Iron in PDB 4s00: Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate

The structure of Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate, PDB code: 4s00 was solved by Y.Zhang, P.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.29 / 2.10
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	175.820, 175.820, 109.637, 90.00, 90.00, 120.00
R / Rfree (%)	15.1 / 17.7

The binding sites of Iron atom in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate (pdb code 4s00). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate, PDB code: 4s00:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate


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 Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:28.0 occ:0.70 OE2 A:GLU421 2.3 16.8 1.0 NE2 A:HIS371 2.4 12.4 1.0 OD2 A:ASP307 2.5 18.7 1.0 FE A:FE502 2.7 35.8 0.7 OE2 A:GLU406 3.0 34.2 1.0 CD A:GLU421 3.2 15.4 1.0 CD2 A:HIS371 3.2 12.6 1.0 OE1 A:GLU406 3.3 30.5 1.0 CD A:GLU406 3.3 30.8 1.0 CG A:ASP307 3.3 15.9 1.0 OE1 A:GLU421 3.4 14.8 1.0 O A:AKR503 3.4 27.9 1.0 CE1 A:HIS371 3.4 12.8 1.0 OD1 A:ASP307 3.6 20.9 1.0 O1 C:GOL504 4.0 38.6 1.0 OD2 A:ASP295 4.2 25.8 1.0 CG A:HIS371 4.4 10.8 1.0 CB A:CYS404 4.4 12.6 1.0 OD2 A:ASP377 4.5 24.7 1.0 C A:AKR503 4.5 37.8 1.0 CG A:GLU406 4.5 17.5 1.0 ND1 A:HIS371 4.5 14.1 1.0 C1 C:GOL504 4.5 29.0 1.0 CG A:GLU421 4.5 9.6 1.0 CB A:ASP307 4.6 11.6 1.0 O A:HOH1068 4.7 33.5 1.0 OXT A:AKR503 4.7 29.4 1.0 OD1 A:ASP297 4.8 19.2 1.0 OD1 A:ASP377 4.8 18.3 1.0 NZ A:LYS419 4.9 10.8 1.0 CG A:ASP377 5.0 21.5 1.0

Iron binding site 2 out of 8 in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate


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 Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:35.8 occ:0.69 OD1 A:ASP297 2.3 19.2 1.0 OD2 A:ASP295 2.4 25.8 1.0 OD1 A:ASP307 2.5 20.9 1.0 O A:AKR503 2.6 27.9 1.0 FE A:FE501 2.7 28.0 0.7 OD2 A:ASP307 2.7 18.7 1.0 CG A:ASP307 2.9 15.9 1.0 OXT A:AKR503 3.0 29.4 1.0 OD1 A:ASP295 3.0 21.0 1.0 CG A:ASP295 3.0 20.7 1.0 C A:AKR503 3.1 37.8 1.0 CG A:ASP297 3.4 17.9 1.0 OE1 A:GLU421 3.7 14.8 1.0 OD2 A:ASP297 3.7 17.7 1.0 OE2 A:GLU421 4.0 16.8 1.0 CD A:GLU421 4.3 15.4 1.0 O A:HOH1190 4.4 21.1 1.0 CB A:ASP295 4.4 14.8 1.0 CB A:ASP307 4.4 11.6 1.0 CA A:AKR503 4.4 26.9 1.0 O A:HOH665 4.5 13.8 1.0 OD2 A:ASP377 4.5 24.7 1.0 OE1 A:GLU406 4.6 30.5 1.0 NE2 A:HIS371 4.6 12.4 1.0 CB A:ASP297 4.7 12.9 1.0 NZ A:LYS419 4.7 10.8 1.0 CA A:ASP297 4.9 15.4 1.0 O A:HOH1068 4.9 33.5 1.0 OD1 A:ASP377 4.9 18.3 1.0

Iron binding site 3 out of 8 in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate


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 Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:24.9 occ:0.68 OE2 B:GLU421 2.3 16.4 1.0 NE2 B:HIS371 2.4 12.0 1.0 OD2 B:ASP307 2.5 17.4 1.0 FE B:FE502 2.7 37.5 0.7 OE2 B:GLU406 2.7 33.1 1.0 CD B:GLU406 3.0 28.5 1.0 CD B:GLU421 3.2 15.0 1.0 CD2 B:HIS371 3.2 13.1 1.0 OE1 B:GLU406 3.3 31.6 1.0 CG B:ASP307 3.3 16.6 1.0 CE1 B:HIS371 3.4 13.2 1.0 OE1 B:GLU421 3.4 15.2 1.0 OXT B:AKR503 3.4 26.7 1.0 OD1 B:ASP307 3.5 20.9 1.0 O3 D:GOL503 3.9 35.7 1.0 CG B:GLU406 3.9 21.9 1.0 OD2 B:ASP295 4.2 28.7 1.0 CB B:CYS404 4.3 11.6 1.0 CG B:HIS371 4.4 11.4 1.0 ND1 B:HIS371 4.5 14.9 1.0 C3 D:GOL503 4.5 33.3 1.0 C B:AKR503 4.5 38.2 1.0 OD2 B:ASP377 4.5 24.2 1.0 CG B:GLU421 4.5 10.2 1.0 CB B:ASP307 4.6 10.2 1.0 O B:AKR503 4.8 29.4 1.0 OD1 B:ASP377 4.8 19.1 1.0 OD1 B:ASP297 4.8 19.0 1.0 NZ B:LYS419 4.9 14.3 1.0

Iron binding site 4 out of 8 in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate


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 Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:37.5 occ:0.71 OD1 B:ASP297 2.3 19.0 1.0 OD2 B:ASP295 2.4 28.7 1.0 OD1 B:ASP307 2.4 20.9 1.0 FE B:FE501 2.7 24.9 0.7 OXT B:AKR503 2.7 26.7 1.0 OD2 B:ASP307 2.7 17.4 1.0 CG B:ASP307 2.9 16.6 1.0 OD1 B:ASP295 2.9 18.5 1.0 O B:AKR503 3.0 29.4 1.0 CG B:ASP295 3.0 19.3 1.0 C B:AKR503 3.1 38.2 1.0 CG B:ASP297 3.4 17.5 1.0 OE1 B:GLU421 3.6 15.2 1.0 OD2 B:ASP297 3.8 17.2 1.0 OE2 B:GLU421 4.0 16.4 1.0 CD B:GLU421 4.3 15.0 1.0 O B:HOH776 4.3 20.2 1.0 CB B:ASP295 4.4 13.0 1.0 CB B:ASP307 4.4 10.2 1.0 CA B:AKR503 4.4 27.6 1.0 OE1 B:GLU406 4.5 31.6 1.0 O B:HOH655 4.5 14.3 1.0 OD2 B:ASP377 4.6 24.2 1.0 OE2 B:GLU406 4.6 33.1 1.0 NE2 B:HIS371 4.6 12.0 1.0 O B:HOH1166 4.6 29.9 1.0 CB B:ASP297 4.7 13.4 1.0 NZ B:LYS419 4.7 14.3 1.0 CD B:GLU406 4.8 28.5 1.0 CA B:ASP297 4.9 14.6 1.0 OD1 B:ASP377 5.0 19.1 1.0

Iron binding site 5 out of 8 in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate


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 Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:30.8 occ:0.74 OE2 C:GLU421 2.3 22.7 1.0 NE2 C:HIS371 2.4 14.5 1.0 OD2 C:ASP307 2.6 25.7 1.0 FE C:FE502 2.7 42.1 0.7 OE2 C:GLU406 3.0 38.7 1.0 CD C:GLU406 3.1 32.4 1.0 CD2 C:HIS371 3.2 11.9 1.0 CD C:GLU421 3.2 22.8 1.0 OE1 C:GLU406 3.3 34.2 1.0 CG C:ASP307 3.3 20.9 1.0 OXT C:AKR503 3.3 27.5 1.0 OE1 C:GLU421 3.4 21.0 1.0 CE1 C:HIS371 3.5 17.6 1.0 OD1 C:ASP307 3.6 23.5 1.0 CG C:GLU406 4.0 27.9 1.0 O3 A:GOL504 4.2 39.5 1.0 OD2 C:ASP295 4.3 24.8 1.0 CB C:CYS404 4.4 13.4 1.0 CG C:HIS371 4.4 13.6 1.0 C3 A:GOL504 4.4 27.6 1.0 C C:AKR503 4.4 36.8 1.0 ND1 C:HIS371 4.5 14.5 1.0 CB C:ASP307 4.5 15.3 1.0 CG C:GLU421 4.6 15.6 1.0 OD2 C:ASP377 4.6 24.1 1.0 OD1 C:ASP377 4.7 21.5 1.0 O C:AKR503 4.8 34.9 1.0 OD1 C:ASP297 4.8 21.8 1.0 O C:HOH1013 4.9 35.7 1.0 NZ C:LYS419 5.0 18.6 1.0 CG C:ASP377 5.0 18.8 1.0

Iron binding site 6 out of 8 in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate


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 Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:42.1 occ:0.73 OD1 C:ASP297 2.4 21.8 1.0 OD2 C:ASP295 2.4 24.8 1.0 OD1 C:ASP307 2.4 23.5 1.0 OXT C:AKR503 2.7 27.5 1.0 FE C:FE501 2.7 30.8 0.7 OD2 C:ASP307 2.8 25.7 1.0 OD1 C:ASP295 2.8 19.0 1.0 CG C:ASP295 2.9 20.5 1.0 CG C:ASP307 2.9 20.9 1.0 O C:AKR503 3.0 34.9 1.0 C C:AKR503 3.2 36.8 1.0 CG C:ASP297 3.3 19.5 1.0 OE1 C:GLU421 3.6 21.0 1.0 OD2 C:ASP297 3.6 18.1 1.0 OE2 C:GLU421 4.0 22.7 1.0 CD C:GLU421 4.2 22.8 1.0 O C:HOH1119 4.3 25.7 1.0 CB C:ASP295 4.3 15.0 1.0 O C:HOH645 4.4 17.3 1.0 CB C:ASP307 4.4 15.3 1.0 OE1 C:GLU406 4.5 34.2 1.0 CA C:AKR503 4.5 30.2 1.0 CB C:ASP297 4.6 15.6 1.0 NZ C:LYS419 4.7 18.6 1.0 NE2 C:HIS371 4.7 14.5 1.0 OD2 C:ASP377 4.7 24.1 1.0 OE2 C:GLU406 4.7 38.7 1.0 CA C:ASP297 4.9 18.8 1.0 CD C:GLU406 4.9 32.4 1.0 N C:ASP297 5.0 16.6 1.0

Iron binding site 7 out of 8 in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:28.5 occ:0.72 OE2 D:GLU421 2.3 21.0 1.0 NE2 D:HIS371 2.4 13.9 1.0 OD2 D:ASP307 2.5 24.0 1.0 OE2 D:GLU406 2.6 38.5 1.0 FE D:FE502 2.7 41.8 0.8 CD D:GLU406 3.1 32.6 1.0 CD2 D:HIS371 3.2 12.7 1.0 CD D:GLU421 3.2 20.9 1.0 CG D:ASP307 3.3 20.6 1.0 O B:AKR504 3.3 26.2 1.0 OE1 D:GLU421 3.4 18.2 1.0 CE1 D:HIS371 3.5 16.3 1.0 OD1 D:ASP307 3.5 22.6 1.0 OE1 D:GLU406 3.5 32.7 1.0 CG D:GLU406 4.0 29.0 1.0 C1 D:GOL504 4.1 35.8 1.0 O1 D:GOL504 4.3 38.8 1.0 OD2 D:ASP295 4.4 24.2 1.0 CB D:CYS404 4.4 12.6 1.0 CG D:HIS371 4.4 15.0 1.0 C B:AKR504 4.4 36.3 1.0 OD2 D:ASP377 4.5 25.8 1.0 CB D:ASP307 4.5 14.1 1.0 ND1 D:HIS371 4.5 14.7 1.0 CG D:GLU421 4.6 15.5 1.0 OD1 D:ASP377 4.7 22.5 1.0 OD1 D:ASP297 4.8 21.9 1.0 OXT B:AKR504 4.8 34.9 1.0 O D:HOH1040 4.9 34.2 1.0 CG D:ASP377 4.9 18.9 1.0 NZ D:LYS419 5.0 17.5 1.0 OD1 D:ASP295 5.0 18.6 1.0 O D:ASP307 5.0 14.1 1.0

Iron binding site 8 out of 8 in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant Y366A in Complex with Acrylate within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe502 b:41.8 occ:0.77 OD1 D:ASP297 2.4 21.9 1.0 OD2 D:ASP295 2.4 24.2 1.0 OD1 D:ASP307 2.4 22.6 1.0 FE D:FE501 2.7 28.5 0.7 O B:AKR504 2.7 26.2 1.0 OD2 D:ASP307 2.7 24.0 1.0 OD1 D:ASP295 2.8 18.6 1.0 CG D:ASP307 2.9 20.6 1.0 CG D:ASP295 2.9 19.2 1.0 OXT B:AKR504 3.2 34.9 1.0 C B:AKR504 3.3 36.3 1.0 CG D:ASP297 3.3 19.0 1.0 OE1 D:GLU421 3.6 18.2 1.0 OD2 D:ASP297 3.6 17.7 1.0 OE2 D:GLU421 4.0 21.0 1.0 O D:HOH827 4.2 24.8 1.0 CD D:GLU421 4.2 20.9 1.0 CB D:ASP295 4.3 15.1 1.0 CB D:ASP307 4.4 14.1 1.0 O D:HOH636 4.4 16.2 1.0 OE2 D:GLU406 4.5 38.5 1.0 CA B:AKR504 4.6 27.9 1.0 NZ D:LYS419 4.7 17.5 1.0 CB D:ASP297 4.7 15.8 1.0 OE1 D:GLU406 4.7 32.7 1.0 NE2 D:HIS371 4.7 13.9 1.0 OD2 D:ASP377 4.7 25.8 1.0 CA D:ASP297 4.9 18.5 1.0 CD D:GLU406 4.9 32.6 1.0 OG D:SER309 5.0 17.2 1.0 N D:ASP297 5.0 16.7 1.0

P.Wang, X.L.Chen, C.Y.Li, X.Gao, D.Y.Zhu, B.B.Xie, Q.L.Qin, X.Y.Zhang, H.N.Su, B.C.Zhou, L.Y.Xun, Y.Z.Zhang. Structural and Molecular Basis For the Novel Catalytic Mechanism and Evolution of Dddp, An Abundant Peptidase-Like Bacterial Dimethylsulfoniopropionate Lyase: A New Enzyme From An Old Fold. Mol.Microbiol. V. 98 289 2015.
ISSN: ISSN 0950-382X
PubMed: 26154071
DOI: 10.1111/MMI.13119