Iron in PDB 4b28: Crystal Structure of Dmsp Lyase Rddddp From Roseobacter Denitrificans

The structure of Crystal Structure of Dmsp Lyase Rddddp From Roseobacter Denitrificans, PDB code: 4b28 was solved by J.H.Hehemann, A.Law, L.Redecke, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.15
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	116.850, 116.850, 133.430, 90.00, 90.00, 120.00
R / Rfree (%)	20.619 / 25.15

The binding sites of Iron atom in the Crystal Structure of Dmsp Lyase Rddddp From Roseobacter Denitrificans (pdb code 4b28). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Dmsp Lyase Rddddp From Roseobacter Denitrificans, PDB code: 4b28:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Dmsp Lyase Rddddp From Roseobacter Denitrificans


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 Dmsp Lyase Rddddp From Roseobacter Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1446 b:33.1 occ:1.00 OD1 A:ASP307 2.0 27.7 1.0 OD2 A:ASP295 2.2 25.0 1.0 OD1 A:ASP297 2.3 27.0 1.0 OD1 A:ASP295 2.4 26.7 1.0 OE1 A:GLU421 2.4 24.5 1.0 CG A:ASP295 2.6 25.0 1.0 FE A:FE1447 2.7 36.7 1.0 CG A:ASP307 2.8 24.4 1.0 OD2 A:ASP307 2.9 25.5 1.0 CD A:GLU421 3.3 24.9 1.0 CG A:ASP297 3.4 24.0 1.0 OE2 A:GLU421 3.4 25.8 1.0 OD2 A:ASP297 3.9 27.0 1.0 CB A:ASP295 4.1 22.9 1.0 OG A:SER309 4.2 24.4 1.0 OE2 A:GLU406 4.2 29.6 1.0 O A:HOH2161 4.2 31.5 1.0 CB A:ASP307 4.2 23.9 1.0 NZ A:LYS419 4.3 28.1 1.0 O A:HOH2151 4.4 28.8 1.0 OH A:TYR366 4.5 31.4 1.0 OE1 A:GLU406 4.6 31.9 1.0 CB A:ASP297 4.6 21.7 1.0 C A:ASP307 4.7 23.0 1.0 NE2 A:HIS371 4.7 28.3 1.0 N A:ASP297 4.7 20.3 1.0 CA A:ASP307 4.7 23.4 1.0 CA A:ASP297 4.7 21.2 1.0 CG A:GLU421 4.8 26.6 1.0 O A:HOH2160 4.8 37.9 1.0 CD A:GLU406 4.8 30.2 1.0 O A:ASP307 4.9 22.9 1.0 N A:ILE308 5.0 22.7 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Dmsp Lyase Rddddp From Roseobacter Denitrificans


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 Dmsp Lyase Rddddp From Roseobacter Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1447 b:36.7 occ:1.00 OE2 A:GLU421 2.1 25.8 1.0 OE2 A:GLU406 2.1 29.6 1.0 NE2 A:HIS371 2.2 28.3 1.0 FE A:FE1446 2.7 33.1 1.0 OD2 A:ASP307 2.7 25.5 1.0 CD A:GLU421 2.9 24.9 1.0 CD A:GLU406 3.1 30.2 1.0 OE1 A:GLU421 3.1 24.5 1.0 CD2 A:HIS371 3.2 26.7 1.0 CE1 A:HIS371 3.2 27.1 1.0 CG A:ASP307 3.4 24.4 1.0 OE1 A:GLU406 3.5 31.9 1.0 OD1 A:ASP307 3.6 27.7 1.0 CG A:GLU406 4.2 29.9 1.0 CG A:GLU421 4.2 26.6 1.0 ND1 A:HIS371 4.3 26.6 1.0 CG A:HIS371 4.3 25.4 1.0 OH A:TYR366 4.3 31.4 1.0 OD1 A:ASP297 4.4 27.0 1.0 OD2 A:ASP295 4.4 25.0 1.0 OD2 A:ASP377 4.5 29.8 1.0 CB A:CYS404 4.5 27.7 1.0 OD1 A:ASP377 4.6 29.6 1.0 CE2 A:TYR366 4.6 30.6 1.0 NZ A:LYS419 4.6 28.1 1.0 CB A:ASP307 4.7 23.9 1.0 O A:HOH2161 4.7 31.5 1.0 CG A:ASP377 4.9 26.0 1.0 CZ A:TYR366 4.9 30.3 1.0

J.H.Hehemann, A.Law, L.Redecke, A.B.Boraston. The Structure of Rddddp From Roseobacter Denitrificans Reveals That Dmsp Lyases in the Dddp-Family Are Metalloenzymes. Plos One V. 9 03128 2014.
ISSN: ISSN 1932-6203
PubMed: 25054772
DOI: 10.1371/JOURNAL.PONE.0103128