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Iron in PDB 7rwy: Crystal Structure of A Fe-Bound RIDC1 Variant in the Presence of Reductant

Protein crystallography data

The structure of Crystal Structure of A Fe-Bound RIDC1 Variant in the Presence of Reductant, PDB code: 7rwy was solved by A.Kakkis, E.Golub, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.65 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.55, 82.68, 74.14, 90, 95.22, 90
R / Rfree (%) 20.2 / 25.9

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of A Fe-Bound RIDC1 Variant in the Presence of Reductant (pdb code 7rwy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Crystal Structure of A Fe-Bound RIDC1 Variant in the Presence of Reductant, PDB code: 7rwy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 7rwy

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Iron binding site 1 out of 10 in the Crystal Structure of A Fe-Bound RIDC1 Variant in the Presence of Reductant


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 Fe-Bound RIDC1 Variant in the Presence of Reductant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:32.9
occ:1.00
FE A:HEC201 0.0 32.9 1.0
NE2 A:HIS102 1.8 32.6 1.0
ND A:HEC201 2.0 39.4 1.0
NA A:HEC201 2.0 42.2 1.0
NB A:HEC201 2.1 38.7 1.0
NC A:HEC201 2.1 34.3 1.0
SD A:MET7 2.2 30.2 1.0
CE1 A:HIS102 2.7 39.4 1.0
CD2 A:HIS102 2.9 32.6 1.0
C4D A:HEC201 3.0 42.8 1.0
C1A A:HEC201 3.0 46.6 1.0
C4A A:HEC201 3.0 42.0 1.0
C1D A:HEC201 3.1 41.5 1.0
C1B A:HEC201 3.1 41.2 1.0
C4B A:HEC201 3.1 36.9 1.0
C1C A:HEC201 3.1 33.3 1.0
CE A:MET7 3.1 33.2 1.0
C4C A:HEC201 3.2 37.0 1.0
CHA A:HEC201 3.3 38.7 1.0
CG A:MET7 3.4 47.3 1.0
CHB A:HEC201 3.4 34.5 1.0
CHC A:HEC201 3.5 36.1 1.0
CHD A:HEC201 3.5 36.5 1.0
ND1 A:HIS102 3.9 38.3 1.0
CG A:HIS102 4.0 33.5 1.0
CB A:MET7 4.1 42.0 1.0
C2A A:HEC201 4.2 46.3 1.0
C3A A:HEC201 4.2 40.6 1.0
C3D A:HEC201 4.2 44.0 1.0
C2D A:HEC201 4.3 40.4 1.0
C3B A:HEC201 4.3 39.6 1.0
C2B A:HEC201 4.3 37.4 1.0
HHA A:HEC201 4.3 46.4 1.0
C2C A:HEC201 4.3 32.5 1.0
C3C A:HEC201 4.4 32.1 1.0
HHB A:HEC201 4.4 41.2 1.0
HHC A:HEC201 4.5 43.2 1.0
HHD A:HEC201 4.5 43.7 1.0

Iron binding site 2 out of 10 in 7rwy

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Iron binding site 2 out of 10 in the Crystal Structure of A Fe-Bound RIDC1 Variant in the Presence of Reductant


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 Fe-Bound RIDC1 Variant in the Presence of Reductant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:33.2
occ:1.00
FE B:HEC202 0.0 33.2 1.0
NE2 B:HIS102 1.8 28.7 1.0
ND B:HEC202 2.0 39.5 1.0
NC B:HEC202 2.0 38.3 1.0
NA B:HEC202 2.1 46.2 1.0
NB B:HEC202 2.2 34.0 1.0
SD B:MET7 2.3 43.2 1.0
CE1 B:HIS102 2.7 34.7 1.0
CD2 B:HIS102 3.0 33.1 1.0
C4C B:HEC202 3.0 30.7 1.0
C1D B:HEC202 3.0 39.8 1.0
C1C B:HEC202 3.0 35.4 1.0
C4D B:HEC202 3.0 42.1 1.0
C1A B:HEC202 3.1 41.8 1.0
C1B B:HEC202 3.1 44.4 1.0
C4A B:HEC202 3.1 45.6 1.0
C4B B:HEC202 3.2 37.5 1.0
CE B:MET7 3.2 33.5 1.0
CG B:MET7 3.3 43.8 1.0
CHD B:HEC202 3.3 42.2 1.0
CHA B:HEC202 3.4 42.6 1.0
CHC B:HEC202 3.5 39.6 1.0
CHB B:HEC202 3.5 32.9 1.0
ND1 B:HIS102 3.9 28.4 1.0
CB B:MET7 4.0 39.4 1.0
CG B:HIS102 4.0 37.2 1.0
C3C B:HEC202 4.2 35.6 1.0
C2C B:HEC202 4.2 39.7 1.0
C2D B:HEC202 4.2 41.7 1.0
C3D B:HEC202 4.2 46.7 1.0
C2B B:HEC202 4.3 40.2 1.0
HHD B:HEC202 4.3 50.6 1.0
C3B B:HEC202 4.3 36.8 1.0
C2A B:HEC202 4.4 42.8 1.0
C3A B:HEC202 4.4 46.5 1.0
HHA B:HEC202 4.4 51.0 1.0
HHC B:HEC202 4.4 47.4 1.0
HHB B:HEC202 4.5 39.4 1.0
CA B:MET7 4.8 36.8 1.0

Iron binding site 3 out of 10 in 7rwy

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Iron binding site 3 out of 10 in the Crystal Structure of A Fe-Bound RIDC1 Variant in the Presence of Reductant


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 Fe-Bound RIDC1 Variant in the Presence of Reductant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:25.9
occ:1.00
NE2 B:HIS73 2.2 25.0 1.0
NE2 C:HIS59 2.2 34.5 1.0
NE2 F:HIS73 2.2 25.5 1.0
NE2 F:HIS77 2.3 36.5 1.0
NE2 C:HIS63 2.3 26.5 1.0
CE1 C:HIS59 2.9 32.9 1.0
CE1 C:HIS63 3.1 25.9 1.0
CD2 F:HIS73 3.1 28.2 1.0
CD2 B:HIS73 3.2 24.4 1.0
CD2 F:HIS77 3.2 27.6 1.0
CE1 B:HIS73 3.2 25.0 1.0
CE1 F:HIS77 3.3 36.5 1.0
CE1 F:HIS73 3.3 32.4 1.0
CD2 C:HIS59 3.4 35.1 1.0
CD2 C:HIS63 3.5 30.2 1.0
O B:HOH326 3.8 31.7 1.0
ND1 C:HIS59 4.1 36.1 1.0
ND1 C:HIS63 4.3 28.7 1.0
ND1 B:HIS73 4.3 24.8 1.0
CG F:HIS73 4.3 23.4 1.0
CG B:HIS73 4.3 27.4 1.0
ND1 F:HIS73 4.3 30.0 1.0
ND1 F:HIS77 4.3 36.8 1.0
CG F:HIS77 4.3 41.5 1.0
H241 B:1PE201 4.4 40.9 1.0
CG C:HIS59 4.4 37.1 1.0
CG C:HIS63 4.5 31.9 1.0
ND1 B:HIS77 4.8 30.1 1.0
H132 B:1PE201 4.9 31.9 1.0

Iron binding site 4 out of 10 in 7rwy

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Iron binding site 4 out of 10 in the Crystal Structure of A Fe-Bound RIDC1 Variant in the Presence of Reductant


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 Fe-Bound RIDC1 Variant in the Presence of Reductant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:32.7
occ:1.00
O C:HOH315 1.9 39.7 1.0
NE2 B:HIS59 1.9 30.4 1.0
NE2 C:HIS77 2.1 27.2 1.0
NE2 C:HIS73 2.5 19.7 1.0
O F:HOH306 2.5 25.4 1.0
CE1 B:HIS59 2.6 28.5 1.0
CE1 C:HIS77 2.8 27.8 1.0
CD2 B:HIS59 3.1 28.6 1.0
CD2 C:HIS73 3.2 19.7 1.0
CD2 C:HIS77 3.4 25.5 1.0
CE1 C:HIS73 3.6 25.8 1.0
ND1 B:HIS59 3.8 35.0 1.0
O B:HOH308 4.0 40.9 1.0
ND1 C:HIS77 4.0 25.9 1.0
CG B:HIS59 4.1 36.5 1.0
CG C:HIS77 4.3 27.1 1.0
CG C:HIS73 4.4 21.8 1.0
ND1 C:HIS73 4.6 20.1 1.0
OD1 F:ASP60 4.6 26.6 1.0
CG F:HIS63 4.7 20.3 1.0
ND1 F:HIS63 4.8 25.1 1.0
CD2 F:HIS63 4.9 18.0 1.0
CE1 F:HIS63 5.0 18.4 1.0

Iron binding site 5 out of 10 in 7rwy

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Iron binding site 5 out of 10 in the Crystal Structure of A Fe-Bound RIDC1 Variant in the Presence of Reductant


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 A Fe-Bound RIDC1 Variant in the Presence of Reductant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe203

b:24.1
occ:1.00
FE C:HEC203 0.0 24.1 1.0
NE2 C:HIS102 1.9 22.1 1.0
ND C:HEC203 2.0 35.5 1.0
NC C:HEC203 2.1 28.5 1.0
SD C:MET7 2.1 21.4 1.0
NA C:HEC203 2.1 33.5 1.0
NB C:HEC203 2.1 34.0 1.0
CE1 C:HIS102 2.9 29.1 1.0
CD2 C:HIS102 2.9 27.3 1.0
C1D C:HEC203 3.0 41.0 1.0
C4D C:HEC203 3.0 36.2 1.0
C1C C:HEC203 3.1 27.0 1.0
C4C C:HEC203 3.1 35.0 1.0
C1A C:HEC203 3.1 30.3 1.0
C4A C:HEC203 3.1 31.1 1.0
C1B C:HEC203 3.1 36.0 1.0
C4B C:HEC203 3.1 38.0 1.0
CE C:MET7 3.3 31.9 1.0
CG C:MET7 3.4 34.4 1.0
CHD C:HEC203 3.4 33.0 1.0
CHA C:HEC203 3.4 31.6 1.0
CHC C:HEC203 3.5 27.0 1.0
CHB C:HEC203 3.5 28.9 1.0
ND1 C:HIS102 4.0 26.9 1.0
CG C:HIS102 4.0 27.6 1.0
CB C:MET7 4.2 24.8 1.0
C2D C:HEC203 4.2 36.0 1.0
C3D C:HEC203 4.3 39.6 1.0
C2C C:HEC203 4.3 39.2 1.0
C3C C:HEC203 4.3 34.4 1.0
C2A C:HEC203 4.3 35.7 1.0
C3A C:HEC203 4.3 29.5 1.0
C2B C:HEC203 4.4 22.5 1.0
C3B C:HEC203 4.4 29.3 1.0
HHD C:HEC203 4.4 39.5 1.0
HHA C:HEC203 4.4 37.9 1.0
HHC C:HEC203 4.4 32.4 1.0
HHB C:HEC203 4.5 34.6 1.0
NH2 C:ARG106 4.9 34.9 1.0

Iron binding site 6 out of 10 in 7rwy

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Iron binding site 6 out of 10 in the Crystal Structure of A Fe-Bound RIDC1 Variant in the Presence of Reductant


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 A Fe-Bound RIDC1 Variant in the Presence of Reductant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:27.0
occ:1.00
NE2 E:HIS73 2.0 28.4 1.0
NE2 D:HIS59 2.2 32.2 1.0
NE2 A:HIS73 2.2 37.2 1.0
NE2 D:HIS63 2.3 36.6 1.0
NE2 E:HIS77 2.3 34.7 1.0
CE1 D:HIS63 3.0 32.5 1.0
CE1 E:HIS73 3.0 22.5 1.0
CD2 A:HIS73 3.0 28.9 1.0
CD2 E:HIS73 3.0 29.1 1.0
CE1 D:HIS59 3.1 31.8 1.0
CE1 E:HIS77 3.1 30.9 1.0
CD2 D:HIS59 3.2 34.8 1.0
CE1 A:HIS73 3.3 30.7 1.0
CD2 E:HIS77 3.4 35.2 1.0
CD2 D:HIS63 3.4 29.8 1.0
ND1 E:HIS73 4.1 37.7 1.0
CG E:HIS73 4.2 29.2 1.0
ND1 D:HIS63 4.2 29.9 1.0
ND1 D:HIS59 4.2 35.7 1.0
CG A:HIS73 4.2 32.1 1.0
ND1 E:HIS77 4.3 33.2 1.0
CG D:HIS59 4.3 43.2 1.0
ND1 A:HIS73 4.3 30.8 1.0
H131 D:1PE203 4.4 46.3 1.0
H132 D:1PE203 4.4 46.3 1.0
CG D:HIS63 4.4 33.4 1.0
CG E:HIS77 4.5 35.6 1.0
H221 D:1PE203 4.5 45.6 1.0
C13 D:1PE203 4.9 38.7 1.0

Iron binding site 7 out of 10 in 7rwy

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Iron binding site 7 out of 10 in the Crystal Structure of A Fe-Bound RIDC1 Variant in the Presence of Reductant


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 A Fe-Bound RIDC1 Variant in the Presence of Reductant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:30.8
occ:1.00
O D:HOH311 1.9 34.1 1.0
NE2 A:HIS59 2.1 37.2 1.0
NE2 D:HIS77 2.2 19.4 1.0
NE2 D:HIS73 2.3 21.5 1.0
O E:HOH320 2.4 30.1 1.0
CE1 D:HIS77 2.9 24.3 1.0
CE1 A:HIS59 3.0 38.8 1.0
CD2 A:HIS59 3.1 30.9 1.0
CD2 D:HIS73 3.2 22.7 1.0
CE1 D:HIS73 3.3 29.5 1.0
CD2 D:HIS77 3.3 23.7 1.0
O A:HOH306 3.4 45.3 1.0
O D:HOH330 3.7 41.8 1.0
ND1 A:HIS59 4.1 44.8 1.0
O D:HOH335 4.1 43.8 1.0
ND1 D:HIS77 4.1 22.6 1.0
CG A:HIS59 4.2 37.0 1.0
CG D:HIS77 4.4 22.7 1.0
CG D:HIS73 4.4 25.8 1.0
ND1 D:HIS73 4.4 23.6 1.0
CG E:HIS63 4.6 24.0 1.0
OD1 E:ASP60 4.6 35.3 1.0
CD2 E:HIS63 4.6 18.5 1.0
ND1 E:HIS63 4.9 21.2 1.0
NE2 E:HIS63 4.9 20.1 1.0
CB E:HIS63 5.0 21.4 1.0

Iron binding site 8 out of 10 in 7rwy

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Iron binding site 8 out of 10 in the Crystal Structure of A Fe-Bound RIDC1 Variant in the Presence of Reductant


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 A Fe-Bound RIDC1 Variant in the Presence of Reductant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe204

b:26.3
occ:1.00
FE D:HEC204 0.0 26.3 1.0
ND D:HEC204 2.0 33.8 1.0
NA D:HEC204 2.0 36.4 1.0
NE2 D:HIS102 2.1 20.0 1.0
NB D:HEC204 2.1 28.5 1.0
NC D:HEC204 2.1 31.2 1.0
SD D:MET7 2.3 28.2 1.0
C1A D:HEC204 3.0 35.5 1.0
C4D D:HEC204 3.0 34.6 1.0
C4B D:HEC204 3.0 33.0 1.0
CD2 D:HIS102 3.1 25.8 1.0
C1C D:HEC204 3.1 27.8 1.0
C4A D:HEC204 3.1 33.6 1.0
CE1 D:HIS102 3.1 33.5 1.0
C1D D:HEC204 3.1 33.0 1.0
C1B D:HEC204 3.1 41.1 1.0
C4C D:HEC204 3.2 31.3 1.0
CHA D:HEC204 3.3 29.8 1.0
CE D:MET7 3.3 30.2 1.0
CHC D:HEC204 3.4 28.6 1.0
CG D:MET7 3.5 31.6 1.0
CHB D:HEC204 3.5 29.5 1.0
CHD D:HEC204 3.5 29.1 1.0
CB D:MET7 4.1 29.3 1.0
ND1 D:HIS102 4.2 25.7 1.0
CG D:HIS102 4.2 27.9 1.0
C2A D:HEC204 4.2 43.6 1.0
C3D D:HEC204 4.2 35.7 1.0
C3B D:HEC204 4.2 34.9 1.0
C3A D:HEC204 4.3 40.6 1.0
C2D D:HEC204 4.3 33.8 1.0
C2B D:HEC204 4.3 30.4 1.0
HHA D:HEC204 4.3 35.7 1.0
C2C D:HEC204 4.3 38.4 1.0
HHC D:HEC204 4.4 34.2 1.0
C3C D:HEC204 4.4 35.0 1.0
HHB D:HEC204 4.5 35.3 1.0
HHD D:HEC204 4.5 34.8 1.0

Iron binding site 9 out of 10 in 7rwy

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Iron binding site 9 out of 10 in the Crystal Structure of A Fe-Bound RIDC1 Variant in the Presence of Reductant


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 A Fe-Bound RIDC1 Variant in the Presence of Reductant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:32.3
occ:1.00
FE E:HEC201 0.0 32.3 1.0
NB E:HEC201 2.0 32.9 1.0
NA E:HEC201 2.0 33.5 1.0
NE2 E:HIS102 2.1 31.7 1.0
NC E:HEC201 2.1 28.0 1.0
ND E:HEC201 2.1 29.0 1.0
SD E:MET7 2.5 32.0 1.0
C1A E:HEC201 3.0 36.8 1.0
C4B E:HEC201 3.0 31.5 1.0
C4A E:HEC201 3.0 37.0 1.0
C1B E:HEC201 3.0 33.9 1.0
CD2 E:HIS102 3.0 27.3 1.0
CE1 E:HIS102 3.0 37.1 1.0
C1C E:HEC201 3.1 24.3 1.0
C4D E:HEC201 3.1 33.3 1.0
C4C E:HEC201 3.1 21.5 1.0
C1D E:HEC201 3.2 33.9 1.0
CHB E:HEC201 3.4 35.7 1.0
CHA E:HEC201 3.4 38.0 1.0
CHC E:HEC201 3.4 28.8 1.0
CE E:MET7 3.5 32.5 1.0
CHD E:HEC201 3.5 29.7 1.0
CG E:MET7 3.6 41.3 1.0
ND1 E:HIS102 4.2 30.6 1.0
CG E:HIS102 4.2 30.5 1.0
C2A E:HEC201 4.2 42.4 1.0
C3A E:HEC201 4.2 37.1 1.0
C3B E:HEC201 4.2 28.2 1.0
C2B E:HEC201 4.2 32.7 1.0
C2C E:HEC201 4.3 25.8 1.0
C3D E:HEC201 4.3 30.8 1.0
C3C E:HEC201 4.3 25.0 1.0
CB E:MET7 4.3 34.0 1.0
HHB E:HEC201 4.4 42.8 1.0
C2D E:HEC201 4.4 28.7 1.0
HHA E:HEC201 4.4 45.5 1.0
HHC E:HEC201 4.4 34.4 1.0
HHD E:HEC201 4.5 35.6 1.0

Iron binding site 10 out of 10 in 7rwy

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Iron binding site 10 out of 10 in the Crystal Structure of A Fe-Bound RIDC1 Variant in the Presence of Reductant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of A Fe-Bound RIDC1 Variant in the Presence of Reductant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:34.2
occ:1.00
FE F:HEC201 0.0 34.2 1.0
NE2 F:HIS102 2.0 38.6 1.0
NC F:HEC201 2.0 34.7 1.0
NB F:HEC201 2.0 37.4 1.0
ND F:HEC201 2.1 38.6 1.0
NA F:HEC201 2.1 46.2 1.0
SD F:MET7 2.6 43.2 1.0
CE1 F:HIS102 2.8 39.5 1.0
C1C F:HEC201 3.0 37.7 1.0
C4B F:HEC201 3.0 40.8 1.0
C4C F:HEC201 3.1 36.8 1.0
C4D F:HEC201 3.1 46.2 1.0
CD2 F:HIS102 3.1 37.2 1.0
C1B F:HEC201 3.1 42.3 1.0
C1A F:HEC201 3.1 50.7 1.0
C1D F:HEC201 3.1 48.0 1.0
C4A F:HEC201 3.1 50.5 1.0
CE F:MET7 3.4 41.1 1.0
CHC F:HEC201 3.4 38.4 1.0
CG F:MET7 3.4 53.4 1.0
CHD F:HEC201 3.4 44.2 1.0
CHB F:HEC201 3.4 42.8 1.0
CHA F:HEC201 3.5 47.1 1.0
ND1 F:HIS102 4.0 38.1 1.0
CG F:HIS102 4.1 40.1 1.0
C2C F:HEC201 4.2 41.2 1.0
C3C F:HEC201 4.3 34.2 1.0
CB F:MET7 4.3 46.3 1.0
C3B F:HEC201 4.3 40.7 1.0
C2B F:HEC201 4.3 40.2 1.0
C3D F:HEC201 4.3 51.4 1.0
C2A F:HEC201 4.3 53.6 1.0
C3A F:HEC201 4.3 55.8 1.0
C2D F:HEC201 4.3 43.5 1.0
HHC F:HEC201 4.4 46.0 1.0
HHD F:HEC201 4.4 52.9 1.0
HHB F:HEC201 4.4 51.3 1.0
HHA F:HEC201 4.4 56.5 1.0

Reference:

A.Kakkis, E.Golub. Crystal Structure of Fe-Bound RIDC1 Variant in the Presence of Reductant To Be Published.
Page generated: Fri Aug 9 00:15:11 2024

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