Iron in PDB 4mln: Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid
Protein crystallography data
The structure of Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid, PDB code: 4mln
was solved by
L.M.Van Staalduinen,
F.R.Mcsorley,
D.L.Zechel,
Z.Jia,
Montreal-Kingstonbacterial Structural Genomics Initiative (Bsgi),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.90 /
2.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
66.630,
74.910,
75.810,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.6 /
25.4
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid
(pdb code 4mln). 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 of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid, PDB code: 4mln:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 4mln
Go back to
Iron Binding Sites List in 4mln
Iron binding site 1 out
of 4 in the Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:22.7
occ:1.00
|
NE2
|
A:HIS58
|
2.1
|
23.1
|
1.0
|
OD1
|
A:ASP161
|
2.1
|
23.6
|
1.0
|
OD2
|
A:ASP59
|
2.1
|
22.0
|
1.0
|
O
|
A:HOH301
|
2.1
|
28.4
|
1.0
|
O
|
A:HOH347
|
2.1
|
26.5
|
1.0
|
NE2
|
A:HIS34
|
2.2
|
24.5
|
1.0
|
CG
|
A:ASP161
|
2.9
|
28.1
|
1.0
|
CG
|
A:ASP59
|
3.0
|
20.4
|
1.0
|
CE1
|
A:HIS58
|
3.0
|
23.6
|
1.0
|
CD2
|
A:HIS58
|
3.1
|
20.3
|
1.0
|
OD2
|
A:ASP161
|
3.2
|
32.1
|
1.0
|
CD2
|
A:HIS34
|
3.2
|
27.2
|
1.0
|
HAC
|
A:ODV203
|
3.2
|
28.2
|
1.0
|
CE1
|
A:HIS34
|
3.2
|
26.8
|
1.0
|
OD1
|
A:ASP59
|
3.4
|
17.6
|
1.0
|
HAG
|
A:ODV203
|
3.6
|
38.3
|
1.0
|
FE
|
A:FE202
|
3.7
|
21.8
|
1.0
|
OAC
|
A:ODV203
|
4.0
|
23.5
|
1.0
|
O
|
A:HOH348
|
4.1
|
31.8
|
1.0
|
ND1
|
A:HIS58
|
4.1
|
20.4
|
1.0
|
CB
|
A:ASP59
|
4.2
|
19.9
|
1.0
|
CG
|
A:HIS58
|
4.2
|
17.8
|
1.0
|
CAG
|
A:ODV203
|
4.2
|
31.9
|
1.0
|
CB
|
A:ASP161
|
4.3
|
23.9
|
1.0
|
O
|
A:HOH363
|
4.3
|
29.1
|
1.0
|
CG
|
A:HIS34
|
4.3
|
24.7
|
1.0
|
ND1
|
A:HIS34
|
4.3
|
22.1
|
1.0
|
NE2
|
A:HIS104
|
4.7
|
21.6
|
1.0
|
CA
|
A:ASP161
|
4.7
|
27.3
|
1.0
|
HAI
|
A:ODV203
|
4.8
|
44.6
|
1.0
|
CD2
|
A:HIS104
|
4.8
|
24.6
|
1.0
|
O
|
A:ASP161
|
4.9
|
30.8
|
1.0
|
|
Iron binding site 2 out
of 4 in 4mln
Go back to
Iron Binding Sites List in 4mln
Iron binding site 2 out
of 4 in the Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe202
b:21.8
occ:1.00
|
HAC
|
A:ODV203
|
1.6
|
28.2
|
1.0
|
O
|
A:HOH301
|
2.1
|
28.4
|
1.0
|
NE2
|
A:HIS104
|
2.1
|
21.6
|
1.0
|
OD1
|
A:ASP59
|
2.2
|
17.6
|
1.0
|
OAC
|
A:ODV203
|
2.2
|
23.5
|
1.0
|
NE2
|
A:HIS80
|
2.2
|
23.5
|
1.0
|
OAE
|
A:ODV203
|
2.3
|
23.0
|
1.0
|
CAG
|
A:ODV203
|
3.0
|
31.9
|
1.0
|
CD2
|
A:HIS104
|
3.1
|
24.6
|
1.0
|
PAH
|
A:ODV203
|
3.1
|
25.6
|
1.0
|
CE1
|
A:HIS104
|
3.2
|
19.3
|
1.0
|
CG
|
A:ASP59
|
3.2
|
20.4
|
1.0
|
CE1
|
A:HIS80
|
3.2
|
20.2
|
1.0
|
CD2
|
A:HIS80
|
3.2
|
21.3
|
1.0
|
HAG
|
A:ODV203
|
3.2
|
38.3
|
1.0
|
OD2
|
A:ASP59
|
3.5
|
22.0
|
1.0
|
FE
|
A:FE201
|
3.7
|
22.7
|
1.0
|
OAD
|
A:ODV203
|
4.0
|
25.9
|
1.0
|
CD2
|
A:HIS58
|
4.0
|
20.3
|
1.0
|
NE2
|
A:HIS62
|
4.2
|
22.1
|
1.0
|
O
|
A:HOH347
|
4.2
|
26.5
|
1.0
|
ND1
|
A:HIS104
|
4.2
|
25.9
|
1.0
|
OD2
|
A:ASP161
|
4.2
|
32.1
|
1.0
|
CG
|
A:HIS104
|
4.3
|
23.2
|
1.0
|
OAB
|
A:ODV203
|
4.3
|
31.1
|
1.0
|
ND1
|
A:HIS80
|
4.3
|
19.9
|
1.0
|
NE2
|
A:HIS58
|
4.4
|
23.1
|
1.0
|
CAF
|
A:ODV203
|
4.4
|
33.7
|
1.0
|
CG
|
A:HIS80
|
4.4
|
20.7
|
1.0
|
NH1
|
A:ARG158
|
4.4
|
30.6
|
1.0
|
HAH
|
A:ODV203
|
4.5
|
40.5
|
1.0
|
CB
|
A:ASP59
|
4.5
|
19.9
|
1.0
|
O
|
A:HOH348
|
4.7
|
31.8
|
1.0
|
CG2
|
A:VAL105
|
4.8
|
25.6
|
1.0
|
HAJ
|
A:ODV203
|
4.8
|
44.6
|
1.0
|
O
|
A:HIS58
|
4.8
|
17.3
|
1.0
|
CA
|
A:ASP59
|
4.9
|
17.4
|
1.0
|
CD2
|
A:HIS62
|
4.9
|
25.2
|
1.0
|
HAF
|
A:ODV203
|
5.0
|
40.5
|
1.0
|
|
Iron binding site 3 out
of 4 in 4mln
Go back to
Iron Binding Sites List in 4mln
Iron binding site 3 out
of 4 in the Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:19.6
occ:1.00
|
OD2
|
B:ASP59
|
2.0
|
19.6
|
1.0
|
NE2
|
B:HIS58
|
2.1
|
15.8
|
1.0
|
OH
|
B:TYR24
|
2.1
|
25.2
|
1.0
|
NE2
|
B:HIS34
|
2.1
|
23.3
|
1.0
|
OD1
|
B:ASP161
|
2.2
|
22.6
|
1.0
|
O
|
B:HOH301
|
2.3
|
19.0
|
1.0
|
CG
|
B:ASP59
|
3.0
|
18.9
|
1.0
|
CG
|
B:ASP161
|
3.0
|
22.0
|
1.0
|
CD2
|
B:HIS58
|
3.0
|
13.9
|
1.0
|
CZ
|
B:TYR24
|
3.1
|
32.6
|
1.0
|
CE1
|
B:HIS58
|
3.1
|
19.2
|
1.0
|
HAC
|
B:ODV203
|
3.1
|
24.9
|
1.0
|
CD2
|
B:HIS34
|
3.1
|
21.6
|
1.0
|
CE1
|
B:HIS34
|
3.1
|
22.5
|
1.0
|
OD2
|
B:ASP161
|
3.3
|
20.5
|
1.0
|
OD1
|
B:ASP59
|
3.4
|
18.7
|
1.0
|
CE1
|
B:TYR24
|
3.7
|
30.2
|
1.0
|
FE
|
B:FE202
|
3.8
|
18.4
|
1.0
|
OAC
|
B:ODV203
|
4.0
|
20.8
|
1.0
|
CE2
|
B:TYR24
|
4.0
|
27.1
|
1.0
|
HAG
|
B:ODV203
|
4.0
|
33.1
|
1.0
|
ND1
|
B:HIS58
|
4.2
|
15.2
|
1.0
|
CG
|
B:HIS58
|
4.2
|
16.8
|
1.0
|
ND1
|
B:HIS34
|
4.2
|
20.9
|
1.0
|
CB
|
B:ASP59
|
4.2
|
16.9
|
1.0
|
CG
|
B:HIS34
|
4.2
|
21.0
|
1.0
|
CB
|
B:ASP161
|
4.4
|
18.5
|
1.0
|
CAG
|
B:ODV203
|
4.5
|
27.6
|
1.0
|
CA
|
B:ASP161
|
4.8
|
17.7
|
1.0
|
NE2
|
B:HIS104
|
4.8
|
17.5
|
1.0
|
O
|
B:ASP161
|
4.9
|
19.3
|
1.0
|
CD1
|
B:TYR24
|
5.0
|
32.9
|
1.0
|
CD2
|
B:HIS104
|
5.0
|
20.0
|
1.0
|
|
Iron binding site 4 out
of 4 in 4mln
Go back to
Iron Binding Sites List in 4mln
Iron binding site 4 out
of 4 in the Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe202
b:18.4
occ:1.00
|
HAC
|
B:ODV203
|
1.9
|
24.9
|
1.0
|
O
|
B:HOH301
|
2.0
|
19.0
|
1.0
|
OAC
|
B:ODV203
|
2.1
|
20.8
|
1.0
|
OD1
|
B:ASP59
|
2.2
|
18.7
|
1.0
|
NE2
|
B:HIS104
|
2.2
|
17.5
|
1.0
|
NE2
|
B:HIS80
|
2.2
|
20.1
|
1.0
|
OAE
|
B:ODV203
|
2.2
|
22.2
|
1.0
|
CAG
|
B:ODV203
|
3.0
|
27.6
|
1.0
|
PAH
|
B:ODV203
|
3.1
|
23.7
|
1.0
|
CD2
|
B:HIS104
|
3.1
|
20.0
|
1.0
|
CE1
|
B:HIS104
|
3.1
|
20.9
|
1.0
|
CE1
|
B:HIS80
|
3.1
|
19.5
|
1.0
|
CD2
|
B:HIS80
|
3.2
|
19.6
|
1.0
|
CG
|
B:ASP59
|
3.2
|
18.9
|
1.0
|
HAG
|
B:ODV203
|
3.4
|
33.1
|
1.0
|
OD2
|
B:ASP59
|
3.5
|
19.6
|
1.0
|
FE
|
B:FE201
|
3.8
|
19.6
|
1.0
|
CD2
|
B:HIS58
|
4.0
|
13.9
|
1.0
|
OAD
|
B:ODV203
|
4.1
|
26.6
|
1.0
|
NE2
|
B:HIS62
|
4.2
|
26.5
|
1.0
|
OD2
|
B:ASP161
|
4.2
|
20.5
|
1.0
|
OAB
|
B:ODV203
|
4.2
|
21.7
|
1.0
|
OH
|
B:TYR24
|
4.2
|
25.2
|
1.0
|
ND1
|
B:HIS104
|
4.3
|
20.0
|
1.0
|
CAF
|
B:ODV203
|
4.3
|
31.6
|
1.0
|
HAH
|
B:ODV203
|
4.3
|
37.9
|
1.0
|
ND1
|
B:HIS80
|
4.3
|
19.0
|
1.0
|
CG
|
B:HIS104
|
4.3
|
18.6
|
1.0
|
CG
|
B:HIS80
|
4.3
|
20.7
|
1.0
|
NH1
|
B:ARG158
|
4.4
|
20.1
|
1.0
|
NE2
|
B:HIS58
|
4.4
|
15.8
|
1.0
|
CB
|
B:ASP59
|
4.5
|
16.9
|
1.0
|
CG2
|
B:VAL105
|
4.7
|
21.1
|
1.0
|
O
|
B:HIS58
|
4.8
|
17.3
|
1.0
|
CD2
|
B:HIS62
|
4.8
|
23.8
|
1.0
|
CA
|
B:ASP59
|
4.8
|
18.7
|
1.0
|
HAF
|
B:ODV203
|
4.8
|
37.9
|
1.0
|
HAJ
|
B:ODV203
|
4.9
|
48.0
|
1.0
|
CE1
|
B:HIS62
|
5.0
|
24.4
|
1.0
|
|
Reference:
L.M.Van Staalduinen,
F.R.Mcsorley,
K.Schiessl,
J.Seguin,
P.B.Wyatt,
F.Hammerschmidt,
D.L.Zechel,
Z.Jia.
Crystal Structure of Phnz in Complex with Substrate Reveals A Di-Iron Oxygenase Mechanism For Catabolism of Organophosphonates. Proc.Natl.Acad.Sci.Usa V. 111 5171 2014.
ISSN: ISSN 0027-8424
PubMed: 24706911
DOI: 10.1073/PNAS.1320039111
Page generated: Mon Aug 5 06:55:59 2024
|