Iron in PDB 4zmc: Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min)

Enzymatic activity of Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min)

All present enzymatic activity of Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min):
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min), PDB code: 4zmc was solved by S.Pfaffen, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.53 / 1.90
Space group P 2 3
Cell size a, b, c (Å), α, β, γ (°) 174.980, 174.980, 174.980, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.8

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min) (pdb code 4zmc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min), PDB code: 4zmc:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in 4zmc

Go back to Iron Binding Sites List in 4zmc
Iron binding site 1 out of 7 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min)


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 the Pmftn Variant E130A Soaked in Iron (5 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:36.5
occ:0.30
OE1 A:GLU15 2.3 34.8 1.0
OE1 A:GLU48 2.3 42.7 1.0
ND1 A:HIS51 3.0 38.5 1.0
CD A:GLU15 3.1 34.1 1.0
ND2 A:ASN97 3.2 27.9 0.5
OE2 A:GLU15 3.3 40.1 1.0
CD A:GLU48 3.4 36.2 1.0
O A:HOH325 3.4 36.6 1.0
OE2 A:GLU48 3.7 47.4 1.0
OE1 A:GLN127 3.8 30.9 1.0
O A:HOH342 3.8 47.3 1.0
CG A:HIS51 3.9 33.0 1.0
CE1 A:HIS51 3.9 38.9 1.0
ND2 A:ASN97 4.0 28.2 0.5
CB A:HIS51 4.1 24.2 1.0
CG A:ASN97 4.3 30.8 0.5
CG A:GLU15 4.6 28.2 1.0
CG A:ASN97 4.6 30.9 0.5
CD A:GLN127 4.7 28.3 1.0
CG A:GLU48 4.7 29.9 1.0
CB A:ASN97 4.9 29.9 0.5
CA A:GLU48 5.0 22.9 1.0
CB A:ASN97 5.0 32.3 0.5
CB A:GLU15 5.0 25.6 1.0

Iron binding site 2 out of 7 in 4zmc

Go back to Iron Binding Sites List in 4zmc
Iron binding site 2 out of 7 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min)


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 the Pmftn Variant E130A Soaked in Iron (5 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:38.3
occ:0.30
OE1 D:GLU15 2.2 28.6 1.0
OE1 D:GLU48 2.3 44.6 1.0
ND1 D:HIS51 3.0 35.1 1.0
ND2 D:ASN97 3.0 26.2 0.3
CD D:GLU15 3.1 27.1 1.0
O D:HOH316 3.2 48.4 1.0
OE2 D:GLU15 3.3 34.1 1.0
CD D:GLU48 3.4 32.5 1.0
O D:HOH363 3.6 36.3 1.0
OE2 D:GLU48 3.8 47.2 1.0
CG D:HIS51 3.9 30.4 1.0
CE1 D:HIS51 3.9 37.3 1.0
CB D:HIS51 4.0 24.9 1.0
OE1 D:GLN127 4.0 26.0 1.0
ND2 D:ASN97 4.1 30.0 0.7
CG D:ASN97 4.2 26.2 0.3
CG D:GLU15 4.5 22.7 1.0
CG D:ASN97 4.5 32.3 0.7
CG D:GLU48 4.7 28.1 1.0
CA D:GLU48 4.8 22.3 1.0
CB D:GLU15 4.9 19.8 1.0
CB D:ASN97 4.9 30.2 0.7
CD D:GLN127 4.9 28.5 1.0
CB D:GLU48 4.9 23.0 1.0
CB D:ASN97 4.9 26.8 0.3
OD1 D:ASN97 5.0 26.9 0.3

Iron binding site 3 out of 7 in 4zmc

Go back to Iron Binding Sites List in 4zmc
Iron binding site 3 out of 7 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min)


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 the Pmftn Variant E130A Soaked in Iron (5 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:40.3
occ:0.35
OE1 C:GLU15 2.2 38.2 1.0
OE1 C:GLU48 2.3 44.7 1.0
ND1 C:HIS51 2.9 46.5 1.0
CD C:GLU15 3.1 33.2 1.0
ND2 C:ASN97 3.2 30.2 0.4
OE2 C:GLU15 3.3 43.5 1.0
CD C:GLU48 3.5 35.3 1.0
O C:HOH360 3.7 40.8 1.0
CG C:HIS51 3.8 35.5 1.0
CB C:HIS51 3.9 28.5 1.0
OE2 C:GLU48 3.9 41.3 1.0
CE1 C:HIS51 3.9 46.1 1.0
OE1 C:GLN127 4.0 28.7 1.0
CG C:ASN97 4.3 29.1 0.4
ND2 C:ASN97 4.3 28.4 0.6
CG C:GLU15 4.5 27.5 1.0
CG C:GLU48 4.8 27.1 1.0
CG C:ASN97 4.8 32.5 0.6
CD C:GLN127 4.8 27.3 1.0
CA C:GLU48 4.8 23.3 1.0
OD1 C:ASN97 4.9 31.2 0.4
CB C:GLU48 4.9 25.3 1.0
CD2 C:HIS51 4.9 42.9 1.0
CB C:GLU15 5.0 23.5 1.0
NE2 C:HIS51 5.0 48.0 1.0

Iron binding site 4 out of 7 in 4zmc

Go back to Iron Binding Sites List in 4zmc
Iron binding site 4 out of 7 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min)


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 the Pmftn Variant E130A Soaked in Iron (5 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:43.6
occ:0.35
OE1 E:GLU15 2.1 39.7 1.0
OE1 E:GLU48 2.4 43.1 1.0
CD E:GLU15 3.0 37.7 1.0
ND1 E:HIS51 3.1 38.4 1.0
O E:HOH308 3.1 44.7 1.0
OE2 E:GLU15 3.2 43.8 1.0
CD E:GLU48 3.2 38.4 1.0
OE2 E:GLU48 3.4 53.3 1.0
O E:HOH337 3.7 32.9 1.0
CG E:HIS51 3.9 35.6 1.0
CB E:HIS51 4.0 26.5 1.0
OE1 E:GLN127 4.0 33.1 1.0
CE1 E:HIS51 4.0 39.7 1.0
ND2 E:ASN97 4.1 38.3 1.0
CG E:GLU15 4.4 29.3 1.0
CG E:ASN97 4.5 35.8 1.0
CG E:GLU48 4.6 32.0 1.0
CB E:ASN97 4.8 29.2 1.0
CA E:GLU48 4.8 25.3 1.0
CD E:GLN127 4.9 28.2 1.0
O E:HOH301 4.9 35.3 1.0
CB E:GLU48 4.9 28.9 1.0
CB E:GLU15 4.9 23.9 1.0

Iron binding site 5 out of 7 in 4zmc

Go back to Iron Binding Sites List in 4zmc
Iron binding site 5 out of 7 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min)


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 the Pmftn Variant E130A Soaked in Iron (5 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:36.1
occ:0.25
O F:HOH1133 2.2 50.0 1.0
OE1 F:GLU15 2.3 38.7 1.0
OE1 F:GLU48 2.5 50.3 1.0
ND1 F:HIS51 2.8 45.1 1.0
OD1 F:ASN97 2.9 39.2 0.4
CD F:GLU15 3.1 37.0 1.0
OE2 F:GLU15 3.1 41.2 1.0
CD F:GLU48 3.5 38.1 1.0
CG F:ASN97 3.6 31.8 0.4
CE1 F:HIS51 3.6 44.1 1.0
O F:HOH1145 3.7 36.7 1.0
O F:HOH1154 3.7 37.4 1.0
CG F:HIS51 3.8 38.5 1.0
OE2 F:GLU48 3.8 53.1 1.0
ND2 F:ASN97 3.9 31.5 0.4
OE1 F:GLN127 3.9 29.9 1.0
CB F:HIS51 4.1 31.5 1.0
ND2 F:ASN97 4.2 30.7 0.6
CG F:GLU15 4.5 27.0 1.0
CG F:ASN97 4.6 30.3 0.6
CB F:ASN97 4.7 32.6 0.4
CD F:GLN127 4.7 31.4 1.0
NE2 F:HIS51 4.8 46.4 1.0
CB F:ASN97 4.8 30.6 0.6
CG F:GLU48 4.8 33.8 1.0
CD2 F:HIS51 4.9 40.7 1.0
CB F:GLU15 4.9 25.9 1.0
CA F:GLU48 5.0 25.9 1.0

Iron binding site 6 out of 7 in 4zmc

Go back to Iron Binding Sites List in 4zmc
Iron binding site 6 out of 7 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min)


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 the Pmftn Variant E130A Soaked in Iron (5 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe201

b:38.8
occ:0.35
OE1 G:GLU15 2.3 31.5 1.0
OE1 G:GLU48 2.3 37.6 1.0
ND2 G:ASN97 2.7 25.6 0.3
ND1 G:HIS51 3.0 37.8 1.0
CD G:GLU15 3.2 32.1 1.0
CD G:GLU48 3.3 30.4 1.0
OE2 G:GLU15 3.4 33.4 1.0
O G:HOH350 3.6 39.1 1.0
OE2 G:GLU48 3.6 41.9 1.0
CG G:ASN97 3.8 25.4 0.3
CE1 G:HIS51 3.8 36.0 1.0
OE1 G:GLN127 3.9 25.7 1.0
CG G:HIS51 3.9 31.9 1.0
ND2 G:ASN97 4.0 23.2 0.7
CB G:HIS51 4.2 25.7 1.0
CG G:ASN97 4.3 26.3 0.7
OD1 G:ASN97 4.6 28.5 0.3
CG G:GLU15 4.6 23.4 1.0
CB G:ASN97 4.6 26.1 0.7
CB G:ASN97 4.7 25.7 0.3
CG G:GLU48 4.7 28.2 1.0
CD G:GLN127 4.7 24.9 1.0
OD1 G:ASN97 4.9 25.8 0.7
CA G:GLU48 4.9 22.1 1.0
CB G:GLU48 5.0 25.1 1.0
NE2 G:HIS51 5.0 42.8 1.0

Iron binding site 7 out of 7 in 4zmc

Go back to Iron Binding Sites List in 4zmc
Iron binding site 7 out of 7 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min)


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 the Pmftn Variant E130A Soaked in Iron (5 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe201

b:36.9
occ:0.35
OE1 H:GLU48 2.2 27.3 0.5
OE1 H:GLU15 2.2 35.4 1.0
ND1 H:HIS51 2.9 37.5 1.0
OE1 H:GLU48 3.0 28.7 0.5
ND2 H:ASN97 3.1 31.1 0.5
CD H:GLU15 3.1 29.4 1.0
OE2 H:GLU15 3.3 37.1 1.0
CD H:GLU48 3.3 26.8 0.5
OE2 H:GLU48 3.4 30.7 0.5
O H:HOH353 3.5 34.8 1.0
CD H:GLU48 3.5 30.3 0.5
OE2 H:GLU48 3.7 25.3 0.5
CE1 H:HIS51 3.8 34.9 1.0
CG H:HIS51 3.9 30.1 1.0
ND2 H:ASN97 3.9 29.8 0.5
OE1 H:GLN127 3.9 27.1 1.0
CB H:HIS51 4.1 27.7 1.0
CG H:ASN97 4.3 31.2 0.5
CG H:GLU15 4.5 25.6 1.0
CG H:ASN97 4.6 30.0 0.5
CG H:GLU48 4.6 26.0 0.5
CD H:GLN127 4.8 27.1 1.0
CB H:GLU48 4.8 24.6 0.5
CA H:GLU48 4.8 23.0 0.5
CG H:GLU48 4.9 28.2 0.5
CA H:GLU48 4.9 24.3 0.5
NE2 H:HIS51 4.9 39.2 1.0
CB H:ASN97 5.0 26.6 0.5
CD2 H:HIS51 5.0 32.9 1.0

Reference:

S.Pfaffen, J.M.Bradley, R.Abdulqadir, M.R.Firme, G.R.Moore, N.E.Le Brun, M.E.Murphy. A Diatom Ferritin Optimized For Iron Oxidation But Not Iron Storage. J.Biol.Chem. V. 290 28416 2015.
ISSN: ESSN 1083-351X
PubMed: 26396187
DOI: 10.1074/JBC.M115.669713
Page generated: Sun Dec 13 15:54:59 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy