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Iron in PDB 2w8s: Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli

Protein crystallography data

The structure of Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli, PDB code: 2w8s was solved by S.Jonas, B.Van Loo, M.Hyvonen, F.Hollfelder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.62 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.700, 200.100, 211.700, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 23.9

Other elements in 2w8s:

The structure of Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli (pdb code 2w8s). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli, PDB code: 2w8s:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2w8s

Go back to Iron Binding Sites List in 2w8s
Iron binding site 1 out of 4 in the Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli


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 A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1516

b:27.7
occ:0.30
ZN A:ZN1515 0.0 28.4 0.3
OD2 A:ASP324 2.1 28.2 1.0
NE2 A:HIS325 2.1 28.4 1.0
OD1 A:ASP12 2.2 26.9 1.0
OD2 A:ASP12 2.3 27.9 1.0
CG A:ASP12 2.5 25.4 1.0
OG2 A:CYS57 2.6 32.0 0.2
SG A:CYS57 2.7 36.4 0.8
CG A:ASP324 3.0 27.4 1.0
OG1 A:CYS57 3.0 31.4 0.2
CD2 A:HIS325 3.0 27.4 1.0
CE1 A:HIS325 3.0 28.8 1.0
CB A:CYS57 3.1 30.2 0.8
OD1 A:ASP324 3.2 29.0 1.0
CB A:CYS57 3.2 32.1 0.2
CA A:CYS57 3.6 29.4 0.8
CA A:CYS57 3.6 32.2 0.2
CB A:ASP12 4.0 23.8 1.0
ND1 A:HIS325 4.1 28.0 1.0
CG A:HIS325 4.1 27.2 1.0
N A:CYS57 4.2 32.3 0.2
N A:CYS57 4.3 27.6 0.8
NH2 A:ARG61 4.3 33.4 1.0
CD2 A:HIS218 4.3 23.4 1.0
CB A:ASP324 4.4 26.4 1.0
NE A:ARG61 4.5 31.1 1.0
OE1 A:GLN13 4.5 25.5 1.0
CA A:ASP12 4.5 23.2 1.0
N A:GLN13 4.7 22.3 1.0
OH A:TYR105 4.7 29.3 1.0
NZ A:LYS337 4.9 27.1 1.0
CZ A:ARG61 4.9 31.7 1.0
NE2 A:HIS218 4.9 23.9 1.0
C A:CYS57 4.9 28.7 0.8
C A:ASP12 5.0 22.8 1.0
CE A:LYS337 5.0 28.0 1.0
C A:CYS57 5.0 32.3 0.2

Iron binding site 2 out of 4 in 2w8s

Go back to Iron Binding Sites List in 2w8s
Iron binding site 2 out of 4 in the Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli


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 A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1516

b:30.0
occ:0.30
ZN B:ZN1515 0.0 30.7 0.3
OD2 B:ASP324 2.0 31.5 1.0
NE2 B:HIS325 2.1 27.9 1.0
OD1 B:ASP12 2.2 28.2 1.0
OG2 B:CYS57 2.3 39.2 0.2
SG B:CYS57 2.3 35.6 0.8
OD2 B:ASP12 2.4 27.1 1.0
CG B:ASP12 2.6 26.2 1.0
CD2 B:HIS325 2.9 28.7 1.0
CG B:ASP324 3.0 24.9 1.0
CB B:CYS57 3.2 39.5 0.2
CE1 B:HIS325 3.2 29.9 1.0
OD1 B:ASP324 3.2 24.0 1.0
CB B:CYS57 3.3 27.0 0.8
OG1 B:CYS57 3.4 39.1 0.2
CA B:CYS57 3.7 39.6 0.2
CA B:CYS57 3.7 26.2 0.8
NH2 B:ARG61 3.8 34.6 1.0
CB B:ASP12 4.0 24.5 1.0
CG B:HIS325 4.1 26.6 1.0
ND1 B:HIS325 4.2 28.7 1.0
N B:CYS57 4.3 24.0 0.8
NE B:ARG61 4.3 30.4 1.0
CB B:ASP324 4.4 22.7 1.0
N B:CYS57 4.4 39.5 0.2
CD2 B:HIS218 4.5 25.2 1.0
CZ B:ARG61 4.6 32.0 1.0
CA B:ASP12 4.6 24.4 1.0
OE1 B:GLN13 4.6 29.6 1.0
CE B:LYS337 4.6 18.9 1.0
NZ B:LYS337 4.6 15.2 1.0
N B:GLN13 4.8 24.9 1.0
OH B:TYR105 4.9 30.1 1.0
C B:CYS57 4.9 39.8 0.2

Iron binding site 3 out of 4 in 2w8s

Go back to Iron Binding Sites List in 2w8s
Iron binding site 3 out of 4 in the Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli


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 A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1516

b:19.2
occ:0.30
ZN C:ZN1515 0.0 20.4 0.3
NE2 C:HIS325 2.0 21.8 1.0
OD2 C:ASP324 2.2 22.3 1.0
OD1 C:ASP12 2.3 21.2 1.0
OG1 C:CYS57 2.4 35.9 0.2
SG C:CYS57 2.4 35.1 0.8
OD2 C:ASP12 2.5 22.6 1.0
CG C:ASP12 2.7 19.6 1.0
CD2 C:HIS325 2.9 18.9 1.0
CG C:ASP324 2.9 20.8 1.0
OD1 C:ASP324 3.0 23.5 1.0
CE1 C:HIS325 3.0 21.4 1.0
CB C:CYS57 3.2 36.0 0.2
CB C:CYS57 3.3 26.3 0.8
CA C:CYS57 3.4 36.0 0.2
OG2 C:CYS57 3.4 35.8 0.2
CA C:CYS57 3.6 25.8 0.8
N C:CYS57 3.9 36.0 0.2
NH2 C:ARG61 3.9 28.2 1.0
CG C:HIS325 4.0 19.1 1.0
N C:CYS57 4.0 23.6 0.8
ND1 C:HIS325 4.0 19.7 1.0
CB C:ASP12 4.1 19.3 1.0
CB C:ASP324 4.4 19.1 1.0
NE C:ARG61 4.4 27.8 1.0
NZ C:LYS337 4.4 15.5 1.0
CE C:LYS337 4.5 18.7 1.0
OE1 C:GLN13 4.5 18.6 1.0
CD2 C:HIS218 4.5 27.1 1.0
CA C:ASP12 4.6 19.1 1.0
CZ C:ARG61 4.7 28.4 1.0
N C:GLN13 4.7 19.2 1.0
C C:CYS57 4.8 36.1 0.2
C C:ASP12 5.0 18.6 1.0
C C:CYS57 5.0 24.4 0.8

Iron binding site 4 out of 4 in 2w8s

Go back to Iron Binding Sites List in 2w8s
Iron binding site 4 out of 4 in the Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli


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 A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1516

b:28.1
occ:0.30
ZN D:ZN1515 0.1 28.4 0.3
NE2 D:HIS325 2.0 26.8 1.0
OD2 D:ASP324 2.2 31.7 1.0
OD1 D:ASP12 2.2 27.0 1.0
OD2 D:ASP12 2.3 24.8 1.0
CG D:ASP12 2.6 22.1 1.0
OG2 D:CYS57 2.6 28.7 0.2
CD2 D:HIS325 2.9 25.0 1.0
SG D:CYS57 2.9 33.6 0.8
CE1 D:HIS325 3.0 25.7 1.0
CB D:CYS57 3.1 23.4 0.8
CG D:ASP324 3.1 27.7 1.0
CB D:CYS57 3.4 28.7 0.2
OD1 D:ASP324 3.4 29.1 1.0
OG1 D:CYS57 3.5 27.9 0.2
CA D:CYS57 3.6 28.7 0.2
CA D:CYS57 3.7 23.0 0.8
NH2 D:ARG61 4.0 27.8 1.0
CG D:HIS325 4.0 23.7 1.0
CB D:ASP12 4.1 20.2 1.0
ND1 D:HIS325 4.1 24.6 1.0
N D:CYS57 4.2 29.0 0.2
N D:CYS57 4.3 20.8 0.8
CE D:LYS337 4.4 19.9 1.0
CD2 D:HIS218 4.4 25.9 1.0
NZ D:LYS337 4.4 19.0 1.0
OE1 D:GLN13 4.5 18.3 1.0
CB D:ASP324 4.5 24.5 1.0
NE D:ARG61 4.6 28.5 1.0
CA D:ASP12 4.7 20.5 1.0
N D:GLN13 4.8 20.2 1.0
CZ D:ARG61 4.8 27.1 1.0
OH D:TYR105 4.9 28.4 1.0
C D:CYS57 4.9 28.8 0.2
C D:CYS57 5.0 21.5 0.8

Reference:

B.Van Loo, S.Jonas, A.C.Babtie, A.Benjdia, O.Berteau, M.Hyvonen, F.Hollfelder. An Efficient, Multiply Promiscuous Hydrolase in the Alkaline Phosphatase Superfamily. Proc.Natl.Acad.Sci.Usa V. 107 2740 2010.
ISSN: ISSN 0027-8424
PubMed: 20133613
DOI: 10.1073/PNAS.0903951107
Page generated: Thu Jul 17 04:57:50 2025

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