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Iron in PDB 6frm: Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4

Protein crystallography data

The structure of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4, PDB code: 6frm was solved by S.Engilberge, F.Riobe, T.Wagner, S.Di Pietro, S.Shima, E.Girard, E.Dumont, O.Maury, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.69 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.170, 147.875, 146.059, 90.00, 90.40, 90.00
R / Rfree (%) 17.7 / 20.9

Other elements in 6frm:

The structure of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 also contains other interesting chemical elements:

Terbium (Tb) 16 atoms
Chlorine (Cl) 17 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 (pdb code 6frm). 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 Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4, PDB code: 6frm:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6frm

Go back to Iron Binding Sites List in 6frm
Iron binding site 1 out of 4 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


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 Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe504

b:53.2
occ:0.60
OE2 C:GLU86 2.1 54.0 1.0
OD2 C:ASP171 2.2 53.9 1.0
NE2 C:HIS152 2.3 78.4 1.0
NE2 C:HIS84 2.7 58.7 1.0
CD2 C:HIS84 2.9 58.5 1.0
TB C:TB503 3.0 61.0 1.0
CD C:GLU86 3.1 75.7 1.0
CD2 C:HIS152 3.3 79.2 1.0
CE1 C:HIS152 3.3 78.1 1.0
CG C:ASP171 3.4 44.9 1.0
CG C:GLU86 3.4 59.3 1.0
CB C:GLU86 3.4 48.1 1.0
OD1 C:ASP171 3.9 39.4 1.0
CE1 C:HIS84 3.9 59.1 1.0
OD1 C:ASP88 4.1 47.2 1.0
OE1 C:GLU86 4.2 78.8 1.0
O C:HOH696 4.2 52.1 1.0
CG C:HIS84 4.3 57.1 1.0
CD2 C:HIS89 4.4 38.7 1.0
CG C:HIS152 4.5 77.9 1.0
ND1 C:HIS152 4.5 79.3 1.0
NE2 C:HIS89 4.5 38.1 1.0
CB C:ASP171 4.6 42.5 1.0
ND1 C:HIS84 4.8 59.9 1.0
OD2 C:ASP88 4.8 49.1 1.0
ND2 C:ASN170 4.9 48.5 1.0
CA C:GLU86 4.9 46.8 1.0
CG C:ASP88 4.9 44.3 1.0

Iron binding site 2 out of 4 in 6frm

Go back to Iron Binding Sites List in 6frm
Iron binding site 2 out of 4 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


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 Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe505

b:54.6
occ:0.40
TB D:TB504 2.5 63.9 1.0
OD2 D:ASP171 2.6 68.2 1.0
OE2 D:GLU86 2.7 81.9 1.0
CG D:GLU86 2.7 70.2 1.0
CB D:GLU86 3.0 53.5 1.0
CD D:GLU86 3.1 95.5 1.0
CE1 D:HIS84 3.2 63.1 1.0
OD1 D:ASP88 3.3 50.6 1.0
ND1 D:HIS84 3.3 63.5 1.0
CG D:ASP171 3.5 55.0 1.0
CD2 D:HIS89 3.7 45.5 1.0
OD1 D:ASP171 3.7 55.1 1.0
NE2 D:HIS89 3.8 44.7 1.0
OD2 D:ASP88 4.0 52.2 1.0
CG D:ASP88 4.1 46.8 1.0
NE2 D:HIS84 4.1 63.8 1.0
O D:HOH1578 4.2 46.0 1.0
CG D:HIS84 4.3 62.0 1.0
OE1 D:GLU86 4.3 0.8 1.0
O D:HOH1637 4.3 72.5 1.0
CA D:GLU86 4.5 52.7 1.0
CD2 D:HIS84 4.7 64.5 1.0
OD1 D:ASN170 4.8 57.1 1.0
CB D:ASP171 4.9 46.8 1.0
CG D:HIS89 4.9 46.0 1.0

Iron binding site 3 out of 4 in 6frm

Go back to Iron Binding Sites List in 6frm
Iron binding site 3 out of 4 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


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 Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe505

b:52.3
occ:0.50
OE1 G:GLU86 2.2 74.1 1.0
OD2 G:ASP171 2.3 54.4 1.0
NE2 G:HIS84 2.5 52.6 1.0
TB G:TB503 2.6 60.6 1.0
NE2 G:HIS152 2.9 89.7 1.0
CD2 G:HIS84 2.9 52.4 1.0
CD G:GLU86 3.1 83.2 1.0
CG G:GLU86 3.3 59.5 1.0
CB G:GLU86 3.3 45.8 1.0
CG G:ASP171 3.4 47.6 1.0
OD1 G:ASP88 3.6 46.2 1.0
CE1 G:HIS84 3.8 53.0 1.0
OD1 G:ASP171 3.8 48.5 1.0
CE1 G:HIS152 3.8 89.3 1.0
CD2 G:HIS89 3.9 44.0 1.0
CD2 G:HIS152 3.9 90.4 1.0
NE2 G:HIS89 4.0 43.2 1.0
CG G:HIS84 4.2 50.5 1.0
OE2 G:GLU86 4.2 83.8 1.0
O G:HOH740 4.3 46.3 1.0
OD2 G:ASP88 4.4 44.9 1.0
CG G:ASP88 4.4 43.8 1.0
ND1 G:HIS84 4.6 53.4 1.0
CB G:ASP171 4.7 39.6 1.0
OD1 G:ASN170 4.7 51.6 1.0
CA G:GLU86 4.8 44.7 1.0

Iron binding site 4 out of 4 in 6frm

Go back to Iron Binding Sites List in 6frm
Iron binding site 4 out of 4 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


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 Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe504

b:46.2
occ:0.50
OE2 H:GLU86 2.0 56.0 1.0
NE2 H:HIS152 2.2 76.9 1.0
OD2 H:ASP171 2.3 42.5 1.0
NE2 H:HIS84 2.6 52.9 1.0
CD2 H:HIS84 3.0 52.9 1.0
CD H:GLU86 3.1 77.5 1.0
TB H:TB503 3.1 57.1 1.0
CE1 H:HIS152 3.2 76.6 1.0
CD2 H:HIS152 3.2 77.3 1.0
CG H:ASP171 3.5 40.2 1.0
CB H:GLU86 3.5 41.6 1.0
CG H:GLU86 3.8 55.0 1.0
CE1 H:HIS84 3.9 52.9 1.0
OE1 H:GLU86 4.0 74.7 1.0
OD1 H:ASP171 4.0 40.7 1.0
OD1 H:ASP88 4.2 38.2 1.0
CG H:HIS84 4.3 50.7 1.0
ND1 H:HIS152 4.3 77.7 1.0
CG H:HIS152 4.4 76.2 1.0
O H:HOH769 4.4 38.2 1.0
CD2 H:HIS89 4.5 35.4 1.0
NE2 H:HIS89 4.6 35.2 1.0
CB H:ASP171 4.6 35.8 1.0
ND1 H:HIS84 4.8 53.3 1.0
OD2 H:ASP88 4.9 45.2 1.0
OD1 H:ASN170 4.9 45.3 1.0
NE1 H:TRP153 4.9 71.9 1.0
CE2 H:TRP153 4.9 73.3 1.0
CG H:ASP88 5.0 37.8 1.0
CA H:GLU86 5.0 40.2 1.0

Reference:

S.Engilberge, F.Riobe, T.Wagner, S.Di Pietro, C.Breyton, B.Franzetti, S.Shima, E.Girard, E.Dumont, O.Maury. Unveiling the Binding Modes of the Crystallophore, A Terbium-Based Nucleating and Phasing Molecular Agent For Protein Crystallography. Chemistry V. 24 9739 2018.
ISSN: ISSN 1521-3765
PubMed: 29806881
DOI: 10.1002/CHEM.201802172
Page generated: Sun Dec 13 16:26:27 2020

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