Atomistry » Iron » PDB 6azu-6bpt » 6b9t
Atomistry »
  Iron »
    PDB 6azu-6bpt »
      6b9t »

Iron in PDB 6b9t: Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound

Enzymatic activity of Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound

All present enzymatic activity of Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound:
1.13.11.73;

Protein crystallography data

The structure of Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound, PDB code: 6b9t was solved by D.A.Born, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.10 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.850, 351.250, 76.870, 90.00, 103.36, 90.00
R / Rfree (%) 19 / 23.8

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound (pdb code 6b9t). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound, PDB code: 6b9t:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 6b9t

Go back to Iron Binding Sites List in 6b9t
Iron binding site 1 out of 9 in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


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 Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:43.2
occ:1.00
 O2 A:2HE502 1.8 42.0 1.0
O4 A:2HE502 1.9 41.7 1.0
NE2 A:HIS148 2.1 38.9 1.0
NE2 A:HIS190 2.1 38.8 1.0
OE1 A:GLN152 2.3 38.2 1.0
O A:HOH601 2.6 37.2 1.0
CE1 A:HIS190 2.9 38.9 1.0
CE1 A:HIS148 3.0 40.5 1.0
CD2 A:HIS148 3.1 38.6 1.0
CB A:2HE502 3.1 45.4 1.0
P A:2HE502 3.2 39.4 1.0
CD A:GLN152 3.3 35.7 1.0
CD2 A:HIS190 3.3 38.8 1.0
CA A:2HE502 3.5 38.8 1.0
NE2 A:GLN152 3.7 35.7 1.0
NZ B:LYS28 3.8 42.2 1.0
ND2 A:ASN145 4.1 39.7 1.0
ND1 A:HIS190 4.1 36.4 1.0
O3 A:2HE502 4.1 38.3 1.0
ND1 A:HIS148 4.2 36.4 1.0
O1 A:2HE502 4.2 40.9 1.0
CG A:HIS148 4.2 39.0 1.0
CG A:HIS190 4.3 37.5 1.0
CG A:GLN152 4.6 34.9 1.0
CE B:LYS28 4.8 40.8 1.0
CB A:GLN152 5.0 36.3 1.0

Iron binding site 2 out of 9 in 6b9t

Go back to Iron Binding Sites List in 6b9t
Iron binding site 2 out of 9 in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


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 Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:40.1
occ:1.00
 O4 B:2HE503 2.0 41.8 1.0
O3 B:2HE503 2.1 38.5 1.0
OE1 B:GLN152 2.1 36.6 1.0
NE2 B:HIS148 2.2 40.2 1.0
NE2 B:HIS190 2.2 38.6 1.0
O B:HOH621 2.4 30.4 1.0
CD2 B:HIS148 2.9 38.5 1.0
CD B:GLN152 3.1 39.1 1.0
CE1 B:HIS190 3.1 39.3 1.0
CB B:2HE503 3.2 42.5 1.0
CD2 B:HIS190 3.3 37.7 1.0
P B:2HE503 3.3 43.4 1.0
CE1 B:HIS148 3.3 37.5 1.0
NE2 B:GLN152 3.4 37.4 1.0
CA B:2HE503 3.5 38.1 1.0
NZ A:LYS28 3.6 38.2 1.0
O1 B:2HE503 4.0 40.0 1.0
ND2 B:ASN145 4.1 40.3 1.0
CG B:HIS148 4.2 38.1 1.0
ND1 B:HIS190 4.3 38.7 1.0
ND1 B:HIS148 4.3 38.1 1.0
CG B:HIS190 4.4 38.9 1.0
CG B:GLN152 4.5 38.4 1.0
O2 B:2HE503 4.5 44.9 1.0
CE A:LYS28 4.7 43.3 1.0
CB B:GLN152 4.9 38.9 1.0

Iron binding site 3 out of 9 in 6b9t

Go back to Iron Binding Sites List in 6b9t
Iron binding site 3 out of 9 in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


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 Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:60.7
occ:1.00
 O B:HOH609 2.0 52.7 1.0
OE1 B:GLU159 3.2 52.7 1.0
O B:HOH707 3.4 39.1 1.0
CD B:GLU159 4.0 51.5 1.0
NE B:ARG195 4.1 40.9 1.0
NH1 B:ARG195 4.5 39.9 1.0
OE2 B:GLU159 4.6 51.8 1.0
CZ B:ARG195 4.8 40.3 1.0
CG B:GLU159 4.9 47.0 1.0

Iron binding site 4 out of 9 in 6b9t

Go back to Iron Binding Sites List in 6b9t
Iron binding site 4 out of 9 in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


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 Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:38.2
occ:1.00
 O4 C:2HE502 2.0 39.3 1.0
NE2 C:HIS148 2.1 35.4 1.0
OE1 C:GLN152 2.1 33.9 1.0
NE2 C:HIS190 2.2 38.6 1.0
O2 C:2HE502 2.2 42.1 1.0
O C:HOH601 2.5 37.5 1.0
CE1 C:HIS190 2.9 35.8 1.0
CD2 C:HIS148 3.0 35.6 1.0
CE1 C:HIS148 3.1 32.7 1.0
CD C:GLN152 3.2 33.8 1.0
CB C:2HE502 3.3 42.9 1.0
CD2 C:HIS190 3.3 36.5 1.0
P C:2HE502 3.4 43.5 1.0
NE2 C:GLN152 3.7 38.2 1.0
CA C:2HE502 3.7 37.1 1.0
NZ D:LYS28 3.8 39.5 1.0
ND2 C:ASN145 4.1 35.4 1.0
ND1 C:HIS190 4.1 34.0 1.0
CG C:HIS148 4.2 34.1 1.0
ND1 C:HIS148 4.2 32.3 1.0
CG C:HIS190 4.4 35.8 1.0
O1 C:2HE502 4.5 38.5 1.0
O3 C:2HE502 4.5 36.7 1.0
CG C:GLN152 4.5 33.2 1.0
CB C:GLN152 4.8 31.1 1.0
CE D:LYS28 4.8 37.9 1.0

Iron binding site 5 out of 9 in 6b9t

Go back to Iron Binding Sites List in 6b9t
Iron binding site 5 out of 9 in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


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 Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:31.0
occ:1.00
 O1 D:2HE502 2.0 32.6 1.0
O4 D:2HE502 2.1 35.3 1.0
NE2 D:HIS148 2.2 30.1 1.0
O D:HOH601 2.2 27.1 1.0
NE2 D:HIS190 2.2 32.4 1.0
OE1 D:GLN152 2.2 28.8 1.0
CE1 D:HIS190 3.1 31.6 1.0
CD2 D:HIS148 3.1 32.9 1.0
CE1 D:HIS148 3.2 30.1 1.0
CD D:GLN152 3.2 30.9 1.0
P D:2HE502 3.2 36.8 1.0
CB D:2HE502 3.2 37.4 1.0
CD2 D:HIS190 3.2 31.9 1.0
CA D:2HE502 3.5 31.2 1.0
NE2 D:GLN152 3.5 27.7 1.0
NZ C:LYS28 3.7 30.8 1.0
O3 D:2HE502 4.0 34.2 1.0
ND2 D:ASN145 4.0 31.3 1.0
ND1 D:HIS190 4.2 32.3 1.0
CG D:HIS148 4.3 32.4 1.0
ND1 D:HIS148 4.3 31.5 1.0
CG D:HIS190 4.3 33.5 1.0
O2 D:2HE502 4.4 33.4 1.0
CG D:GLN152 4.6 29.1 1.0
CE C:LYS28 4.8 30.5 1.0
CE1 D:PHE192 4.9 33.3 1.0
CB D:GLN152 5.0 26.9 1.0

Iron binding site 6 out of 9 in 6b9t

Go back to Iron Binding Sites List in 6b9t
Iron binding site 6 out of 9 in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


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 Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:34.0
occ:1.00
 O4 E:2HE502 1.9 39.2 1.0
O2 E:2HE502 2.0 33.3 1.0
NE2 E:HIS148 2.1 32.2 1.0
OE1 E:GLN152 2.2 36.0 1.0
NE2 E:HIS190 2.2 35.3 1.0
O E:HOH608 2.4 32.5 1.0
CD2 E:HIS148 2.9 32.5 1.0
CE1 E:HIS190 3.0 34.8 1.0
CE1 E:HIS148 3.2 32.5 1.0
CB E:2HE502 3.2 38.1 1.0
CD E:GLN152 3.2 36.2 1.0
CD2 E:HIS190 3.4 34.0 1.0
P E:2HE502 3.4 38.5 1.0
NE2 E:GLN152 3.6 35.2 1.0
NZ F:LYS28 3.6 37.2 1.0
CA E:2HE502 3.8 34.9 1.0
CG E:HIS148 4.1 32.7 1.0
ND2 E:ASN145 4.2 31.2 1.0
ND1 E:HIS148 4.2 31.8 1.0
O3 E:2HE502 4.2 39.2 1.0
ND1 E:HIS190 4.2 36.7 1.0
CG E:HIS190 4.4 37.3 1.0
O1 E:2HE502 4.5 33.7 1.0
CG E:GLN152 4.6 32.5 1.0
CE F:LYS28 4.8 40.0 1.0
CB E:GLN152 4.9 29.9 1.0

Iron binding site 7 out of 9 in 6b9t

Go back to Iron Binding Sites List in 6b9t
Iron binding site 7 out of 9 in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


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 Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:42.4
occ:1.00
 O F:HOH601 1.9 34.9 1.0
NE2 F:HIS190 2.0 38.3 1.0
O4 F:2HE502 2.1 42.0 1.0
O1 F:2HE502 2.2 43.1 1.0
OE1 F:GLN152 2.2 39.3 1.0
NE2 F:HIS148 2.2 41.6 1.0
CE1 F:HIS190 2.8 40.7 1.0
CD2 F:HIS148 3.0 40.5 1.0
CD F:GLN152 3.2 38.1 1.0
CD2 F:HIS190 3.2 41.7 1.0
CB F:2HE502 3.2 44.5 1.0
P F:2HE502 3.2 45.3 1.0
CE1 F:HIS148 3.3 42.0 1.0
CA F:2HE502 3.3 42.4 1.0
NE2 F:GLN152 3.5 41.9 1.0
NZ E:LYS28 3.7 40.1 1.0
ND1 F:HIS190 4.0 43.1 1.0
ND2 F:ASN145 4.1 41.9 1.0
O2 F:2HE502 4.2 39.1 1.0
CG F:HIS190 4.2 43.3 1.0
CG F:HIS148 4.2 42.9 1.0
ND1 F:HIS148 4.3 39.1 1.0
O3 F:2HE502 4.4 43.0 1.0
CG F:GLN152 4.5 38.9 1.0
CE E:LYS28 4.8 38.0 1.0
CB F:GLN152 4.9 35.5 1.0

Iron binding site 8 out of 9 in 6b9t

Go back to Iron Binding Sites List in 6b9t
Iron binding site 8 out of 9 in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


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 Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe501

b:56.3
occ:1.00
 NE2 G:HIS148 2.0 57.7 1.0
O4 G:2HE502 2.1 59.8 1.0
O2 G:2HE502 2.2 68.4 1.0
NE2 G:HIS190 2.4 58.6 1.0
OE1 G:GLN152 2.4 52.1 1.0
CD2 G:HIS148 2.8 58.2 1.0
CB G:2HE502 3.0 62.8 1.0
CE1 G:HIS190 3.0 58.0 1.0
CE1 G:HIS148 3.1 56.1 1.0
P G:2HE502 3.4 69.8 1.0
NZ H:LYS28 3.4 64.2 1.0
CD G:GLN152 3.5 52.8 1.0
CD2 G:HIS190 3.5 59.0 1.0
CA G:2HE502 3.6 56.2 1.0
NE2 G:GLN152 4.0 55.0 1.0
CG G:HIS148 4.0 55.8 1.0
ND1 G:HIS148 4.1 56.0 1.0
ND2 G:ASN145 4.1 61.9 1.0
ND1 G:HIS190 4.3 56.0 1.0
O1 G:2HE502 4.3 67.4 1.0
O3 G:2HE502 4.5 65.4 1.0
CG G:HIS190 4.5 56.3 1.0
CE H:LYS28 4.7 65.2 1.0
CG G:GLN152 4.8 47.9 1.0
CG2 G:THR208 5.0 53.4 1.0

Iron binding site 9 out of 9 in 6b9t

Go back to Iron Binding Sites List in 6b9t
Iron binding site 9 out of 9 in the Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Mpns with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe501

b:48.2
occ:1.00
 O4 H:2HE502 1.9 46.6 1.0
O2 H:2HE502 2.1 51.2 1.0
NE2 H:HIS190 2.1 46.6 1.0
NE2 H:HIS148 2.1 48.2 1.0
OE1 H:GLN152 2.2 46.1 1.0
O H:HOH601 2.9 48.6 1.0
CD2 H:HIS148 3.0 50.0 1.0
CD2 H:HIS190 3.1 47.4 1.0
CB H:2HE502 3.1 50.9 1.0
CE1 H:HIS190 3.1 46.9 1.0
P H:2HE502 3.2 53.6 1.0
CE1 H:HIS148 3.2 47.2 1.0
CD H:GLN152 3.2 42.7 1.0
CA H:2HE502 3.3 50.5 1.0
NE2 H:GLN152 3.6 42.8 1.0
NZ G:LYS28 3.7 58.9 1.0
ND2 H:ASN145 4.1 51.7 1.0
O1 H:2HE502 4.1 53.4 1.0
CG H:HIS148 4.2 49.7 1.0
ND1 H:HIS190 4.2 46.1 1.0
CG H:HIS190 4.2 47.6 1.0
ND1 H:HIS148 4.3 48.4 1.0
O3 H:2HE502 4.3 54.2 1.0
CG H:GLN152 4.6 42.3 1.0
CE G:LYS28 4.9 57.6 1.0
CB H:GLN152 4.9 42.8 1.0

Reference:

D.A.Born, E.C.Ulrich, K.S.Ju, S.C.Peck, W.A.Van Der Donk, C.L.Drennan. Structural Basis For Methylphosphonate Biosynthesis. Science V. 358 1336 2017.
ISSN: ESSN 1095-9203
PubMed: 29217579
DOI: 10.1126/SCIENCE.AAO3435
Page generated: Tue Aug 6 14:08:52 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy