B:HIS250 4.5 59.3 1.0 ND1 B:HIS276 4.5 49.6 1.0 CG B:HIS250 4.5 58.8 1.0 CB B:ASP222 4.6 46.4 1.0 NE2 B:HIS221 4.6 54.6 1.0 C5A B:C2E402 4.8 85.5 1.0 CA B:ASP222 4.8 43.9 1.0 CE B:LYS225 5.0 60.0 1.0

D.Bellini, D.L.Caly, Y.Mccarthy, M.Bumann, S.Q.An, J.M.Dow, R.P.Ryan, M.A.Walsh. Crystal Structure of An Hd-Gyp Domain Cyclic-Di-Gmp Phosphodiesterase Reveals An Enzyme with A Novel Trinuclear Catalytic Iron Centre. Mol.Microbiol. V. 91 26 2014.
ISSN: ISSN 0950-382X
PubMed: 24176013
DOI: 10.1111/MMI.12447