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

Protein crystallography data

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

Iron Binding Sites:

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 4s00

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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 4s00

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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 4s00

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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 4s00

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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 4s00

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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 4s00

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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 4s00

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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 4s00

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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

Reference:

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
Page generated: Sun Dec 13 15:46:30 2020

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