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

All present enzymatic activity of Metallo-Enzyme From P. Marina:
3.1.4.1;

The structure of Metallo-Enzyme From P. Marina, PDB code: 4mcw 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)	71.75 / 2.03
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	69.830, 182.380, 232.470, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.3

The binding sites of Iron atom in the Metallo-Enzyme From P. Marina (pdb code 4mcw). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Metallo-Enzyme From P. Marina, PDB code: 4mcw:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 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:36.0 occ:1.00 NE2 A:HIS277 2.1 35.3 1.0 NE2 A:HIS250 2.1 40.0 1.0 NE2 A:HIS276 2.1 41.8 1.0 O A:HOH575 2.2 27.8 1.0 OD1 A:ASP222 2.2 31.2 1.0 O4 A:SIN404 2.4 34.9 0.8 CE1 A:HIS250 3.0 37.8 1.0 CD2 A:HIS277 3.1 34.6 1.0 CE1 A:HIS277 3.1 35.1 1.0 CD2 A:HIS276 3.1 37.4 1.0 CE1 A:HIS276 3.1 37.5 1.0 CD2 A:HIS250 3.2 35.3 1.0 CG A:ASP222 3.4 32.6 1.0 C4 A:SIN404 3.4 33.7 0.8 FE A:FE402 3.7 30.9 0.7 O3 A:SIN404 3.8 32.9 0.8 OD2 A:ASP222 3.8 34.2 1.0 ND1 A:HIS277 4.2 35.1 1.0 ND1 A:HIS250 4.2 37.9 1.0 CG A:HIS277 4.2 34.8 1.0 ND1 A:HIS276 4.3 37.0 1.0 CG A:HIS276 4.3 38.9 1.0 CG A:HIS250 4.3 38.0 1.0 CD2 A:HIS221 4.3 42.6 1.0 O A:HOH584 4.4 47.7 1.0 CB A:ASP222 4.7 31.1 1.0 O A:HOH576 4.7 26.9 0.9 C3 A:SIN404 4.7 37.2 0.8 C1 A:SIN404 4.8 45.1 0.8 NE2 A:HIS221 4.9 41.6 1.0 CE A:LYS225 4.9 39.8 1.0 C2 A:SIN404 4.9 36.6 0.8 O1 A:SIN404 4.9 47.5 0.8 CA A:ASP222 4.9 32.3 1.0

Iron binding site 2 out of 6 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:30.9 occ:0.73 O A:HOH575 1.8 27.8 1.0 OE1 A:GLU185 2.0 33.6 1.0 OD2 A:ASP222 2.2 34.2 1.0 O3 A:SIN404 2.2 32.9 0.8 O4 A:SIN405 2.2 32.4 0.8 O A:HOH576 2.4 26.9 0.9 CD A:GLU185 3.0 38.6 1.0 CG A:ASP222 3.1 32.6 1.0 C4 A:SIN405 3.1 37.2 0.8 C4 A:SIN404 3.1 33.7 0.8 O3 A:SIN405 3.3 33.8 0.8 OD1 A:ASP222 3.3 31.2 1.0 OE2 A:GLU185 3.3 44.6 1.0 FE A:FE403 3.4 32.3 0.8 O4 A:SIN404 3.5 34.9 0.8 NZ A:LYS225 3.6 42.1 1.0 FE A:FE401 3.7 36.0 1.0 O A:HOH636 3.8 48.1 1.0 O A:HOH592 4.0 57.7 1.0 O A:HOH584 4.2 47.7 1.0 NE2 A:HIS221 4.2 41.6 1.0 OD2 A:ASP305 4.2 36.6 1.0 CE A:LYS225 4.3 39.8 1.0 CG A:GLU185 4.4 36.3 1.0 C2 A:IMD407 4.4 43.1 0.8 CB A:ASP222 4.4 31.1 1.0 C3 A:SIN404 4.5 37.2 0.8 N1 A:IMD407 4.5 44.4 0.8 C3 A:SIN405 4.5 34.1 0.8 O2 A:SIN406 4.5 40.5 0.6 CD2 A:HIS221 4.7 42.6 1.0 OD1 A:ASP305 4.8 38.1 1.0 CG A:ASP305 4.9 35.6 1.0 NE2 A:HIS276 5.0 41.8 1.0

Iron binding site 3 out of 6 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:32.3 occ:0.76 O A:HOH576 1.9 26.9 0.9 NE2 A:HIS189 2.0 33.8 1.0 OE2 A:GLU185 2.2 44.6 1.0 N1 A:IMD407 2.2 44.4 0.8 O3 A:SIN405 2.2 33.8 0.8 OD1 A:ASP305 2.3 38.1 1.0 CE1 A:HIS189 2.9 34.1 1.0 CD A:GLU185 3.1 38.6 1.0 C2 A:IMD407 3.1 43.1 0.8 CD2 A:HIS189 3.1 36.1 1.0 C5 A:IMD407 3.2 40.9 0.8 CG A:ASP305 3.2 35.6 1.0 C4 A:SIN405 3.2 37.2 0.8 OE1 A:GLU185 3.4 33.6 1.0 FE A:FE402 3.4 30.9 0.7 OD2 A:ASP305 3.4 36.6 1.0 O4 A:SIN405 3.6 32.4 0.8 NE2 A:HIS221 3.7 41.6 1.0 O A:HOH587 4.0 41.3 1.0 CE1 A:HIS221 4.0 43.6 1.0 ND1 A:HIS189 4.1 35.7 1.0 OD2 A:ASP222 4.1 34.2 1.0 CG A:HIS189 4.2 33.6 1.0 N3 A:IMD407 4.3 43.1 0.8 C4 A:IMD407 4.3 43.9 0.8 CG A:GLU185 4.4 36.3 1.0 O A:HOH575 4.5 27.8 1.0 C3 A:SIN405 4.5 34.1 0.8 CB A:ASP305 4.6 30.8 1.0 CG2 A:VAL193 4.9 36.1 1.0 CB A:GLU185 4.9 35.7 1.0 CD2 A:HIS221 5.0 42.6 1.0

Iron binding site 4 out of 6 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:40.0 occ:1.00 O B:HOH628 2.1 31.3 1.0 NE2 B:HIS250 2.1 39.0 1.0 NE2 B:HIS277 2.2 43.0 1.0 NE2 B:HIS276 2.2 46.3 1.0 OD1 B:ASP222 2.2 36.6 1.0 O4 B:SIN404 2.4 40.3 0.6 CD2 B:HIS277 3.0 38.9 1.0 CD2 B:HIS276 3.1 43.1 1.0 CD2 B:HIS250 3.1 35.6 1.0 CE1 B:HIS250 3.1 39.0 1.0 CE1 B:HIS276 3.2 44.0 1.0 CE1 B:HIS277 3.3 41.2 1.0 CG B:ASP222 3.3 36.9 1.0 C4 B:SIN404 3.5 41.2 0.6 FE B:FE402 3.7 34.2 0.5 OD2 B:ASP222 3.8 39.6 1.0 O3 B:SIN404 3.9 39.2 0.6 ND1 B:HIS250 4.2 39.4 1.0 CG B:HIS277 4.2 40.3 1.0 CG B:HIS250 4.3 39.1 1.0 O B:HOH542 4.3 34.2 0.9 CG B:HIS276 4.3 42.2 1.0 ND1 B:HIS276 4.3 41.4 1.0 CD2 B:HIS221 4.3 45.4 1.0 ND1 B:HIS277 4.3 41.5 1.0 O4 B:SIN405 4.5 51.9 0.7 CB B:ASP222 4.6 34.3 1.0 CE B:LYS225 4.8 43.2 1.0 C3 B:SIN404 4.8 46.1 0.6 CA B:ASP222 4.8 33.9 1.0 C1 B:SIN404 4.9 56.3 0.6 C2 B:SIN404 4.9 50.3 0.6 O B:HIS221 4.9 30.0 1.0

Iron binding site 5 out of 6 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 5 of Metallo-Enzyme From P. Marina within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:34.2 occ:0.49 O B:HOH628 1.8 31.3 1.0 O3 B:SIN404 2.0 39.2 0.6 O B:HOH542 2.0 34.2 0.9 OE2 B:GLU185 2.2 53.5 1.0 OD2 B:ASP222 2.2 39.6 1.0 O4 B:SIN405 2.5 51.9 0.7 O3 B:SIN405 2.5 47.0 0.7 C4 B:SIN405 2.8 53.0 0.7 C4 B:SIN404 2.9 41.2 0.6 O4 B:SIN404 3.2 40.3 0.6 CG B:ASP222 3.2 36.9 1.0 FE B:FE403 3.2 42.8 0.7 CD B:GLU185 3.2 60.4 1.0 OD1 B:ASP222 3.4 36.6 1.0 OE1 B:GLU185 3.5 63.9 1.0 O B:HOH545 3.5 54.9 0.9 O B:HOH654 3.6 67.2 1.0 FE B:FE401 3.7 40.0 1.0 NZ B:LYS225 3.7 46.9 1.0 OD2 B:ASP305 4.0 42.7 1.0 NE2 B:HIS221 4.1 47.0 1.0 C3 B:SIN404 4.2 46.1 0.6 C3 B:SIN405 4.3 54.5 0.7 OD1 B:ASP305 4.4 44.0 1.0 O B:HOH630 4.4 64.0 1.0 CE B:LYS225 4.4 43.2 1.0 CD2 B:HIS221 4.5 45.4 1.0 CB B:ASP222 4.6 34.3 1.0 CG B:GLU185 4.6 54.9 1.0 CG B:ASP305 4.6 42.3 1.0 NE2 B:HIS277 4.9 43.0 1.0 O B:HOH544 4.9 67.0 1.0 NE2 B:HIS189 5.0 40.4 1.0

Iron binding site 6 out of 6 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 6 of Metallo-Enzyme From P. Marina within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe403 b:42.8 occ:0.65 O B:HOH542 2.0 34.2 0.9 NE2 B:HIS189 2.0 40.4 1.0 OD1 B:ASP305 2.1 44.0 1.0 O B:HOH545 2.4 54.9 0.9 OE1 B:GLU185 2.5 63.9 1.0 O3 B:SIN405 2.6 47.0 0.7 CE1 B:HIS189 2.9 42.0 1.0 CD2 B:HIS189 3.1 43.4 1.0 NE2 B:HIS221 3.1 47.0 1.0 CG B:ASP305 3.1 42.3 1.0 CD B:GLU185 3.2 60.4 1.0 O B:HOH546 3.2 63.6 1.0 FE B:FE402 3.2 34.2 0.5 O B:HOH544 3.2 67.0 1.0 OE2 B:GLU185 3.4 53.5 1.0 OD2 B:ASP305 3.5 42.7 1.0 CE1 B:HIS221 3.6 51.0 1.0 C4 B:SIN405 3.8 53.0 0.7 OD2 B:ASP222 4.0 39.6 1.0 ND1 B:HIS189 4.1 42.9 1.0 CG B:HIS189 4.2 40.2 1.0 O B:HOH629 4.2 49.5 0.8 O B:HOH628 4.3 31.3 1.0 CD2 B:HIS221 4.3 45.4 1.0 O4 B:SIN405 4.3 51.9 0.7 CB B:ASP305 4.4 37.3 1.0 CG B:GLU185 4.5 54.9 1.0 CG2 B:VAL193 4.7 37.3 1.0 CG B:ASP222 4.8 36.9 1.0 C3 B:SIN405 4.9 54.5 0.7 CA B:ASP305 4.9 36.4 1.0 ND1 B:HIS221 4.9 42.8 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