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Iron in PDB 4s01: Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant D377N in Complex with Acrylate

Protein crystallography data

The structure of Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant D377N in Complex with Acrylate, PDB code: 4s01 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) 34.31 / 2.10
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 175.963, 175.963, 109.679, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / 20.5

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant D377N in Complex with Acrylate (pdb code 4s01). 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 D377N in Complex with Acrylate, PDB code: 4s01:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4s01

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Iron binding site 1 out of 8 in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant D377N 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 D377N in Complex with Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:43.0
occ:0.42
 FE A:FE502 2.3 49.2 0.7
OE2 A:GLU406 2.3 30.8 1.0
OE2 A:GLU421 2.4 28.0 1.0
O A:HOH1079 2.5 40.7 1.0
OD2 A:ASP307 2.5 36.4 1.0
NE2 A:HIS371 2.5 25.2 1.0
CD A:GLU421 3.0 28.6 1.0
CG A:ASP307 3.1 32.2 1.0
OE1 A:GLU421 3.1 27.4 1.0
OD1 A:ASP307 3.2 35.8 1.0
CD A:GLU406 3.2 30.4 1.0
CE1 A:HIS371 3.4 25.6 1.0
CD2 A:HIS371 3.5 23.1 1.0
OE1 A:GLU406 3.5 25.8 1.0
OXT A:AKR503 3.7 48.8 1.0
OD2 A:ASP295 4.0 43.8 1.0
ND2 A:ASN377 4.3 35.6 1.0
CB A:ASP307 4.4 25.0 1.0
OH A:TYR366 4.4 32.3 1.0
OD1 A:ASP297 4.4 36.5 1.0
CG A:GLU421 4.4 25.0 1.0
CG A:GLU406 4.5 24.3 1.0
OD1 A:ASP295 4.5 35.5 1.0
ND1 A:HIS371 4.5 22.2 1.0
C A:AKR503 4.6 54.3 1.0
CG A:HIS371 4.6 23.2 1.0
NZ A:LYS419 4.7 25.1 1.0
CG A:ASP295 4.7 37.1 1.0
CB A:CYS404 4.7 25.2 1.0
O A:AKR503 4.7 45.1 1.0
CE2 A:TYR366 4.8 32.6 1.0
OD1 A:ASN377 4.8 31.1 1.0
O C:HOH1019 4.9 52.0 1.0
O A:ASP307 4.9 25.2 1.0
CG A:ASN377 5.0 30.4 1.0
CZ A:TYR366 5.0 30.4 1.0

Iron binding site 2 out of 8 in 4s01

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Iron binding site 2 out of 8 in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant D377N 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 D377N in Complex with Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:49.2
occ:0.66
 FE A:FE501 2.3 43.0 0.4
OD1 A:ASP297 2.5 36.5 1.0
OD2 A:ASP295 2.5 43.8 1.0
OD1 A:ASP307 2.7 35.8 1.0
OXT A:AKR503 2.7 48.8 1.0
O A:HOH1079 2.7 40.7 1.0
OD2 A:ASP307 2.9 36.4 1.0
OD1 A:ASP295 3.0 35.5 1.0
O A:AKR503 3.0 45.1 1.0
CG A:ASP295 3.1 37.1 1.0
CG A:ASP307 3.2 32.2 1.0
C A:AKR503 3.3 54.3 1.0
CG A:ASP297 3.4 30.2 1.0
OD2 A:ASP297 3.6 31.8 1.0
OE1 A:GLU421 3.6 27.4 1.0
OH A:TYR366 4.0 32.3 1.0
OE2 A:GLU421 4.1 28.0 1.0
OE2 A:GLU406 4.2 30.8 1.0
O A:HOH612 4.3 31.3 1.0
CD A:GLU421 4.3 28.6 1.0
CB A:ASP295 4.5 29.0 1.0
NE2 A:HIS371 4.5 25.2 1.0
ND2 A:ASN377 4.6 35.6 1.0
O A:HOH1040 4.6 38.7 1.0
O A:HOH1083 4.6 37.9 1.0
CB A:ASP307 4.7 25.0 1.0
NZ A:LYS419 4.7 25.1 1.0
CB A:ASP297 4.7 26.1 1.0
CA A:AKR503 4.8 40.8 1.0
OE1 A:GLU406 4.8 25.8 1.0
CD A:GLU406 5.0 30.4 1.0
CA A:ASP297 5.0 26.4 1.0

Iron binding site 3 out of 8 in 4s01

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Iron binding site 3 out of 8 in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant D377N 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 D377N in Complex with Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:39.0
occ:0.43
 FE B:FE502 2.3 46.5 0.7
OE2 B:GLU406 2.3 32.0 1.0
OE2 B:GLU421 2.3 26.1 1.0
NE2 B:HIS371 2.4 23.4 1.0
O B:HOH1091 2.4 39.4 1.0
OD2 B:ASP307 2.5 33.3 1.0
CG B:ASP307 3.1 31.2 1.0
O B:AKR503 3.1 37.7 1.0
CD B:GLU421 3.1 27.6 1.0
OD1 B:ASP307 3.3 35.7 1.0
CD B:GLU406 3.3 31.1 1.0
OE1 B:GLU421 3.3 28.1 1.0
CD2 B:HIS371 3.3 24.9 1.0
CE1 B:HIS371 3.3 24.5 1.0
OE1 B:GLU406 3.7 29.4 1.0
ND2 B:ASN377 4.2 34.0 1.0
C B:AKR503 4.3 46.6 1.0
OD2 B:ASP295 4.3 41.0 1.0
CB B:ASP307 4.3 22.1 1.0
O B:HOH1093 4.4 44.4 1.0
ND1 B:HIS371 4.4 23.8 1.0
CG B:GLU421 4.5 24.6 1.0
CG B:HIS371 4.5 23.7 1.0
OD1 B:ASP297 4.5 32.3 1.0
CB B:CYS404 4.5 21.5 1.0
CG B:GLU406 4.5 24.5 1.0
OH B:TYR366 4.6 32.7 1.0
OXT B:AKR503 4.6 41.8 1.0
OD1 B:ASN377 4.6 29.7 1.0
OD1 B:ASP295 4.7 35.4 1.0
CG B:ASN377 4.9 30.9 1.0
O B:ASP307 4.9 24.3 1.0
CG B:ASP295 4.9 36.9 1.0
NZ B:LYS419 4.9 25.1 1.0
CE2 B:TYR366 5.0 30.5 1.0
SG B:CYS404 5.0 24.8 1.0

Iron binding site 4 out of 8 in 4s01

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Iron binding site 4 out of 8 in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant D377N 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 D377N in Complex with Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:46.5
occ:0.67
 FE B:FE501 2.3 39.0 0.4
OD1 B:ASP307 2.5 35.7 1.0
OD1 B:ASP297 2.5 32.3 1.0
OD2 B:ASP295 2.5 41.0 1.0
O B:AKR503 2.5 37.7 1.0
O B:HOH1091 2.6 39.4 1.0
OD2 B:ASP307 2.7 33.3 1.0
OD1 B:ASP295 2.8 35.4 1.0
CG B:ASP307 2.9 31.2 1.0
CG B:ASP295 3.0 36.9 1.0
OXT B:AKR503 3.1 41.8 1.0
C B:AKR503 3.1 46.6 1.0
CG B:ASP297 3.5 32.3 1.0
OE1 B:GLU421 3.5 28.1 1.0
OD2 B:ASP297 3.8 32.4 1.0
OE2 B:GLU421 3.9 26.1 1.0
CD B:GLU421 4.1 27.6 1.0
OH B:TYR366 4.2 32.7 1.0
OE2 B:GLU406 4.2 32.0 1.0
O B:HOH1096 4.2 40.2 1.0
O B:HOH610 4.4 29.8 1.0
CB B:ASP295 4.4 27.7 1.0
CB B:ASP307 4.4 22.1 1.0
NE2 B:HIS371 4.5 23.4 1.0
CA B:AKR503 4.5 38.6 1.0
NZ B:LYS419 4.7 25.1 1.0
ND2 B:ASN377 4.7 34.0 1.0
O B:HOH1097 4.8 34.7 1.0
CB B:ASP297 4.8 22.4 1.0
OE1 B:GLU406 4.8 29.4 1.0
CD B:GLU406 4.9 31.1 1.0
CA B:ASP297 5.0 26.1 1.0
OG B:SER309 5.0 21.7 1.0

Iron binding site 5 out of 8 in 4s01

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Iron binding site 5 out of 8 in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant D377N 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 D377N in Complex with Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:44.0
occ:0.48
 OE2 C:GLU421 2.4 31.9 1.0
FE C:FE502 2.4 47.6 0.7
OE2 C:GLU406 2.4 37.1 1.0
NE2 C:HIS371 2.4 30.7 1.0
O C:HOH658 2.5 41.4 1.0
OD2 C:ASP307 2.5 40.0 1.0
CG C:ASP307 3.0 33.9 1.0
O C:AKR503 3.1 43.1 1.0
OD1 C:ASP307 3.2 36.7 1.0
CD C:GLU421 3.2 35.4 1.0
CD2 C:HIS371 3.3 25.9 1.0
OE1 C:GLU421 3.3 33.2 1.0
CD C:GLU406 3.3 38.1 1.0
CE1 C:HIS371 3.4 27.9 1.0
OE1 C:GLU406 3.7 33.0 1.0
CB C:ASP307 4.2 31.5 1.0
C C:AKR503 4.2 51.6 1.0
ND2 C:ASN377 4.2 35.7 1.0
O C:HOH1022 4.3 44.0 1.0
OD2 C:ASP295 4.4 36.9 1.0
OD1 C:ASP297 4.4 34.8 1.0
CG C:HIS371 4.5 26.0 1.0
ND1 C:HIS371 4.5 26.1 1.0
OH C:TYR366 4.6 34.7 1.0
CB C:CYS404 4.6 26.0 1.0
CG C:GLU406 4.6 32.9 1.0
CG C:GLU421 4.6 28.3 1.0
OXT C:AKR503 4.6 48.7 1.0
OD1 C:ASN377 4.6 34.1 1.0
OD1 C:ASP295 4.6 32.4 1.0
O C:ASP307 4.7 27.7 1.0
CG C:ASN377 4.8 32.9 1.0
CE2 C:TYR366 4.9 34.8 1.0
CG C:ASP295 4.9 33.1 1.0

Iron binding site 6 out of 8 in 4s01

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Iron binding site 6 out of 8 in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant D377N 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 D377N in Complex with Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:47.6
occ:0.66
 FE C:FE501 2.4 44.0 0.5
OD1 C:ASP297 2.4 34.8 1.0
OD1 C:ASP307 2.4 36.7 1.0
OD2 C:ASP295 2.5 36.9 1.0
O C:HOH658 2.6 41.4 1.0
O C:AKR503 2.6 43.1 1.0
OD1 C:ASP295 2.7 32.4 1.0
OD2 C:ASP307 2.9 40.0 1.0
CG C:ASP295 2.9 33.1 1.0
CG C:ASP307 3.0 33.9 1.0
OXT C:AKR503 3.0 48.7 1.0
C C:AKR503 3.2 51.6 1.0
CG C:ASP297 3.4 28.6 1.0
OE1 C:GLU421 3.5 33.2 1.0
OD2 C:ASP297 3.7 29.7 1.0
OE2 C:GLU421 4.0 31.9 1.0
OH C:TYR366 4.1 34.7 1.0
CD C:GLU421 4.2 35.4 1.0
OE2 C:GLU406 4.2 37.1 1.0
CB C:ASP295 4.4 29.5 1.0
O C:HOH963 4.4 43.0 1.0
O C:HOH620 4.4 33.1 1.0
CB C:ASP307 4.5 31.5 1.0
CA C:AKR503 4.6 41.6 1.0
NE2 C:HIS371 4.6 30.7 1.0
NZ C:LYS419 4.7 32.3 1.0
CB C:ASP297 4.7 26.9 1.0
ND2 C:ASN377 4.8 35.7 1.0
OE1 C:GLU406 4.8 33.0 1.0
OG C:SER309 4.9 30.1 1.0
CA C:ASP297 4.9 26.6 1.0
CD C:GLU406 4.9 38.1 1.0

Iron binding site 7 out of 8 in 4s01

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Iron binding site 7 out of 8 in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant D377N 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 D377N in Complex with Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:42.9
occ:0.51
 NE2 D:HIS371 2.3 29.5 1.0
OE2 D:GLU421 2.4 33.9 1.0
FE D:FE502 2.4 48.0 0.6
OE2 D:GLU406 2.4 37.7 1.0
O D:HOH683 2.5 39.3 1.0
OD2 D:ASP307 2.6 42.1 1.0
CG D:ASP307 3.0 37.1 1.0
CD D:GLU421 3.1 36.1 1.0
OXT D:AKR503 3.2 41.8 1.0
OD1 D:ASP307 3.2 36.7 1.0
CE1 D:HIS371 3.2 27.9 1.0
OE1 D:GLU421 3.3 33.1 1.0
CD2 D:HIS371 3.4 26.1 1.0
CD D:GLU406 3.4 36.6 1.0
OE1 D:GLU406 3.8 32.7 1.0
ND2 D:ASN377 4.1 36.3 1.0
CB D:ASP307 4.2 30.1 1.0
O D:HOH1018 4.2 41.0 1.0
C D:AKR503 4.3 50.8 1.0
OD2 D:ASP295 4.4 36.6 1.0
ND1 D:HIS371 4.4 25.7 1.0
CG D:HIS371 4.5 27.4 1.0
CB D:CYS404 4.5 25.1 1.0
OD1 D:ASP297 4.5 34.8 1.0
CG D:GLU421 4.5 30.0 1.0
CG D:GLU406 4.6 30.4 1.0
OD1 D:ASN377 4.6 33.8 1.0
OH D:TYR366 4.6 32.6 1.0
O D:AKR503 4.7 50.7 1.0
OD1 D:ASP295 4.7 32.7 1.0
CG D:ASN377 4.8 32.7 1.0
O D:ASP307 4.8 28.8 1.0
SG D:CYS404 4.9 29.4 1.0
CG D:ASP295 5.0 34.0 1.0
CE2 D:TYR366 5.0 34.3 1.0

Iron binding site 8 out of 8 in 4s01

Go back to Iron Binding Sites List in 4s01
Iron binding site 8 out of 8 in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp Mutant D377N 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 D377N in Complex with Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe502

b:48.0
occ:0.62
 OD1 D:ASP307 2.4 36.7 1.0
FE D:FE501 2.4 42.9 0.5
OD2 D:ASP295 2.4 36.6 1.0
OD1 D:ASP297 2.5 34.8 1.0
O D:HOH683 2.5 39.3 1.0
OXT D:AKR503 2.7 41.8 1.0
OD1 D:ASP295 2.8 32.7 1.0
OD2 D:ASP307 2.8 42.1 1.0
CG D:ASP295 2.9 34.0 1.0
CG D:ASP307 3.0 37.1 1.0
O D:AKR503 3.1 50.7 1.0
C D:AKR503 3.2 50.8 1.0
OE1 D:GLU421 3.5 33.1 1.0
CG D:ASP297 3.5 32.3 1.0
OD2 D:ASP297 3.8 33.9 1.0
OE2 D:GLU421 3.9 33.9 1.0
CD D:GLU421 4.1 36.1 1.0
OH D:TYR366 4.1 32.6 1.0
OE2 D:GLU406 4.1 37.7 1.0
O D:HOH624 4.3 31.7 1.0
CB D:ASP295 4.4 28.5 1.0
CB D:ASP307 4.4 30.1 1.0
O D:HOH1019 4.5 42.7 1.0
NE2 D:HIS371 4.6 29.5 1.0
NZ D:LYS419 4.6 31.4 1.0
CA D:AKR503 4.7 42.4 1.0
ND2 D:ASN377 4.8 36.3 1.0
CB D:ASP297 4.8 28.8 1.0
OE1 D:GLU406 4.8 32.7 1.0
OG D:SER309 4.9 29.5 1.0
CD D:GLU406 4.9 36.6 1.0
CA D:ASP297 5.0 28.9 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: Mon Aug 5 10:06:51 2024

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