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Iron in PDB 4rzy: Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp in Complex with Mes

Protein crystallography data

The structure of Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp in Complex with Mes, PDB code: 4rzy 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) 34.24 / 1.95
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 175.301, 175.301, 109.689, 90.00, 90.00, 120.00
R / Rfree (%) 16.3 / 18.8

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 4rzy

Go back to Iron Binding Sites List in 4rzy
Iron binding site 1 out of 8 in the Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp in Complex with Mes


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 in Complex with Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:25.9
occ:1.00
 OD1 A:ASP307 2.2 21.8 1.0
OD1 A:ASP295 2.3 19.9 1.0
OD2 A:ASP295 2.3 16.3 1.0
OD1 A:ASP297 2.4 19.6 1.0
O A:HOH615 2.4 22.8 1.0
OE1 A:GLU421 2.5 12.0 1.0
CG A:ASP295 2.6 15.1 1.0
FE A:FE502 2.9 19.8 1.0
CG A:ASP307 3.0 17.8 1.0
OD2 A:ASP307 3.1 18.4 1.0
CD A:GLU421 3.3 14.1 1.0
CG A:ASP297 3.4 19.9 1.0
OE2 A:GLU421 3.4 16.7 1.0
O3S A:MES503 3.5 21.9 0.6
OD2 A:ASP297 3.8 20.2 1.0
O2S A:MES503 3.9 26.0 0.6
OG A:SER309 4.1 14.2 1.0
CB A:ASP295 4.1 13.6 1.0
NZ A:LYS419 4.2 12.9 1.0
S A:MES503 4.3 40.9 0.6
CB A:ASP307 4.3 11.3 1.0
O A:HOH608 4.4 18.3 1.0
OE1 A:GLU406 4.5 18.4 1.0
OH A:TYR366 4.5 21.8 1.0
O A:HOH754 4.5 24.5 1.0
N A:ASP297 4.5 12.5 1.0
OE2 A:GLU406 4.5 14.3 1.0
CB A:ASP297 4.6 14.5 1.0
C A:ASP307 4.6 15.4 1.0
CA A:ASP297 4.7 16.8 1.0
CA A:ASP307 4.7 11.5 1.0
CG A:GLU421 4.8 13.6 1.0
O A:ASP307 4.9 14.3 1.0
CA A:ASP295 4.9 12.5 1.0
N A:ILE308 4.9 12.6 1.0
CD A:GLU406 4.9 18.9 1.0

Iron binding site 2 out of 8 in 4rzy

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


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 in Complex with Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:19.8
occ:1.00
 OE2 A:GLU421 2.1 16.7 1.0
OE1 A:GLU406 2.2 18.4 1.0
NE2 A:HIS371 2.3 10.8 1.0
O A:HOH615 2.3 22.8 1.0
OD2 A:ASP307 2.3 18.4 1.0
FE A:FE501 2.9 25.9 1.0
CD A:GLU421 2.9 14.1 1.0
CD A:GLU406 3.1 18.9 1.0
CD2 A:HIS371 3.2 16.1 1.0
CG A:ASP307 3.2 17.8 1.0
OE1 A:GLU421 3.2 12.0 1.0
CE1 A:HIS371 3.3 14.2 1.0
OE2 A:GLU406 3.5 14.3 1.0
OD1 A:ASP307 3.6 21.8 1.0
O3S A:MES503 3.6 21.9 0.6
CB A:CYS404 4.2 13.6 1.0
CG A:GLU421 4.3 13.6 1.0
CG A:GLU406 4.3 14.9 1.0
C7 A:MES503 4.3 30.5 0.6
CG A:HIS371 4.4 13.0 1.0
ND1 A:HIS371 4.4 13.9 1.0
OH A:TYR366 4.5 21.8 1.0
CB A:ASP307 4.5 11.3 1.0
OD2 A:ASP377 4.5 27.6 1.0
OD1 A:ASP297 4.5 19.6 1.0
OD2 A:ASP295 4.7 16.3 1.0
OD1 A:ASP377 4.7 17.9 1.0
SG A:CYS404 4.8 16.8 1.0
S A:MES503 4.8 40.9 0.6
CE2 A:TYR366 4.8 22.9 1.0
O A:ASP307 4.9 14.3 1.0
NZ A:LYS419 5.0 12.9 1.0
CG A:ASP377 5.0 21.6 1.0

Iron binding site 3 out of 8 in 4rzy

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


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 in Complex with Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:21.0
occ:1.00
 OE2 B:GLU421 2.1 16.6 1.0
OE2 B:GLU406 2.2 15.3 1.0
NE2 B:HIS371 2.2 11.7 1.0
O B:HOH624 2.3 23.2 1.0
OD2 B:ASP307 2.3 19.1 1.0
FE B:FE502 2.9 26.9 1.0
CD B:GLU421 2.9 18.0 1.0
CD B:GLU406 3.1 19.1 1.0
OE1 B:GLU421 3.2 13.8 1.0
CG B:ASP307 3.2 15.7 1.0
CD2 B:HIS371 3.2 14.8 1.0
CE1 B:HIS371 3.2 10.6 1.0
O3S B:MES503 3.5 22.5 0.6
OD1 B:ASP307 3.5 21.6 1.0
OE1 B:GLU406 3.5 15.3 1.0
CB B:CYS404 4.1 15.7 1.0
CG B:GLU421 4.3 12.8 1.0
CG B:GLU406 4.3 13.2 1.0
ND1 B:HIS371 4.3 14.7 1.0
CG B:HIS371 4.4 13.2 1.0
OH B:TYR366 4.4 22.0 1.0
CB B:ASP307 4.5 14.1 1.0
C7 B:MES503 4.5 30.0 0.6
OD1 B:ASP297 4.5 19.1 1.0
OD2 B:ASP377 4.5 25.4 1.0
OD1 B:ASP377 4.7 18.7 1.0
S B:MES503 4.7 36.1 0.6
SG B:CYS404 4.8 16.9 1.0
OD2 B:ASP295 4.8 18.9 1.0
CE2 B:TYR366 4.8 18.5 1.0
O2S B:MES503 4.9 22.0 0.6
O B:ASP307 4.9 15.3 1.0
CG B:ASP377 5.0 22.2 1.0
NZ B:LYS419 5.0 12.1 1.0

Iron binding site 4 out of 8 in 4rzy

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


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 in Complex with Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:26.9
occ:1.00
 OD1 B:ASP307 2.2 21.6 1.0
OD1 B:ASP295 2.4 16.7 1.0
OD2 B:ASP295 2.4 18.9 1.0
O B:HOH624 2.4 23.2 1.0
OD1 B:ASP297 2.4 19.1 1.0
OE1 B:GLU421 2.5 13.8 1.0
CG B:ASP295 2.7 18.2 1.0
FE B:FE501 2.9 21.0 1.0
CG B:ASP307 3.0 15.7 1.0
OD2 B:ASP307 3.1 19.1 1.0
CD B:GLU421 3.3 18.0 1.0
OE2 B:GLU421 3.4 16.6 1.0
CG B:ASP297 3.4 20.2 1.0
O3S B:MES503 3.5 22.5 0.6
O2S B:MES503 3.7 22.0 0.6
OD2 B:ASP297 3.8 19.1 1.0
OG B:SER309 4.1 14.5 1.0
CB B:ASP295 4.1 13.1 1.0
NZ B:LYS419 4.2 12.1 1.0
S B:MES503 4.2 36.1 0.6
CB B:ASP307 4.3 14.1 1.0
O B:HOH602 4.4 16.1 1.0
OE2 B:GLU406 4.4 15.3 1.0
O B:HOH778 4.4 25.7 1.0
OH B:TYR366 4.5 22.0 1.0
N B:ASP297 4.5 14.4 1.0
OE1 B:GLU406 4.5 15.3 1.0
C B:ASP307 4.6 17.3 1.0
CB B:ASP297 4.6 14.7 1.0
CA B:ASP297 4.7 17.0 1.0
CA B:ASP307 4.7 12.4 1.0
CG B:GLU421 4.8 12.8 1.0
O B:ASP307 4.8 15.3 1.0
CD B:GLU406 4.9 19.1 1.0
N B:ILE308 4.9 12.2 1.0
CA B:ASP295 4.9 13.2 1.0
NE2 B:HIS371 5.0 11.7 1.0

Iron binding site 5 out of 8 in 4rzy

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


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 in Complex with Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:20.9
occ:1.00
 OE2 C:GLU421 2.1 18.0 1.0
NE2 C:HIS371 2.3 13.5 1.0
OE2 C:GLU406 2.3 21.1 1.0
OD2 C:ASP307 2.3 19.9 1.0
O C:HOH681 2.4 30.8 1.0
FE C:FE502 2.9 25.6 1.0
CD C:GLU421 3.0 19.9 1.0
CD C:GLU406 3.1 22.3 1.0
CD2 C:HIS371 3.1 15.2 1.0
CG C:ASP307 3.2 21.8 1.0
OE1 C:GLU421 3.3 17.8 1.0
CE1 C:HIS371 3.3 16.1 1.0
OE1 C:GLU406 3.5 19.9 1.0
O2S C:MES503 3.6 23.0 0.6
OD1 C:ASP307 3.6 22.7 1.0
C7 C:MES503 4.1 29.9 0.6
CB C:CYS404 4.1 15.2 1.0
CG C:GLU406 4.2 20.7 1.0
CG C:HIS371 4.3 13.7 1.0
CG C:GLU421 4.3 16.0 1.0
ND1 C:HIS371 4.4 15.4 1.0
CB C:ASP307 4.4 16.2 1.0
OD2 C:ASP377 4.5 28.8 1.0
OD1 C:ASP297 4.5 19.9 1.0
OH C:TYR366 4.6 27.3 1.0
SG C:CYS404 4.7 18.1 1.0
OD1 C:ASP377 4.7 21.0 1.0
S C:MES503 4.8 35.9 0.6
OD2 C:ASP295 4.8 19.3 1.0
O C:ASP307 4.9 16.7 1.0
CE2 C:TYR366 4.9 23.4 1.0
CG C:ASP377 4.9 23.3 1.0

Iron binding site 6 out of 8 in 4rzy

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


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 in Complex with Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:25.6
occ:1.00
 OD1 C:ASP307 2.2 22.7 1.0
OD1 C:ASP295 2.3 18.9 1.0
OD2 C:ASP295 2.4 19.3 1.0
OD1 C:ASP297 2.4 19.9 1.0
O C:HOH681 2.4 30.8 1.0
OE1 C:GLU421 2.5 17.8 1.0
CG C:ASP295 2.6 17.9 1.0
CG C:ASP307 2.9 21.8 1.0
FE C:FE501 2.9 20.9 1.0
OD2 C:ASP307 3.0 19.9 1.0
CD C:GLU421 3.3 19.9 1.0
OE2 C:GLU421 3.4 18.0 1.0
CG C:ASP297 3.4 20.9 1.0
O2S C:MES503 3.5 23.0 0.6
OD2 C:ASP297 3.8 19.8 1.0
O1S C:MES503 3.9 25.3 0.6
OG C:SER309 4.0 17.9 1.0
CB C:ASP295 4.1 15.0 1.0
NZ C:LYS419 4.2 16.3 1.0
O C:HOH605 4.3 19.4 1.0
CB C:ASP307 4.3 16.2 1.0
S C:MES503 4.4 35.9 0.6
OE2 C:GLU406 4.4 21.1 1.0
OE1 C:GLU406 4.5 19.9 1.0
N C:ASP297 4.5 16.4 1.0
OH C:TYR366 4.6 27.3 1.0
CB C:ASP297 4.6 18.0 1.0
O C:HOH792 4.6 25.9 1.0
C C:ASP307 4.6 19.6 1.0
CA C:ASP297 4.6 16.1 1.0
CA C:ASP307 4.7 14.8 1.0
CG C:GLU421 4.8 16.0 1.0
CD C:GLU406 4.8 22.3 1.0
O C:ASP307 4.8 16.7 1.0
N C:ILE308 4.9 14.8 1.0
CA C:ASP295 4.9 13.4 1.0
NE2 C:HIS371 5.0 13.5 1.0

Iron binding site 7 out of 8 in 4rzy

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


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 in Complex with Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:20.2
occ:1.00
 OE2 D:GLU421 2.1 15.9 1.0
OE2 D:GLU406 2.3 20.6 1.0
NE2 D:HIS371 2.3 15.5 1.0
OD2 D:ASP307 2.3 18.0 1.0
O D:HOH672 2.3 29.3 1.0
FE D:FE502 2.9 29.0 1.0
CD D:GLU421 3.0 22.1 1.0
CD D:GLU406 3.1 19.9 1.0
CG D:ASP307 3.2 21.8 1.0
CD2 D:HIS371 3.2 15.4 1.0
CE1 D:HIS371 3.3 16.3 1.0
OE1 D:GLU421 3.3 16.5 1.0
OE1 D:GLU406 3.5 22.7 1.0
O2S D:MES503 3.5 26.1 0.6
OD1 D:ASP307 3.6 22.7 1.0
C7 D:MES503 4.0 27.6 0.6
CB D:CYS404 4.1 16.8 1.0
CG D:GLU406 4.3 17.9 1.0
CG D:HIS371 4.4 15.2 1.0
CG D:GLU421 4.4 17.8 1.0
ND1 D:HIS371 4.4 15.7 1.0
CB D:ASP307 4.4 15.2 1.0
OD2 D:ASP377 4.5 30.6 1.0
OD1 D:ASP297 4.5 21.0 1.0
OH D:TYR366 4.6 27.3 1.0
SG D:CYS404 4.7 19.5 1.0
OD1 D:ASP377 4.7 22.0 1.0
OD2 D:ASP295 4.8 20.9 1.0
S D:MES503 4.8 39.4 0.6
CE2 D:TYR366 4.9 24.9 1.0
CG D:ASP377 4.9 22.8 1.0
O D:ASP307 4.9 15.1 1.0
N4 D:MES503 5.0 30.4 0.6

Iron binding site 8 out of 8 in 4rzy

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


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 in Complex with Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe502

b:29.0
occ:1.00
 OD1 D:ASP307 2.2 22.7 1.0
OD1 D:ASP295 2.3 18.6 1.0
OD2 D:ASP295 2.4 20.9 1.0
O D:HOH672 2.4 29.3 1.0
OD1 D:ASP297 2.4 21.0 1.0
OE1 D:GLU421 2.5 16.5 1.0
CG D:ASP295 2.6 20.8 1.0
CG D:ASP307 2.9 21.8 1.0
FE D:FE501 2.9 20.2 1.0
OD2 D:ASP307 3.0 18.0 1.0
CD D:GLU421 3.3 22.1 1.0
CG D:ASP297 3.4 20.6 1.0
OE2 D:GLU421 3.4 15.9 1.0
O2S D:MES503 3.4 26.1 0.6
OD2 D:ASP297 3.8 21.3 1.0
O1S D:MES503 4.1 28.1 0.6
OG D:SER309 4.1 15.2 1.0
CB D:ASP295 4.1 16.4 1.0
NZ D:LYS419 4.3 18.9 1.0
CB D:ASP307 4.3 15.2 1.0
O D:HOH608 4.4 19.7 1.0
S D:MES503 4.4 39.4 0.6
OE2 D:GLU406 4.4 20.6 1.0
OH D:TYR366 4.5 27.3 1.0
OE1 D:GLU406 4.5 22.7 1.0
N D:ASP297 4.5 14.0 1.0
O D:HOH832 4.6 26.5 1.0
CB D:ASP297 4.6 16.5 1.0
C D:ASP307 4.6 17.1 1.0
CA D:ASP297 4.6 13.9 1.0
CA D:ASP307 4.7 13.2 1.0
CG D:GLU421 4.8 17.8 1.0
O D:ASP307 4.9 15.1 1.0
N D:ILE308 4.9 14.0 1.0
CD D:GLU406 4.9 19.9 1.0
CA D:ASP295 4.9 14.7 1.0
NE2 D:HIS371 5.0 15.5 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 10:06:52 2024

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