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

Protein crystallography data

The structure of Crystal Structure of Metallopeptidase-Like Dimethylsulphoniopropionate (Dmsp) Lyase Rldddp in Complex with Phosphate, PDB code: 4rzz 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) 38.02 / 2.10
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 175.610, 175.610, 109.574, 90.00, 90.00, 120.00
R / Rfree (%) 16.8 / 19.4

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 4rzz

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


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 Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:30.6
occ:1.00
OE2 A:GLU406 2.1 25.4 1.0
OE2 A:GLU421 2.2 26.8 1.0
NE2 A:HIS371 2.2 21.8 1.0
OD2 A:ASP307 2.3 27.2 1.0
O A:HOH663 2.4 29.5 1.0
O2 A:PO4503 2.6 37.0 0.7
O1 A:PO4503 2.7 37.1 0.7
CD A:GLU406 3.0 26.9 1.0
CD A:GLU421 3.1 24.2 1.0
CD2 A:HIS371 3.1 21.8 1.0
CE1 A:HIS371 3.2 22.8 1.0
P A:PO4503 3.2 34.5 0.7
CG A:ASP307 3.2 25.6 1.0
FE A:FE502 3.3 39.1 1.0
OE1 A:GLU421 3.4 19.7 1.0
OE1 A:GLU406 3.4 23.4 1.0
OD1 A:ASP307 3.6 29.1 1.0
O4 A:PO4503 3.9 31.7 0.7
CG A:GLU406 4.2 22.6 1.0
ND1 A:HIS371 4.2 21.5 1.0
CG A:HIS371 4.2 23.3 1.0
CB A:CYS404 4.3 20.5 1.0
CG A:GLU421 4.4 21.5 1.0
O3 A:PO4503 4.4 35.9 0.7
CB A:ASP307 4.5 21.9 1.0
OH A:TYR366 4.7 31.1 1.0
OD2 A:ASP377 4.7 36.8 1.0
OD1 A:ASP377 4.7 29.6 1.0
OD2 A:ASP295 4.7 32.9 1.0
CE2 A:TYR366 4.8 29.5 1.0
O A:ASP307 4.8 25.2 1.0
SG A:CYS404 4.9 22.7 1.0
O A:HOH1107 4.9 42.7 1.0
NZ A:LYS419 5.0 22.8 1.0
OD1 A:ASP297 5.0 26.6 1.0

Iron binding site 2 out of 8 in 4rzz

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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 Phosphate


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 Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:39.1
occ:1.00
O A:HOH663 1.9 29.5 1.0
OD1 A:ASP297 2.0 26.6 1.0
OD1 A:ASP307 2.2 29.1 1.0
OD2 A:ASP295 2.4 32.9 1.0
O4 A:PO4503 2.5 31.7 0.7
OD1 A:ASP295 2.6 26.8 1.0
O2 A:PO4503 2.7 37.0 0.7
CG A:ASP295 2.8 28.8 1.0
CG A:ASP307 2.9 25.6 1.0
CG A:ASP297 3.0 27.9 1.0
OD2 A:ASP307 3.0 27.2 1.0
P A:PO4503 3.1 34.5 0.7
FE A:FE501 3.3 30.6 1.0
OD2 A:ASP297 3.4 27.2 1.0
O A:HOH1108 3.4 38.6 1.0
O1 A:PO4503 3.8 37.1 0.7
OE1 A:GLU421 3.8 19.7 1.0
O A:HOH832 4.0 34.1 1.0
O A:HOH1000 4.2 33.9 1.0
CB A:ASP297 4.2 22.8 1.0
CB A:ASP295 4.3 21.9 1.0
OE2 A:GLU421 4.3 26.8 1.0
CA A:ASP297 4.3 23.9 1.0
CB A:ASP307 4.4 21.9 1.0
N A:ASP297 4.4 23.1 1.0
O3 A:PO4503 4.4 35.9 0.7
CD A:GLU421 4.5 24.2 1.0
O A:HOH602 4.5 23.0 1.0
OH A:TYR366 4.5 31.1 1.0
OE2 A:GLU406 4.8 25.4 1.0
CA A:ASP307 4.9 21.0 1.0
NZ A:LYS419 4.9 22.8 1.0

Iron binding site 3 out of 8 in 4rzz

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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 Phosphate


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 Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:30.1
occ:1.00
OE2 B:GLU406 2.1 25.6 1.0
OE2 B:GLU421 2.1 26.6 1.0
NE2 B:HIS371 2.2 21.1 1.0
OD2 B:ASP307 2.2 26.6 1.0
O B:HOH687 2.3 30.8 1.0
O4 B:PO4503 2.3 32.7 0.7
CD B:GLU406 3.0 25.9 1.0
CD B:GLU421 3.1 25.3 1.0
CD2 B:HIS371 3.1 20.5 1.0
CE1 B:HIS371 3.2 22.6 1.0
CG B:ASP307 3.2 23.8 1.0
FE B:FE502 3.4 39.8 1.0
OE1 B:GLU421 3.4 22.3 1.0
P B:PO4503 3.4 33.0 0.7
OE1 B:GLU406 3.5 22.7 1.0
OD1 B:ASP307 3.5 28.1 1.0
O3 B:PO4503 3.6 30.3 0.7
O2 B:PO4503 4.1 35.9 0.7
CG B:GLU406 4.2 21.8 1.0
CB B:CYS404 4.2 22.5 1.0
ND1 B:HIS371 4.2 23.0 1.0
CG B:HIS371 4.3 22.7 1.0
CG B:GLU421 4.4 20.1 1.0
OD2 B:ASP377 4.4 36.8 1.0
CB B:ASP307 4.4 20.7 1.0
O1 B:PO4503 4.6 38.5 0.7
OH B:TYR366 4.7 29.6 1.0
OD2 B:ASP295 4.7 31.7 1.0
CE2 B:TYR366 4.8 26.4 1.0
O B:ASP307 4.8 24.4 1.0
OD1 B:ASP377 4.8 28.5 1.0
SG B:CYS404 4.9 23.0 1.0
CG B:ASP377 5.0 32.7 1.0

Iron binding site 4 out of 8 in 4rzz

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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 Phosphate


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 Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:39.8
occ:1.00
O B:HOH687 1.9 30.8 1.0
OD1 B:ASP297 2.0 26.1 1.0
O3 B:PO4503 2.1 30.3 0.7
OD1 B:ASP307 2.1 28.1 1.0
OD2 B:ASP295 2.3 31.7 1.0
OD1 B:ASP295 2.5 28.3 1.0
CG B:ASP295 2.7 29.1 1.0
CG B:ASP307 2.9 23.8 1.0
CG B:ASP297 3.0 26.3 1.0
OD2 B:ASP307 3.1 26.6 1.0
P B:PO4503 3.3 33.0 0.7
FE B:FE501 3.4 30.1 1.0
OD2 B:ASP297 3.4 26.7 1.0
O4 B:PO4503 3.5 32.7 0.7
O B:HOH1144 3.7 40.0 1.0
OE1 B:GLU421 3.8 22.3 1.0
CB B:ASP297 4.2 21.7 1.0
O B:HOH861 4.2 30.8 1.0
CB B:ASP295 4.2 24.3 1.0
O2 B:PO4503 4.2 35.9 0.7
CA B:ASP297 4.3 23.1 1.0
O B:HOH876 4.3 33.0 1.0
N B:ASP297 4.3 22.0 1.0
CB B:ASP307 4.4 20.7 1.0
OE2 B:GLU421 4.4 26.6 1.0
O1 B:PO4503 4.4 38.5 0.7
CD B:GLU421 4.5 25.3 1.0
OH B:TYR366 4.5 29.6 1.0
O B:HOH601 4.6 24.7 1.0
OE2 B:GLU406 4.9 25.6 1.0
CA B:ASP307 4.9 20.5 1.0
OD2 B:ASP377 4.9 36.8 1.0
NZ B:LYS419 5.0 20.9 1.0
OG B:SER309 5.0 23.5 1.0

Iron binding site 5 out of 8 in 4rzz

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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 Phosphate


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 Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:33.6
occ:1.00
OE2 C:GLU406 2.1 32.9 1.0
OD2 C:ASP307 2.2 32.8 1.0
NE2 C:HIS371 2.2 25.7 1.0
OE2 C:GLU421 2.3 32.9 1.0
O C:HOH661 2.3 28.6 1.0
O4 C:PO4503 2.5 38.2 0.8
CD C:GLU406 3.0 34.2 1.0
CD C:GLU421 3.1 31.5 1.0
CG C:ASP307 3.2 32.7 1.0
CD2 C:HIS371 3.2 25.0 1.0
CE1 C:HIS371 3.2 27.9 1.0
OE1 C:GLU421 3.3 27.8 1.0
FE C:FE502 3.4 40.1 1.0
P C:PO4503 3.4 37.7 0.8
OE1 C:GLU406 3.5 31.0 1.0
O3 C:PO4503 3.5 42.9 0.8
OD1 C:ASP307 3.6 34.2 1.0
O2 C:PO4503 3.6 39.7 0.8
CG C:GLU406 4.2 32.5 1.0
CB C:CYS404 4.2 23.4 1.0
CG C:HIS371 4.3 26.2 1.0
ND1 C:HIS371 4.3 24.6 1.0
CB C:ASP307 4.4 26.7 1.0
CG C:GLU421 4.4 27.3 1.0
OD2 C:ASP377 4.6 40.7 1.0
OH C:TYR366 4.6 36.6 1.0
OD1 C:ASP377 4.7 35.5 1.0
OD2 C:ASP295 4.7 28.4 1.0
O1 C:PO4503 4.7 45.1 0.8
O C:ASP307 4.8 27.5 1.0
CE2 C:TYR366 4.8 33.9 1.0
SG C:CYS404 4.8 28.6 1.0

Iron binding site 6 out of 8 in 4rzz

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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 Phosphate


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 Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:40.1
occ:1.00
O C:HOH661 1.9 28.6 1.0
OD1 C:ASP297 2.0 30.4 1.0
OD1 C:ASP307 2.1 34.2 1.0
OD2 C:ASP295 2.3 28.4 1.0
OD1 C:ASP295 2.5 28.9 1.0
O2 C:PO4503 2.6 39.7 0.8
CG C:ASP295 2.7 29.3 1.0
O3 C:PO4503 2.9 42.9 0.8
CG C:ASP297 2.9 29.4 1.0
CG C:ASP307 2.9 32.7 1.0
OD2 C:ASP307 3.1 32.8 1.0
P C:PO4503 3.2 37.7 0.8
OD2 C:ASP297 3.3 29.9 1.0
FE C:FE501 3.4 33.6 1.0
O C:HOH1043 3.4 42.4 1.0
O4 C:PO4503 3.8 38.2 0.8
OE1 C:GLU421 3.9 27.8 1.0
O C:HOH872 3.9 36.2 1.0
CB C:ASP295 4.2 25.4 1.0
CB C:ASP297 4.2 26.4 1.0
O C:HOH850 4.3 36.3 1.0
CA C:ASP297 4.3 26.2 1.0
CB C:ASP307 4.3 26.7 1.0
N C:ASP297 4.4 26.5 1.0
OE2 C:GLU421 4.4 32.9 1.0
OH C:TYR366 4.5 36.6 1.0
O C:HOH608 4.5 26.9 1.0
O1 C:PO4503 4.6 45.1 0.8
CD C:GLU421 4.6 31.5 1.0
OE2 C:GLU406 4.8 32.9 1.0
CA C:ASP307 4.9 26.0 1.0
OD2 C:ASP377 5.0 40.7 1.0
OG C:SER309 5.0 30.5 1.0
NZ C:LYS419 5.0 30.4 1.0

Iron binding site 7 out of 8 in 4rzz

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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 Phosphate


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 Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:32.9
occ:1.00
OD2 D:ASP307 2.2 31.8 1.0
OE2 D:GLU406 2.2 34.5 1.0
OE2 D:GLU421 2.2 32.3 1.0
NE2 D:HIS371 2.2 26.8 1.0
O D:HOH1024 2.3 33.5 1.0
O1 D:PO4503 2.4 33.9 0.8
CD D:GLU421 3.0 32.6 1.0
CD D:GLU406 3.1 33.9 1.0
CD2 D:HIS371 3.1 25.4 1.0
CG D:ASP307 3.2 30.6 1.0
CE1 D:HIS371 3.2 27.1 1.0
OE1 D:GLU421 3.3 32.1 1.0
FE D:FE502 3.4 42.4 1.0
P D:PO4503 3.5 40.2 0.8
OE1 D:GLU406 3.5 31.8 1.0
OD1 D:ASP307 3.6 34.4 1.0
O2 D:PO4503 3.7 35.7 0.8
O3 D:PO4503 3.9 39.9 0.8
CG D:GLU406 4.2 31.4 1.0
CB D:CYS404 4.2 25.2 1.0
CG D:HIS371 4.3 25.7 1.0
ND1 D:HIS371 4.3 24.2 1.0
CG D:GLU421 4.4 29.0 1.0
CB D:ASP307 4.4 26.0 1.0
OD2 D:ASP377 4.6 40.4 1.0
OH D:TYR366 4.6 36.9 1.0
O D:ASP307 4.6 25.7 1.0
OD1 D:ASP377 4.7 32.8 1.0
OD2 D:ASP295 4.7 29.8 1.0
O4 D:PO4503 4.7 40.0 0.8
CE2 D:TYR366 4.8 35.5 1.0
SG D:CYS404 4.8 28.8 1.0
CG D:ASP377 5.0 33.0 1.0

Iron binding site 8 out of 8 in 4rzz

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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 Phosphate


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 Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe502

b:42.4
occ:1.00
O D:HOH1024 1.9 33.5 1.0
OD1 D:ASP297 2.1 30.7 1.0
O2 D:PO4503 2.1 35.7 0.8
OD1 D:ASP307 2.2 34.4 1.0
OD2 D:ASP295 2.3 29.8 1.0
OD1 D:ASP295 2.5 29.9 1.0
CG D:ASP295 2.7 28.6 1.0
CG D:ASP297 3.0 27.6 1.0
CG D:ASP307 3.0 30.6 1.0
OD2 D:ASP307 3.1 31.8 1.0
O D:HOH933 3.3 42.6 1.0
OD2 D:ASP297 3.3 28.3 1.0
P D:PO4503 3.3 40.2 0.8
FE D:FE501 3.4 32.9 1.0
O1 D:PO4503 3.6 33.9 0.8
O3 D:PO4503 3.8 39.9 0.8
OE1 D:GLU421 3.9 32.1 1.0
O D:HOH791 4.0 33.3 1.0
CB D:ASP295 4.2 25.3 1.0
CB D:ASP297 4.2 27.0 1.0
O D:HOH928 4.3 38.3 1.0
CA D:ASP297 4.4 27.3 1.0
OE2 D:GLU421 4.4 32.3 1.0
CB D:ASP307 4.4 26.0 1.0
N D:ASP297 4.5 27.2 1.0
OH D:TYR366 4.5 36.9 1.0
O D:HOH607 4.5 27.1 1.0
O4 D:PO4503 4.6 40.0 0.8
CD D:GLU421 4.6 32.6 1.0
OE2 D:GLU406 4.8 34.5 1.0
OG D:SER309 4.9 30.8 1.0
CA D:ASP307 4.9 28.6 1.0
OD2 D:ASP377 5.0 40.4 1.0
NZ D:LYS419 5.0 31.6 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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