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Iron in PDB 9j9v: Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe)

Enzymatic activity of Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe)

All present enzymatic activity of Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe):
5.1.3.13;

Protein crystallography data

The structure of Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe), PDB code: 9j9v was solved by W.J.Jeong, W.J.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.27 / 2.04
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 52.012, 63.999, 73.218, 90.01, 90.04, 113.85
R / Rfree (%) 23.9 / 26.7

Iron Binding Sites:

The binding sites of Iron atom in the Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe) (pdb code 9j9v). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe), PDB code: 9j9v:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 9j9v

Go back to Iron Binding Sites List in 9j9v
Iron binding site 1 out of 8 in the Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:39.0
occ:1.00
 OD1 A:ASP78 1.9 31.0 1.0
NE2 A:HIS132 2.2 46.0 1.0
O A:HOH320 2.2 40.0 1.0
CG A:ASP78 2.7 32.1 1.0
OD2 A:ASP78 3.0 39.5 1.0
CD2 A:HIS132 3.1 43.3 1.0
CB A:HIS130 3.2 32.2 1.0
CE1 A:HIS132 3.3 53.4 1.0
ND1 A:HIS130 3.7 50.3 1.0
CG A:HIS130 3.9 40.1 1.0
CB A:ASP78 4.1 35.4 1.0
CG A:HIS132 4.3 40.6 1.0
ND1 A:HIS132 4.3 51.4 1.0
O A:HIS130 4.4 27.1 1.0
CA A:HIS130 4.4 29.1 1.0
C A:ASP78 4.5 27.2 1.0
C A:HIS130 4.5 26.1 1.0
CA A:ASP78 4.6 29.8 1.0
O A:ASP78 4.6 31.9 1.0
N A:ASP78 4.7 25.8 1.0
N A:ARG79 4.9 22.0 1.0
CE1 A:HIS130 5.0 46.0 1.0

Iron binding site 2 out of 8 in 9j9v

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Iron binding site 2 out of 8 in the Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:48.1
occ:1.00
 O A:HOH355 2.1 33.6 1.0
NE2 A:HIS64 2.2 48.5 1.0
OD2 A:ASP172 2.2 31.6 1.0
OD1 A:ASP172 2.2 29.6 1.0
CG A:ASP172 2.4 30.1 1.0
CE1 A:HIS64 2.5 46.6 1.0
O A:HOH349 2.7 36.4 1.0
CD2 A:HIS64 3.5 41.9 1.0
ND1 A:HIS64 3.8 48.2 1.0
CB A:ASP172 3.9 30.4 1.0
N A:GLY62 4.0 26.4 1.0
OG A:SER169 4.0 35.0 1.0
O A:HOH378 4.0 38.9 1.0
CG A:HIS64 4.3 39.3 1.0
O A:HOH340 4.4 23.9 1.0
O A:GLY62 4.4 26.7 1.0
CA A:GLY62 4.6 26.1 1.0
CA A:ASP172 4.7 33.6 1.0
N A:ASP172 4.8 30.6 1.0
CA A:ARG61 4.8 21.8 1.0
C A:ARG61 4.9 23.6 1.0
C A:GLY62 4.9 28.0 1.0
NE1 A:TRP175 4.9 23.8 1.0
CB A:ARG61 5.0 20.9 1.0

Iron binding site 3 out of 8 in 9j9v

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Iron binding site 3 out of 8 in the Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:39.6
occ:1.00
 OD1 B:ASP78 2.0 36.3 1.0
NE2 B:HIS132 2.3 50.1 1.0
O B:HOH333 2.4 38.2 1.0
CG B:ASP78 2.8 35.5 1.0
CD2 B:HIS132 3.1 46.1 1.0
OD2 B:ASP78 3.1 44.2 1.0
CB B:HIS130 3.2 31.9 1.0
CE1 B:HIS132 3.4 56.8 1.0
ND1 B:HIS130 3.8 44.6 1.0
CG B:HIS130 3.8 39.0 1.0
NH2 B:ARG79 4.1 37.7 1.0
CB B:ASP78 4.2 36.2 1.0
CG B:HIS132 4.3 40.9 1.0
CA B:HIS130 4.4 28.3 1.0
ND1 B:HIS132 4.4 53.9 1.0
O B:HIS130 4.4 32.1 1.0
C B:HIS130 4.5 28.9 1.0
C B:ASP78 4.6 25.4 1.0
O B:ASP78 4.6 34.3 1.0
CA B:ASP78 4.6 30.4 1.0
N B:ASP78 4.8 23.8 1.0
CZ B:ARG79 4.9 49.6 1.0
N B:ARG79 4.9 25.5 1.0
CE1 B:HIS130 5.0 46.0 1.0

Iron binding site 4 out of 8 in 9j9v

Go back to Iron Binding Sites List in 9j9v
Iron binding site 4 out of 8 in the Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:39.8
occ:1.00
 NE2 B:HIS64 2.2 39.0 1.0
O B:HOH357 2.3 35.5 1.0
OD2 B:ASP172 2.3 23.6 1.0
OD1 B:ASP172 2.4 27.8 1.0
CE1 B:HIS64 2.6 48.3 1.0
CG B:ASP172 2.6 27.4 1.0
O B:HOH350 2.7 30.2 1.0
CD2 B:HIS64 3.5 32.4 1.0
ND1 B:HIS64 3.9 44.0 1.0
OG B:SER169 4.1 27.7 1.0
N B:GLY62 4.1 22.0 1.0
CB B:ASP172 4.1 27.6 1.0
O B:HOH328 4.3 26.2 1.0
CG B:HIS64 4.3 29.9 1.0
O B:GLY62 4.7 26.7 1.0
CA B:GLY62 4.8 21.4 1.0
CA B:ARG61 4.8 20.8 1.0
CB B:ARG61 4.8 20.6 1.0
C B:ARG61 4.9 22.5 1.0
CA B:ASP172 4.9 29.6 1.0
N B:ASP172 5.0 25.0 1.0

Iron binding site 5 out of 8 in 9j9v

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Iron binding site 5 out of 8 in the Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:45.4
occ:1.00
 OD1 C:ASP78 1.9 35.9 1.0
NE2 C:HIS132 2.2 51.5 1.0
CG C:ASP78 2.8 37.9 1.0
CD2 C:HIS132 3.1 44.3 1.0
OD2 C:ASP78 3.2 39.8 1.0
CE1 C:HIS132 3.3 56.4 1.0
CB C:HIS130 3.3 32.2 1.0
O C:HOH349 3.8 51.8 1.0
ND1 C:HIS130 3.8 49.4 1.0
CG C:HIS130 4.0 41.2 1.0
FE C:FE202 4.1 42.6 1.0
CB C:ASP78 4.2 37.7 1.0
CG C:HIS132 4.3 40.5 1.0
ND1 C:HIS132 4.4 50.8 1.0
C C:ASP78 4.5 30.6 1.0
O C:HIS130 4.6 28.9 1.0
CA C:HIS130 4.6 29.1 1.0
CA C:ASP78 4.6 32.9 1.0
C C:HIS130 4.6 25.8 1.0
O C:ASP78 4.6 33.6 1.0
N C:ASP78 4.8 30.1 1.0
N C:ARG79 4.9 25.8 1.0
CE1 C:HIS130 5.0 45.0 1.0

Iron binding site 6 out of 8 in 9j9v

Go back to Iron Binding Sites List in 9j9v
Iron binding site 6 out of 8 in the Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:42.6
occ:1.00
 OD2 C:ASP78 2.6 39.8 1.0
CG C:ASP78 3.6 37.9 1.0
FE C:FE201 4.1 45.4 1.0
OD1 C:ASP78 4.1 35.9 1.0
CB C:ASP78 4.7 37.7 1.0

Iron binding site 7 out of 8 in 9j9v

Go back to Iron Binding Sites List in 9j9v
Iron binding site 7 out of 8 in the Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe203

b:48.3
occ:1.00
 OD2 C:ASP172 2.1 29.9 1.0
NE2 C:HIS64 2.2 51.4 1.0
OD1 C:ASP172 2.3 36.9 1.0
CG C:ASP172 2.4 34.1 1.0
CE1 C:HIS64 2.5 53.1 1.0
O C:HOH337 2.8 37.5 1.0
CD2 C:HIS64 3.5 47.9 1.0
ND1 C:HIS64 3.8 52.3 1.0
N C:GLY62 3.9 32.9 1.0
CB C:ASP172 3.9 32.7 1.0
OG C:SER169 4.0 32.5 1.0
CG C:HIS64 4.3 43.4 1.0
O C:GLY62 4.4 30.6 1.0
CA C:GLY62 4.6 29.6 1.0
CA C:ARG61 4.7 25.4 1.0
CA C:ASP172 4.7 36.5 1.0
C C:ARG61 4.8 29.9 1.0
N C:ASP172 4.8 33.1 1.0
CB C:ARG61 4.9 22.9 1.0
C C:GLY62 4.9 32.2 1.0
NE1 C:TRP175 5.0 29.8 1.0

Iron binding site 8 out of 8 in 9j9v

Go back to Iron Binding Sites List in 9j9v
Iron binding site 8 out of 8 in the Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Artificial Dinuclear Fe-Bound Metalloprotein 2 (D2:Fe) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:41.8
occ:1.00
 NE2 D:HIS64 2.2 36.0 1.0
OD2 D:ASP172 2.3 26.9 1.0
O D:HOH360 2.4 39.0 1.0
OD1 D:ASP172 2.4 29.7 1.0
CE1 D:HIS64 2.6 46.3 1.0
CG D:ASP172 2.6 30.8 1.0
O D:HOH346 2.8 34.2 1.0
CD2 D:HIS64 3.5 31.1 1.0
ND1 D:HIS64 3.9 42.0 1.0
OG D:SER169 4.0 26.5 1.0
N D:GLY62 4.1 22.2 1.0
CB D:ASP172 4.1 28.0 1.0
CG D:HIS64 4.3 31.0 1.0
O D:HOH339 4.4 27.7 1.0
O D:GLY62 4.6 30.6 1.0
CA D:GLY62 4.8 22.6 1.0
CA D:ARG61 4.8 22.4 1.0
CB D:ARG61 4.8 20.1 1.0
CA D:ASP172 4.9 33.3 1.0
C D:ARG61 4.9 22.4 1.0
N D:ASP172 4.9 26.6 1.0

Reference:

W.J.Jeong, W.J.Song. Metal-Installer: A Protein Designer Tool to Create Metal-Binding Sites To Be Published.
Page generated: Fri Aug 8 06:55:45 2025

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