Iron in PDB 7cnv: Crystal Structure of Iscu H106C Variant

The structure of Crystal Structure of Iscu H106C Variant, PDB code: 7cnv was solved by K.Kunichika, Y.Takahashi, T.Fujishiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.51 / 2.23
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.82, 104.08, 65.28, 90, 106.12, 90
R / Rfree (%)	21 / 23.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Iscu H106C Variant (pdb code 7cnv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 22 binding sites of Iron where determined in the Crystal Structure of Iscu H106C Variant, PDB code: 7cnv:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 22 in the Crystal Structure of Iscu H106C Variant


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 Iscu H106C Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:41.3 occ:1.00 FE1 A:FES201 0.0 41.3 1.0 OD2 A:ASP40 2.0 50.7 1.0 S1 A:FES201 2.2 40.5 1.0 S2 A:FES201 2.2 38.9 1.0 SG A:CYS38 2.4 51.4 1.0 FE2 A:FES201 2.7 40.6 1.0 CG A:ASP40 3.0 47.4 1.0 CB A:CYS38 3.3 48.2 1.0 CB A:ASP40 3.3 46.6 1.0 ND2 A:ASN35 4.1 45.8 1.0 OD1 A:ASP40 4.2 47.4 1.0 N A:CYS63 4.3 43.4 1.0 CA A:GLY62 4.3 43.0 1.0 SG A:CYS107 4.4 51.2 1.0 N A:ASP40 4.5 46.2 1.0 S2 B:FES201 4.5 38.7 1.0 CA A:ASP40 4.5 46.5 1.0 SG A:CYS63 4.6 47.6 1.0 CB A:CYS63 4.6 44.2 1.0 CG A:ASN35 4.7 46.2 1.0 CA A:CYS38 4.7 48.7 1.0 CB A:ASN35 4.8 46.2 1.0 C A:GLY62 4.8 43.2 1.0 NZ B:LYS104 4.8 49.6 1.0

Iron binding site 2 out of 22 in the Crystal Structure of Iscu H106C Variant


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 Iscu H106C Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:40.6 occ:1.00 FE2 A:FES201 0.0 40.6 1.0 S2 A:FES201 2.1 38.9 1.0 S1 A:FES201 2.2 40.5 1.0 SG A:CYS107 2.2 51.2 1.0 SG A:CYS63 2.4 47.6 1.0 FE1 A:FES201 2.7 41.3 1.0 CB A:CYS107 3.1 51.0 1.0 CB A:CYS63 3.3 44.2 1.0 N A:CYS63 3.9 43.4 1.0 NZ A:LYS104 4.0 46.1 1.0 ND2 A:ASN35 4.1 45.8 1.0 CA A:CYS107 4.2 52.2 1.0 CA A:CYS63 4.2 43.9 1.0 CB A:ALA66 4.4 43.2 1.0 SG A:CYS38 4.4 51.4 1.0 OD2 A:ASP40 4.4 50.7 1.0 O A:HOH304 4.6 44.7 1.0 CD A:LYS104 4.6 47.7 1.0 O A:HOH307 4.8 43.4 1.0 N A:CYS107 4.9 54.1 1.0 N A:ALA66 4.9 43.7 1.0 C A:GLY62 5.0 43.2 1.0 CE A:LYS104 5.0 46.7 1.0

Iron binding site 3 out of 22 in the Crystal Structure of Iscu H106C Variant


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 Iscu H106C Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:69.3 occ:1.00 SG A:CYS106 2.3 99.6 0.5 SG A:CYS106 2.3 65.8 0.5 CB A:CYS106 3.3 59.5 0.5 O A:CYS106 3.4 56.8 0.5 O A:CYS106 3.4 54.6 0.5 CA A:CYS106 3.5 57.8 0.5 CB A:CYS106 3.5 69.4 0.5 CA A:CYS106 3.6 62.5 0.5 CB A:ASN109 3.8 52.7 1.0 C A:CYS106 3.9 55.5 0.5 C A:CYS106 3.9 58.1 0.5 FE A:FE2203 4.2 96.0 1.0 ND2 A:ASN109 4.3 57.3 1.0 CD A:PRO36 4.4 49.0 1.0 OD2 A:ASP113 4.6 51.7 1.0 CG A:ASN109 4.6 55.0 1.0 O A:GLY34 4.9 47.6 1.0 CD2 A:LEU110 4.9 46.2 1.0 N A:CYS106 4.9 58.1 0.5 N A:CYS106 4.9 61.0 0.5 CA A:ASN109 4.9 51.4 1.0

Iron binding site 4 out of 22 in the Crystal Structure of Iscu H106C Variant


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 Iscu H106C Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:96.0 occ:1.00 SG A:CYS106 2.3 99.6 0.5 CB A:CYS106 3.3 69.4 0.5 CB A:CYS106 3.3 59.5 0.5 SG A:CYS106 3.9 65.8 0.5 FE A:FE2202 4.2 69.3 1.0 CA A:CYS106 4.2 62.5 0.5 CA A:CYS106 4.2 57.8 0.5 CG A:PRO36 4.3 50.1 1.0 CD A:PRO36 4.7 49.0 1.0 N A:CYS106 4.8 58.1 0.5 N A:CYS106 4.8 61.0 0.5 CG2 A:VAL37 5.0 49.1 1.0

Iron binding site 5 out of 22 in the Crystal Structure of Iscu H106C Variant


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 Iscu H106C Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:40.3 occ:1.00 FE1 B:FES201 0.0 40.3 1.0 S2 B:FES201 2.1 38.7 1.0 S1 B:FES201 2.2 40.0 1.0 SG B:CYS63 2.3 52.8 1.0 SG B:CYS107 2.3 55.7 1.0 FE2 B:FES201 2.6 42.6 1.0 CB B:CYS107 3.2 55.4 1.0 CB B:CYS63 3.3 49.5 1.0 NZ B:LYS104 3.8 49.6 1.0 N B:CYS63 3.8 48.1 1.0 ND2 B:ASN35 4.1 50.5 1.0 CA B:CYS63 4.2 48.3 1.0 CA B:CYS107 4.3 55.7 1.0 OD2 B:ASP40 4.4 55.8 1.0 SG B:CYS38 4.4 55.0 1.0 CB B:ALA66 4.4 51.4 1.0 CD B:LYS104 4.6 51.2 1.0 O A:HOH301 4.8 39.0 1.0 CE B:LYS104 4.8 50.5 1.0 N B:ALA66 4.9 51.7 1.0 C B:GLY62 4.9 48.4 1.0 N B:CYS107 5.0 56.2 1.0

Iron binding site 6 out of 22 in the Crystal Structure of Iscu H106C Variant


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 Iscu H106C Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:42.6 occ:1.00 FE2 B:FES201 0.0 42.6 1.0 OD2 B:ASP40 2.0 55.8 1.0 S2 B:FES201 2.2 38.7 1.0 S1 B:FES201 2.2 40.0 1.0 SG B:CYS38 2.3 55.0 1.0 FE1 B:FES201 2.6 40.3 1.0 CG B:ASP40 3.0 51.2 1.0 CB B:CYS38 3.3 51.4 1.0 CB B:ASP40 3.4 50.4 1.0 ND2 B:ASN35 4.0 50.5 1.0 OD1 B:ASP40 4.1 50.0 1.0 N B:CYS63 4.3 48.1 1.0 CA B:GLY62 4.3 48.6 1.0 SG B:CYS107 4.4 55.7 1.0 SG B:CYS63 4.5 52.8 1.0 N B:ASP40 4.6 49.3 1.0 CA B:ASP40 4.6 50.0 1.0 S2 A:FES201 4.6 38.9 1.0 CB B:CYS63 4.6 49.5 1.0 CG B:ASN35 4.7 51.6 1.0 CA B:CYS38 4.8 50.9 1.0 CB B:ASN35 4.8 51.8 1.0 C B:GLY62 4.8 48.4 1.0 NZ A:LYS104 4.9 46.1 1.0

Iron binding site 7 out of 22 in the Crystal Structure of Iscu H106C Variant


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 Iscu H106C Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:67.5 occ:1.00 SG B:CYS106 2.2 71.9 1.0 CB B:CYS106 3.2 63.7 1.0 CG B:PRO36 3.7 58.0 1.0 CA B:CYS106 3.9 60.8 1.0 CD B:PRO36 4.3 56.0 1.0 N B:CYS106 4.7 61.5 1.0

Iron binding site 8 out of 22 in the Crystal Structure of Iscu H106C Variant


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 Iscu H106C Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:45.4 occ:1.00 FE1 C:FES201 0.0 45.4 1.0 S2 C:FES201 2.2 42.9 1.0 S1 C:FES201 2.2 47.6 1.0 SG C:CYS107 2.2 71.5 1.0 SG C:CYS63 2.4 54.5 1.0 FE2 C:FES201 2.7 47.7 1.0 CB C:CYS107 3.2 72.4 1.0 CB C:CYS63 3.4 51.0 1.0 N C:CYS63 3.9 54.7 1.0 NZ C:LYS104 3.9 63.5 1.0 ND2 C:ASN35 4.0 58.8 1.0 CA C:CYS107 4.2 75.3 1.0 CA C:CYS63 4.2 52.6 1.0 O C:HOH302 4.3 61.4 1.0 SG C:CYS38 4.4 59.0 1.0 CB C:ALA66 4.4 52.7 1.0 OD2 C:ASP40 4.4 57.3 1.0 CD C:LYS104 4.6 66.9 1.0 CE C:LYS104 4.9 65.7 1.0 O C:HOH307 4.9 53.1 1.0 N C:CYS107 4.9 76.8 1.0 C C:GLY62 4.9 54.2 1.0 N C:ALA66 4.9 53.5 1.0

Iron binding site 9 out of 22 in the Crystal Structure of Iscu H106C Variant


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 Iscu H106C Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:47.7 occ:1.00 FE2 C:FES201 0.0 47.7 1.0 OD2 C:ASP40 2.0 57.3 1.0 S2 C:FES201 2.2 42.9 1.0 S1 C:FES201 2.2 47.6 1.0 SG C:CYS38 2.4 59.0 1.0 FE1 C:FES201 2.7 45.4 1.0 CG C:ASP40 3.0 54.2 1.0 CB C:CYS38 3.3 54.9 1.0 CB C:ASP40 3.4 55.1 1.0 ND2 C:ASN35 4.1 58.8 1.0 OD1 C:ASP40 4.1 53.2 1.0 N C:CYS63 4.3 54.7 1.0 CA C:GLY62 4.3 52.3 1.0 SG C:CYS107 4.4 71.5 1.0 S1 D:FES201 4.5 46.2 1.0 N C:ASP40 4.5 53.1 1.0 SG C:CYS63 4.5 54.5 1.0 CA C:ASP40 4.6 54.8 1.0 CB C:CYS63 4.6 51.0 1.0 CA C:CYS38 4.7 55.1 1.0 CG C:ASN35 4.7 58.6 1.0 NZ D:LYS104 4.8 47.5 1.0 C C:GLY62 4.8 54.2 1.0 CB C:ASN35 4.8 58.1 1.0

Iron binding site 10 out of 22 in the Crystal Structure of Iscu H106C Variant


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 Iscu H106C Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe202 b:102.8 occ:1.00 SG C:CYS106 2.3 110.8 0.4 SG C:CYS106 3.1 120.4 0.6 O C:CYS106 3.5 81.8 1.0 CB C:ASN109 3.6 75.6 1.0 CA C:CYS106 3.6 85.9 0.4 CB C:CYS106 3.7 91.3 0.4 CA C:CYS106 3.7 86.4 0.6 FE C:FE2203 3.8 90.2 1.0 C C:CYS106 4.0 83.3 1.0 CB C:CYS106 4.0 93.1 0.6 ND2 C:ASN109 4.0 79.7 1.0 CD C:PRO36 4.3 62.6 1.0 CG C:ASN109 4.4 76.9 1.0 OD2 C:ASP113 4.6 84.6 1.0 CA C:ASN109 4.8 78.4 1.0 N C:CYS106 4.9 85.6 1.0 O C:GLY34 4.9 61.3 1.0 C C:ASN109 5.0 77.6 1.0 CG C:PRO36 5.0 62.0 1.0

K.Kunichika, T.Fujishiro, Y.Takahashi. [2FE-2S] Clusters-Assembled Dimeric Structures of Iscu Iron-Sulfur Scaffold To Be Published.