Iron in PDB 7c8m: Crystal Structure of Iscu Wild-Type

The structure of Crystal Structure of Iscu Wild-Type, PDB code: 7c8m 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)	48.79 / 3.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	85.29, 67.14, 47.42, 90, 123.61, 90
R / Rfree (%)	22.1 / 29.2

The binding sites of Iron atom in the Crystal Structure of Iscu Wild-Type (pdb code 7c8m). 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 Iscu Wild-Type, PDB code: 7c8m:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Iscu Wild-Type


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 Wild-Type within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:98.1 occ:1.00 FE1 A:FES201 0.0 98.1 1.0 S1 A:FES201 2.2 111.7 1.0 S2 A:FES201 2.3 90.0 1.0 SG A:CYS107 2.3 118.8 1.0 SG A:CYS63 2.3 103.0 1.0 FE2 A:FES201 3.1 94.7 1.0 CB A:CYS63 3.2 99.7 1.0 CB A:CYS107 3.5 110.7 1.0 NZ A:LYS104 3.6 110.3 1.0 N A:CYS63 4.0 98.6 1.0 CA A:CYS63 4.2 97.7 1.0 SG A:CYS38 4.2 98.8 1.0 CD A:LYS104 4.5 113.7 1.0 CA A:CYS107 4.6 115.8 1.0 CE A:LYS104 4.6 109.4 1.0 ND2 A:ASN35 4.6 126.6 1.0 CB A:ALA66 4.8 125.3 1.0 OD2 A:ASP40 4.8 111.1 1.0 CB A:CYS38 5.0 95.7 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Iscu Wild-Type


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 Wild-Type within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:94.7 occ:1.00 FE2 A:FES201 0.0 94.7 1.0 OD2 A:ASP40 2.0 111.1 1.0 S2 A:FES201 2.2 90.0 1.0 S1 A:FES201 2.2 111.7 1.0 SG A:CYS38 2.3 98.8 1.0 CG A:ASP40 2.8 114.1 1.0 CB A:ASP40 2.9 107.8 1.0 CB A:CYS38 3.0 95.7 1.0 FE1 A:FES201 3.1 98.1 1.0 OD1 A:ASP40 4.0 117.6 1.0 CA A:GLY62 4.0 109.1 1.0 N A:CYS63 4.1 98.6 1.0 CA A:ASP40 4.2 105.8 1.0 N A:ASP40 4.2 99.3 1.0 CA A:CYS38 4.4 102.2 1.0 C A:GLY62 4.5 102.9 1.0 CB A:CYS63 4.6 99.7 1.0 C A:CYS38 4.7 101.4 1.0 SG A:CYS63 4.8 103.0 1.0 SG A:CYS107 4.9 118.8 1.0 ND2 A:ASN35 4.9 126.6 1.0 CB A:ASN35 4.9 118.2 1.0 CA A:CYS63 5.0 97.7 1.0 O A:CYS38 5.0 109.8 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Iscu Wild-Type


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 Wild-Type within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:104.6 occ:1.00 FE1 C:FES201 0.0 104.6 1.0 S1 C:FES201 2.2 117.4 1.0 S2 C:FES201 2.2 94.4 1.0 SG C:CYS63 2.3 108.0 1.0 SG C:CYS107 2.3 109.5 1.0 CB C:CYS63 3.1 109.4 1.0 FE2 C:FES201 3.1 96.8 1.0 NZ C:LYS104 3.4 114.7 1.0 CB C:CYS107 3.5 98.2 1.0 N C:CYS63 4.1 119.2 1.0 CA C:CYS63 4.2 112.3 1.0 SG C:CYS38 4.3 105.4 1.0 CD C:LYS104 4.5 111.8 1.0 CE C:LYS104 4.5 113.4 1.0 CA C:CYS107 4.6 110.6 1.0 ND2 C:ASN35 4.6 142.8 1.0 OD2 C:ASP40 4.9 123.2 1.0 CB C:ALA66 4.9 112.9 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Iscu Wild-Type


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 Wild-Type within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:96.8 occ:1.00 FE2 C:FES201 0.0 96.8 1.0 OD2 C:ASP40 2.0 123.2 1.0 S2 C:FES201 2.2 94.4 1.0 S1 C:FES201 2.2 117.4 1.0 SG C:CYS38 2.3 105.4 1.0 CG C:ASP40 2.8 128.6 1.0 CB C:ASP40 3.0 121.7 1.0 CB C:CYS38 3.1 104.5 1.0 FE1 C:FES201 3.1 104.6 1.0 CA C:GLY62 4.0 121.8 1.0 N C:CYS63 4.0 119.2 1.0 OD1 C:ASP40 4.1 128.3 1.0 CA C:ASP40 4.2 121.5 1.0 N C:ASP40 4.3 115.2 1.0 C C:GLY62 4.4 123.1 1.0 CA C:CYS38 4.5 109.1 1.0 CB C:CYS63 4.5 109.4 1.0 SG C:CYS63 4.7 108.0 1.0 C C:CYS38 4.8 111.6 1.0 SG C:CYS107 4.9 109.5 1.0 ND2 C:ASN35 4.9 142.8 1.0 CA C:CYS63 4.9 112.3 1.0 CB C:ASN35 4.9 128.9 1.0

K.Kunichika, R.Nakamura, T.Fujishiro, Y.Takahashi. The Structure of the Dimeric State of Iscu Harboring Two Adjacent [2FE-2S] Clusters Provides Mechanistic Insights Into Cluster Conversion to [4FE-4S]. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 33938220
DOI: 10.1021/ACS.BIOCHEM.1C00112