Iron in PDB 3t81: Crystal Structure of Diiron Adenine Deaminase

All present enzymatic activity of Crystal Structure of Diiron Adenine Deaminase:
3.5.4.2;

The structure of Crystal Structure of Diiron Adenine Deaminase, PDB code: 3t81 was solved by A.Bagaria, D.Kumaran, S.K.Burley, S.Swaminathan, New York Sgx Researchcenter For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.89 / 2.63
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.662, 131.845, 69.628, 90.00, 97.04, 90.00
R / Rfree (%)	18.5 / 28.7

The binding sites of Iron atom in the Crystal Structure of Diiron Adenine Deaminase (pdb code 3t81). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of Diiron Adenine Deaminase, PDB code: 3t81:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Crystal Structure of Diiron Adenine Deaminase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Diiron Adenine Deaminase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe606 b:49.8 occ:1.00 NE2 A:HIS239 2.1 42.9 1.0 OE2 A:GLU240 2.2 33.3 1.0 O A:HOH630 2.2 27.1 1.0 OE1 A:GLU187 2.2 44.1 1.0 ND1 A:HIS218 2.3 37.8 1.0 CE1 A:HIS218 2.7 40.3 1.0 CE1 A:HIS239 3.0 43.5 1.0 CD2 A:HIS239 3.2 39.4 1.0 CD A:GLU240 3.3 36.7 1.0 CD A:GLU187 3.3 39.9 1.0 CG A:HIS218 3.4 38.0 1.0 OE2 A:GLU187 3.7 49.2 1.0 CG A:GLU240 3.7 34.9 1.0 FE A:FE607 3.9 45.8 1.0 NE2 A:HIS218 3.9 41.3 1.0 CB A:HIS218 4.1 41.2 1.0 ND1 A:HIS239 4.2 41.5 1.0 CG A:HIS239 4.3 35.4 1.0 CD2 A:HIS218 4.3 44.9 1.0 OE1 A:GLU240 4.4 33.0 1.0 OD2 A:ASP289 4.4 45.2 1.0 CE A:MSE189 4.6 78.9 1.0 CG A:GLU187 4.6 39.7 1.0 CA A:HIS218 4.8 40.6 1.0 NE2 A:HIS92 4.8 40.1 1.0 CB A:GLU187 4.9 46.4 1.0 NH1 A:ARG260 4.9 23.9 1.0

Iron binding site 2 out of 6 in the Crystal Structure of Diiron Adenine Deaminase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Diiron Adenine Deaminase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe607 b:45.8 occ:1.00 NE2 A:HIS92 2.2 40.1 1.0 OD1 A:ASP289 2.3 45.3 1.0 NE2 A:HIS94 2.3 42.2 1.0 OE2 A:GLU187 2.4 49.2 1.0 CG A:ASP289 3.0 40.7 1.0 OD2 A:ASP289 3.0 45.2 1.0 CE1 A:HIS92 3.2 38.7 1.0 CD2 A:HIS92 3.2 39.8 1.0 CD A:GLU187 3.3 39.9 1.0 CD2 A:HIS94 3.3 38.6 1.0 CE1 A:HIS94 3.3 41.9 1.0 OE1 A:GLU187 3.6 44.1 1.0 NE2 A:HIS239 3.7 42.9 1.0 FE A:FE606 3.9 49.8 1.0 O A:HOH630 4.2 27.1 1.0 OD1 A:ASP290 4.2 63.6 1.0 CE1 A:HIS239 4.2 43.5 1.0 CD2 A:HIS239 4.3 39.4 1.0 ND1 A:HIS92 4.3 38.5 1.0 CB A:ASP289 4.3 36.3 1.0 CG A:HIS92 4.4 30.8 1.0 ND1 A:HIS94 4.4 35.4 1.0 CG A:HIS94 4.5 35.6 1.0 CG A:GLU187 4.5 39.7 1.0 CA A:ASP289 4.8 37.8 1.0 CG A:HIS239 4.9 35.4 1.0 ND1 A:HIS239 4.9 41.5 1.0

Iron binding site 3 out of 6 in the Crystal Structure of Diiron Adenine Deaminase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Diiron Adenine Deaminase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe608 b:51.0 occ:1.00 OE1 A:GLU123 2.0 39.3 1.0 OD1 A:ASP478 2.2 42.9 1.0 NE2 A:HIS122 2.3 34.9 1.0 ND1 A:HIS477 2.4 46.7 1.0 OE2 A:GLU123 2.5 44.0 1.0 CD A:GLU123 2.5 42.0 1.0 CE1 A:HIS477 2.9 43.8 1.0 CD2 A:HIS122 3.2 34.8 1.0 CE1 A:HIS122 3.3 33.6 1.0 CG A:ASP478 3.3 45.7 1.0 CG A:HIS477 3.5 42.7 1.0 OD2 A:ASP478 3.7 46.2 1.0 CG A:GLU123 4.0 41.3 1.0 CB A:HIS477 4.1 39.7 1.0 NE2 A:HIS477 4.1 48.5 1.0 CG A:HIS122 4.3 37.5 1.0 ND1 A:HIS122 4.3 41.1 1.0 CD2 A:HIS477 4.4 47.1 1.0 CE1 A:HIS480 4.5 36.1 1.0 NE2 A:HIS480 4.5 31.4 1.0 CB A:ASP478 4.6 40.7 1.0 CA A:HIS477 4.6 41.4 1.0 CA A:ASP478 4.7 44.1 1.0 CB A:GLU123 4.9 40.8 1.0

Iron binding site 4 out of 6 in the Crystal Structure of Diiron Adenine Deaminase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Diiron Adenine Deaminase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe606 b:52.6 occ:1.00 NE2 B:HIS94 1.9 41.1 1.0 O B:HOH635 2.1 38.7 1.0 NE2 B:HIS92 2.1 51.4 1.0 OD1 B:ASP289 2.2 36.8 1.0 CE1 B:HIS94 2.9 40.2 1.0 CD2 B:HIS94 3.0 37.6 1.0 OE1 B:GLU187 3.0 51.1 1.0 CE1 B:HIS92 3.0 45.0 1.0 CD2 B:HIS92 3.1 50.2 1.0 CG B:ASP289 3.3 41.6 1.0 CD B:GLU187 3.6 48.9 1.0 OD2 B:ASP289 3.6 47.8 1.0 OE2 B:GLU187 3.7 41.1 1.0 FE B:FE608 3.9 59.3 1.0 CE1 B:HIS239 4.0 55.0 1.0 ND1 B:HIS94 4.0 41.5 1.0 NE2 B:HIS239 4.0 58.6 1.0 CG B:HIS94 4.1 38.5 1.0 ND1 B:HIS92 4.2 38.5 1.0 CG B:HIS92 4.2 42.2 1.0 CB B:ASP289 4.5 40.0 1.0 OD2 B:ASP290 4.6 56.0 1.0 ND1 B:HIS239 4.7 53.3 1.0 CA B:ASP289 4.7 44.6 1.0 CD2 B:HIS239 4.8 54.0 1.0 CG B:GLU187 4.8 51.4 1.0 CE1 B:HIS122 4.9 48.6 1.0

Iron binding site 5 out of 6 in the Crystal Structure of Diiron Adenine Deaminase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Diiron Adenine Deaminase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe607 b:64.2 occ:1.00 ND1 B:HIS477 1.9 50.0 1.0 OE2 B:GLU123 2.2 45.0 1.0 OD1 B:ASP478 2.2 56.4 1.0 OE1 B:GLU123 2.5 54.0 1.0 CE1 B:HIS477 2.6 52.2 1.0 CD B:GLU123 2.7 49.6 1.0 NE2 B:HIS122 2.7 46.2 1.0 CG B:HIS477 3.1 54.7 1.0 CG B:ASP478 3.1 58.9 1.0 OD2 B:ASP478 3.5 57.6 1.0 CD2 B:HIS122 3.6 44.3 1.0 CB B:HIS477 3.7 54.7 1.0 CE1 B:HIS122 3.7 48.6 1.0 NE2 B:HIS477 3.8 53.3 1.0 CD2 B:HIS477 4.1 51.4 1.0 CG B:GLU123 4.2 49.6 1.0 CA B:HIS477 4.4 55.8 1.0 CE1 B:HIS480 4.4 59.0 1.0 CB B:ASP478 4.4 58.3 1.0 NE2 B:HIS480 4.6 58.5 1.0 CA B:ASP478 4.6 58.7 1.0 CG B:HIS122 4.8 41.4 1.0 ND1 B:HIS122 4.8 48.6 1.0

Iron binding site 6 out of 6 in the Crystal Structure of Diiron Adenine Deaminase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Diiron Adenine Deaminase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe608 b:59.3 occ:1.00 OE2 B:GLU187 1.5 41.1 1.0 OE2 B:GLU240 1.9 36.8 1.0 ND1 B:HIS218 2.3 54.1 1.0 O B:HOH635 2.3 38.7 1.0 NE2 B:HIS239 2.7 58.6 1.0 CD B:GLU187 2.8 48.9 1.0 CE1 B:HIS218 3.1 47.1 1.0 CD B:GLU240 3.1 44.8 1.0 CD2 B:HIS239 3.2 54.0 1.0 CG B:HIS218 3.4 50.1 1.0 OE1 B:GLU187 3.6 51.1 1.0 CG B:GLU240 3.8 43.2 1.0 CE1 B:HIS239 3.8 55.0 1.0 CB B:HIS218 3.8 45.6 1.0 CG B:GLU187 3.8 51.4 1.0 FE B:FE606 3.9 52.6 1.0 OE1 B:GLU240 4.2 36.7 1.0 NE2 B:HIS218 4.3 49.8 1.0 CG B:HIS239 4.4 51.7 1.0 CD2 B:HIS218 4.5 50.3 1.0 NH1 B:ARG260 4.5 44.3 1.0 OD2 B:ASP289 4.6 47.8 1.0 ND1 B:HIS239 4.7 53.3 1.0 CA B:HIS218 4.7 45.1 1.0 NE2 B:HIS92 4.9 51.4 1.0

A.Bagaria, D.Kumaran, S.K.Burley, S.Swaminathan. Crystal Structure of Diiron Adenine Deaminase To Be Published.