Iron in PDB 4me4: Metallo-Enzyme From P. Marina

The structure of Metallo-Enzyme From P. Marina, PDB code: 4me4 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)	71.00 / 2.55
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	70.090, 181.120, 231.510, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 21.8

The binding sites of Iron atom in the Metallo-Enzyme From P. Marina (pdb code 4me4). 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: 4me4:
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:33.9 occ:1.00 O A:HOH501 1.9 30.7 1.0 NE2 A:HIS277 2.1 36.0 1.0 O4 A:SIN404 2.1 36.7 0.8 OD1 A:ASP222 2.1 36.3 1.0 NE2 A:HIS276 2.2 34.4 1.0 NE2 A:HIS250 2.2 36.9 1.0 CD2 A:HIS277 3.1 36.2 1.0 CE1 A:HIS277 3.1 36.0 1.0 CE1 A:HIS250 3.1 38.6 1.0 CG A:ASP222 3.1 37.1 1.0 CD2 A:HIS276 3.1 34.6 1.0 FE A:FE402 3.1 54.4 1.0 CE1 A:HIS276 3.3 33.9 1.0 CD2 A:HIS250 3.3 37.8 1.0 C4 A:SIN404 3.3 41.1 0.8 OD2 A:ASP222 3.3 41.0 1.0 O3 A:SIN404 4.0 43.5 0.8 ND1 A:HIS277 4.2 35.2 1.0 CG A:HIS277 4.2 36.4 1.0 CD2 A:HIS221 4.3 41.5 1.0 ND1 A:HIS250 4.3 37.6 1.0 CG A:HIS276 4.3 35.1 1.0 ND1 A:HIS276 4.4 35.3 1.0 C3 A:SIN404 4.4 45.2 0.8 CG A:HIS250 4.4 37.8 1.0 CB A:ASP222 4.5 35.0 1.0 O A:HOH502 4.6 29.4 1.0 NE2 A:HIS221 4.7 43.4 1.0 CE A:LYS225 4.8 35.5 1.0 O2 A:SIN404 4.9 60.4 0.8 O1 A:SIN405 4.9 25.7 0.5 C1 A:SIN404 4.9 61.4 0.8 CA A:ASP222 4.9 35.0 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:54.4 occ:1.00 OD2 A:ASP222 2.0 41.0 1.0 O A:HOH501 2.1 30.7 1.0 O A:HOH502 2.3 29.4 1.0 OE1 A:GLU185 2.4 41.2 1.0 O1 A:SIN405 2.4 25.7 0.5 O3 A:SIN404 2.5 43.5 0.8 O4 A:SIN404 2.7 36.7 0.8 C4 A:SIN404 3.0 41.1 0.8 CG A:ASP222 3.0 37.1 1.0 FE A:FE401 3.1 33.9 1.0 OD1 A:ASP222 3.3 36.3 1.0 C1 A:SIN405 3.3 27.6 0.5 N3 A:IMD407 3.4 42.8 1.0 CD A:GLU185 3.4 40.4 1.0 C2 A:IMD407 3.5 51.9 1.0 NZ A:LYS225 3.6 34.5 1.0 O2 A:SIN405 3.6 25.8 0.5 OE2 A:GLU185 3.6 41.8 1.0 FE A:FE403 3.6 30.6 0.5 O A:HOH510 3.8 52.4 1.0 OD2 A:ASP305 4.1 39.3 1.0 O A:HOH562 4.1 43.2 1.0 NE2 A:HIS221 4.2 43.4 1.0 CE A:LYS225 4.2 35.5 1.0 CB A:ASP222 4.4 35.0 1.0 C3 A:SIN404 4.5 45.2 0.8 NE2 A:HIS277 4.5 36.0 1.0 O2 A:SIN404 4.6 60.4 0.8 CE1 A:HIS277 4.6 36.0 1.0 CD2 A:HIS221 4.6 41.5 1.0 C2 A:SIN405 4.7 28.7 0.5 C4 A:IMD407 4.7 50.9 1.0 NE2 A:HIS276 4.7 34.4 1.0 OD1 A:ASP305 4.7 33.6 1.0 O A:HOH512 4.8 49.5 1.0 CG A:GLU185 4.8 36.2 1.0 N1 A:IMD407 4.8 64.4 1.0 CG A:ASP305 4.9 36.1 1.0 NE2 A:HIS250 4.9 36.9 1.0 C3 A:SIN405 4.9 28.1 0.5

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:30.6 occ:0.50 O A:HOH502 1.7 29.4 1.0 N3 A:IMD407 1.8 42.8 1.0 NE2 A:HIS189 2.0 32.7 1.0 OE2 A:GLU185 2.2 41.8 1.0 C4 A:IMD407 2.2 50.9 1.0 OD1 A:ASP305 2.3 33.6 1.0 O2 A:SIN405 2.4 25.8 0.5 CE1 A:HIS189 2.7 33.6 1.0 C2 A:IMD407 2.9 51.9 1.0 O A:HOH513 3.0 66.9 1.0 CD A:GLU185 3.0 40.4 1.0 CD2 A:HIS189 3.1 31.6 1.0 C1 A:SIN405 3.2 27.6 0.5 CG A:ASP305 3.3 36.1 1.0 C5 A:IMD407 3.4 61.8 1.0 OE1 A:GLU185 3.4 41.2 1.0 O1 A:SIN405 3.5 25.7 0.5 OD2 A:ASP305 3.6 39.3 1.0 FE A:FE402 3.6 54.4 1.0 N1 A:IMD407 3.6 64.4 1.0 O A:HOH503 3.7 55.3 1.0 NE2 A:HIS221 3.8 43.4 1.0 ND1 A:HIS189 3.9 33.9 1.0 CE1 A:HIS221 4.1 40.2 1.0 OD2 A:ASP222 4.1 41.0 1.0 CG A:HIS189 4.1 31.4 1.0 CG A:GLU185 4.3 36.2 1.0 O A:HOH506 4.3 44.6 1.0 C2 A:SIN405 4.4 28.7 0.5 O A:HOH501 4.6 30.7 1.0 CB A:ASP305 4.7 34.6 1.0 CG2 A:VAL193 4.9 29.4 1.0 CB A:GLU185 4.9 34.1 1.0 C3 A:SIN405 5.0 28.1 0.5

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:39.1 occ:1.00 O B:HOH501 1.9 36.5 1.0 NE2 B:HIS277 2.0 42.2 1.0 NE2 B:HIS276 2.1 35.5 1.0 OD1 B:ASP222 2.1 36.0 1.0 NE2 B:HIS250 2.2 44.5 1.0 O4 B:SIN405 2.5 61.0 1.0 CE1 B:HIS277 3.0 41.0 1.0 CD2 B:HIS277 3.0 43.4 1.0 CE1 B:HIS276 3.1 35.6 1.0 CD2 B:HIS276 3.1 37.0 1.0 CE1 B:HIS250 3.1 43.4 1.0 FE B:FE402 3.2 74.8 1.0 CD2 B:HIS250 3.2 41.4 1.0 CG B:ASP222 3.2 38.6 1.0 OD2 B:ASP222 3.6 43.1 1.0 C4 B:SIN405 3.7 72.2 1.0 ND1 B:HIS277 4.2 40.0 1.0 O B:HOH502 4.2 27.3 1.0 CG B:HIS277 4.2 41.3 1.0 ND1 B:HIS276 4.2 35.3 1.0 ND1 B:HIS250 4.3 42.7 1.0 CG B:HIS276 4.3 36.8 1.0 CG B:HIS250 4.3 42.3 1.0 C3 B:SIN405 4.6 73.8 1.0 CB B:ASP222 4.6 36.5 1.0 CE B:LYS225 4.6 42.9 1.0 O3 B:SIN405 4.6 75.6 1.0 CD2 B:HIS221 4.6 38.0 1.0 CA B:ASP222 4.9 33.9 1.0 OD2 B:ASP305 5.0 37.8 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:74.8 occ:1.00 O B:HOH501 2.0 36.5 1.0 O3P B:5GP404 2.3 98.9 1.0 OD2 B:ASP222 2.4 43.1 1.0 O4 B:SIN405 2.5 61.0 1.0 O B:HOH502 2.6 27.3 1.0 OE2 B:GLU185 3.0 58.4 1.0 O3 B:SIN405 3.0 75.6 1.0 C4 B:SIN405 3.1 72.2 1.0 FE B:FE401 3.2 39.1 1.0 CG B:ASP222 3.2 38.6 1.0 OD1 B:ASP222 3.3 36.0 1.0 NZ B:LYS225 3.4 45.3 1.0 P B:5GP404 3.5 94.0 1.0 N1 B:IMD407 3.6 33.5 1.0 C2 B:IMD407 3.8 38.0 1.0 CD B:GLU185 3.8 55.5 1.0 FE B:FE403 3.9 38.9 0.5 C5' B:5GP404 3.9 92.6 1.0 O1P B:5GP404 3.9 95.5 1.0 OE1 B:GLU185 3.9 66.6 1.0 O5' B:5GP404 4.0 89.2 1.0 CE B:LYS225 4.1 42.9 1.0 OD2 B:ASP305 4.4 37.8 1.0 NE2 B:HIS277 4.4 42.2 1.0 CE1 B:HIS277 4.4 41.0 1.0 C3 B:SIN405 4.6 73.8 1.0 CB B:ASP222 4.6 36.5 1.0 O1 B:SIN405 4.6 84.9 1.0 C5 B:IMD407 4.7 40.5 1.0 NE2 B:HIS221 4.7 38.9 1.0 NE2 B:HIS276 4.7 35.5 1.0 O2P B:5GP404 4.8 0.0 1.0 CD2 B:HIS221 4.8 38.0 1.0 NE2 B:HIS250 4.9 44.5 1.0 N3 B:IMD407 4.9 47.6 1.0 O B:HOH503 4.9 56.6 1.0 OD1 B:ASP305 5.0 34.3 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:38.9 occ:0.50 N1 B:IMD407 1.7 33.5 1.0 O B:HOH502 1.9 27.3 1.0 NE2 B:HIS189 2.0 36.8 1.0 OD1 B:ASP305 2.1 34.3 1.0 O1P B:5GP404 2.4 95.5 1.0 CE1 B:HIS189 2.6 37.9 1.0 C5 B:IMD407 2.6 40.5 1.0 C2 B:IMD407 2.6 38.0 1.0 OE2 B:GLU185 2.8 58.4 1.0 NE2 B:HIS221 2.9 38.9 1.0 CG B:ASP305 3.2 35.9 1.0 CD2 B:HIS189 3.3 37.0 1.0 OD2 B:ASP305 3.5 37.8 1.0 P B:5GP404 3.6 94.0 1.0 CE1 B:HIS221 3.7 37.6 1.0 CD B:GLU185 3.7 55.5 1.0 N3 B:IMD407 3.7 47.6 1.0 C4 B:IMD407 3.7 44.7 1.0 FE B:FE402 3.9 74.8 1.0 ND1 B:HIS189 3.9 39.0 1.0 CD2 B:HIS221 4.0 38.0 1.0 OD2 B:ASP222 4.0 43.1 1.0 O3P B:5GP404 4.0 98.9 1.0 O5' B:5GP404 4.1 89.2 1.0 CG B:HIS189 4.2 37.6 1.0 OE1 B:GLU185 4.3 66.6 1.0 O B:HOH501 4.3 36.5 1.0 CB B:ASP305 4.5 36.1 1.0 CG B:GLU185 4.6 52.1 1.0 CG2 B:VAL193 4.6 35.6 1.0 O B:HOH504 4.7 45.2 1.0 ND1 B:HIS221 4.9 36.3 1.0 O2P B:5GP404 4.9 0.0 1.0 CA B:ASP305 4.9 35.7 1.0 CG B:ASP222 4.9 38.6 1.0 C5' B:5GP404 4.9 92.6 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