Iron in PDB 8cp4: [4FE-4S] Cluster Containing Lare in Complex with Amp

The structure of [4FE-4S] Cluster Containing Lare in Complex with Amp, PDB code: 8cp4 was solved by P.Zecchin, L.Pecqueur, B.Golinelli-Pimpaneau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.87 / 3.19
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	186.17, 212.69, 196.74, 90, 90, 90
R / Rfree (%)	21.6 / 25.3

The structure of [4FE-4S] Cluster Containing Lare in Complex with Amp also contains other interesting chemical elements:

Chlorine

(Cl)

11 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Iron atom in the [4FE-4S] Cluster Containing Lare in Complex with Amp (pdb code 8cp4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the [4FE-4S] Cluster Containing Lare in Complex with Amp, PDB code: 8cp4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in the [4FE-4S] Cluster Containing Lare in Complex with Amp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of [4FE-4S] Cluster Containing Lare in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:100.3 occ:1.00 FE1 A:SF4301 0.0 100.3 1.0 SG A:CYS99 2.1 107.2 1.0 S3 A:SF4301 2.2 116.5 1.0 S4 A:SF4301 2.2 100.3 1.0 S2 A:SF4301 2.2 112.8 1.0 FE3 A:SF4301 2.6 100.3 1.0 FE2 A:SF4301 2.7 100.3 1.0 FE4 A:SF4301 2.7 100.3 1.0 CB A:CYS99 2.9 108.5 1.0 S1 A:SF4301 3.8 100.3 1.0 CD2 A:PHE56 4.4 100.8 1.0 CA A:CYS99 4.4 109.2 1.0 ND2 A:ASN54 4.5 107.5 1.0 SG A:CYS96 4.5 121.6 1.0 CA A:CYS96 4.6 112.8 1.0 CE2 A:PHE56 4.7 97.9 1.0 SG A:CYS174 4.7 105.2 1.0 O A:CYS96 4.7 116.1 1.0 CG A:LYS100 4.7 111.7 1.0 C A:CYS99 4.7 109.7 1.0 N A:LYS100 4.7 114.1 1.0 O2P A:AMP302 4.9 132.1 0.8

Iron binding site 2 out of 28 in the [4FE-4S] Cluster Containing Lare in Complex with Amp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of [4FE-4S] Cluster Containing Lare in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:100.3 occ:1.00 FE2 A:SF4301 0.0 100.3 1.0 S4 A:SF4301 2.2 100.3 1.0 S1 A:SF4301 2.2 100.3 1.0 S3 A:SF4301 2.3 116.5 1.0 O1P A:AMP302 2.5 134.4 0.8 FE3 A:SF4301 2.6 100.3 1.0 FE1 A:SF4301 2.7 100.3 1.0 FE4 A:SF4301 2.7 100.3 1.0 O2P A:AMP302 2.8 132.1 0.8 P A:AMP302 3.2 157.7 0.8 S2 A:SF4301 3.8 112.8 1.0 O4' A:AMP302 4.0 137.7 0.8 O5' A:AMP302 4.2 159.1 0.8 SG A:CYS96 4.3 121.6 1.0 O3P A:AMP302 4.3 152.7 0.8 C4' A:AMP302 4.4 141.6 0.8 CB A:CYS174 4.6 108.3 1.0 C5' A:AMP302 4.6 146.1 0.8 SG A:CYS99 4.6 107.2 1.0 SG A:CYS174 4.7 105.2 1.0 CE A:LYS100 4.9 146.6 1.0

Iron binding site 3 out of 28 in the [4FE-4S] Cluster Containing Lare in Complex with Amp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of [4FE-4S] Cluster Containing Lare in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:100.3 occ:1.00 FE3 A:SF4301 0.0 100.3 1.0 S1 A:SF4301 2.2 100.3 1.0 S4 A:SF4301 2.2 100.3 1.0 SG A:CYS96 2.2 121.6 1.0 S2 A:SF4301 2.3 112.8 1.0 FE2 A:SF4301 2.6 100.3 1.0 FE1 A:SF4301 2.6 100.3 1.0 FE4 A:SF4301 2.7 100.3 1.0 CB A:CYS96 3.6 127.4 1.0 CA A:CYS96 3.7 112.8 1.0 S3 A:SF4301 3.8 116.5 1.0 N A:CYS96 4.5 113.9 1.0 SG A:CYS174 4.5 105.2 1.0 NE A:ARG95 4.6 109.0 1.0 SG A:CYS99 4.6 107.2 1.0 CB A:CYS99 4.6 108.5 1.0 O1P A:AMP302 4.7 134.4 0.8 CG A:ARG95 4.8 110.1 1.0 C A:CYS96 4.9 113.6 1.0 O A:CYS96 5.0 116.1 1.0

Iron binding site 4 out of 28 in the [4FE-4S] Cluster Containing Lare in Complex with Amp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of [4FE-4S] Cluster Containing Lare in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:100.3 occ:1.00 FE4 A:SF4301 0.0 100.3 1.0 SG A:CYS174 2.1 105.2 1.0 S1 A:SF4301 2.2 100.3 1.0 S2 A:SF4301 2.2 112.8 1.0 S3 A:SF4301 2.3 116.5 1.0 FE2 A:SF4301 2.7 100.3 1.0 FE3 A:SF4301 2.7 100.3 1.0 FE1 A:SF4301 2.7 100.3 1.0 CB A:CYS174 2.8 108.3 1.0 S4 A:SF4301 3.9 100.3 1.0 O2P A:AMP302 4.1 132.1 0.8 CD2 A:PHE56 4.2 100.8 1.0 CA A:CYS174 4.2 108.2 1.0 CG2 A:THR177 4.5 96.0 1.0 SG A:CYS99 4.6 107.2 1.0 CB A:PHE56 4.8 101.5 1.0 CG A:PHE56 4.9 102.9 1.0 SG A:CYS96 4.9 121.6 1.0 CE2 A:PHE56 4.9 97.9 1.0 O1P A:AMP302 4.9 134.4 0.8 CZ A:PHE57 5.0 131.6 1.0 CB A:ALA176 5.0 95.9 1.0

Iron binding site 5 out of 28 in the [4FE-4S] Cluster Containing Lare in Complex with Amp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of [4FE-4S] Cluster Containing Lare in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:100.3 occ:1.00 FE1 B:SF4301 0.0 100.3 1.0 S4 B:SF4301 2.2 100.3 1.0 SG B:CYS99 2.2 99.7 1.0 S3 B:SF4301 2.2 103.8 1.0 S2 B:SF4301 2.2 100.3 1.0 FE3 B:SF4301 2.6 100.3 1.0 FE4 B:SF4301 2.7 100.3 1.0 FE2 B:SF4301 2.7 100.3 1.0 CB B:CYS99 3.0 100.3 1.0 S1 B:SF4301 3.8 100.3 1.0 CD2 B:PHE56 4.3 92.1 1.0 SG B:CYS96 4.4 100.7 1.0 CA B:CYS99 4.4 101.1 1.0 CA B:CYS96 4.5 101.3 1.0 SG B:CYS174 4.6 97.6 1.0 O B:CYS96 4.7 102.5 1.0 CE2 B:PHE56 4.7 91.8 1.0 CL B:CL302 4.8 113.8 1.0 N B:LYS100 4.9 102.6 1.0 C B:CYS99 4.9 101.9 1.0 CE B:LYS100 4.9 120.0 1.0 CB B:CYS96 5.0 101.7 1.0

Iron binding site 6 out of 28 in the [4FE-4S] Cluster Containing Lare in Complex with Amp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of [4FE-4S] Cluster Containing Lare in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:100.3 occ:1.00 FE2 B:SF4301 0.0 100.3 1.0 S4 B:SF4301 2.2 100.3 1.0 S1 B:SF4301 2.2 100.3 1.0 CL B:CL302 2.2 113.8 1.0 S3 B:SF4301 2.3 103.8 1.0 FE3 B:SF4301 2.6 100.3 1.0 FE4 B:SF4301 2.7 100.3 1.0 FE1 B:SF4301 2.7 100.3 1.0 S2 B:SF4301 3.8 100.3 1.0 CE B:LYS100 4.1 120.0 1.0 CB B:CYS174 4.4 100.4 1.0 NZ B:LYS100 4.5 103.6 1.0 SG B:CYS96 4.5 100.7 1.0 SG B:CYS99 4.6 99.7 1.0 SG B:CYS174 4.7 97.6 1.0

Iron binding site 7 out of 28 in the [4FE-4S] Cluster Containing Lare in Complex with Amp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of [4FE-4S] Cluster Containing Lare in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:100.3 occ:1.00 FE3 B:SF4301 0.0 100.3 1.0 SG B:CYS96 2.1 100.7 1.0 S1 B:SF4301 2.2 100.3 1.0 S4 B:SF4301 2.2 100.3 1.0 S2 B:SF4301 2.2 100.3 1.0 FE2 B:SF4301 2.6 100.3 1.0 FE4 B:SF4301 2.6 100.3 1.0 FE1 B:SF4301 2.6 100.3 1.0 CB B:CYS96 3.4 101.7 1.0 S3 B:SF4301 3.7 103.8 1.0 CA B:CYS96 3.7 101.3 1.0 NE B:ARG95 4.3 99.2 1.0 CL B:CL302 4.5 113.8 1.0 N B:CYS96 4.6 103.7 1.0 SG B:CYS99 4.7 99.7 1.0 CB B:CYS99 4.8 100.3 1.0 SG B:CYS174 4.8 97.6 1.0 NH2 B:ARG95 4.8 99.7 1.0 C B:CYS96 4.8 102.4 1.0 O B:CYS96 4.9 102.5 1.0 CZ B:ARG95 4.9 99.2 1.0

Iron binding site 8 out of 28 in the [4FE-4S] Cluster Containing Lare in Complex with Amp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of [4FE-4S] Cluster Containing Lare in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:100.3 occ:1.00 FE4 B:SF4301 0.0 100.3 1.0 S1 B:SF4301 2.2 100.3 1.0 S2 B:SF4301 2.2 100.3 1.0 S3 B:SF4301 2.2 103.8 1.0 SG B:CYS174 2.3 97.6 1.0 FE3 B:SF4301 2.6 100.3 1.0 FE2 B:SF4301 2.7 100.3 1.0 FE1 B:SF4301 2.7 100.3 1.0 CB B:CYS174 2.7 100.4 1.0 S4 B:SF4301 3.8 100.3 1.0 CA B:CYS174 4.2 97.6 1.0 CG2 B:THR177 4.3 85.3 1.0 CL B:CL302 4.5 113.8 1.0 CD2 B:PHE56 4.5 92.1 1.0 SG B:CYS96 4.6 100.7 1.0 SG B:CYS99 4.7 99.7 1.0 CB B:PHE56 4.8 93.3 1.0 C B:CYS174 5.0 97.5 1.0 CG B:PHE56 5.0 92.7 1.0

Iron binding site 9 out of 28 in the [4FE-4S] Cluster Containing Lare in Complex with Amp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of [4FE-4S] Cluster Containing Lare in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:101.4 occ:1.00 FE1 C:SF4301 0.0 101.4 1.0 S4 C:SF4301 2.2 100.3 1.0 S3 C:SF4301 2.2 100.3 1.0 S2 C:SF4301 2.3 117.8 1.0 SG C:CYS99 2.3 109.6 1.0 FE2 C:SF4301 2.6 100.8 1.0 FE3 C:SF4301 2.7 100.3 1.0 FE4 C:SF4301 2.7 100.3 1.0 CB C:CYS99 3.0 110.3 1.0 S1 C:SF4301 3.8 100.8 1.0 CD2 C:PHE56 4.4 103.6 1.0 CA C:CYS99 4.4 112.0 1.0 SG C:CYS96 4.5 108.8 1.0 O C:CYS96 4.6 108.2 1.0 SG C:CYS174 4.6 108.3 1.0 CE2 C:PHE56 4.7 96.5 1.0 CL C:CL302 4.8 117.0 1.0 CG C:LYS100 4.8 105.7 1.0 CA C:CYS96 4.8 112.8 1.0 C C:CYS99 4.9 111.3 1.0 N C:LYS100 4.9 112.2 1.0 ND2 C:ASN54 5.0 109.4 1.0

Iron binding site 10 out of 28 in the [4FE-4S] Cluster Containing Lare in Complex with Amp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of [4FE-4S] Cluster Containing Lare in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:100.8 occ:1.00 FE2 C:SF4301 0.0 100.8 1.0 S4 C:SF4301 2.2 100.3 1.0 S1 C:SF4301 2.3 100.8 1.0 S3 C:SF4301 2.3 100.3 1.0 CL C:CL302 2.4 117.0 1.0 FE1 C:SF4301 2.6 101.4 1.0 FE3 C:SF4301 2.6 100.3 1.0 FE4 C:SF4301 2.7 100.3 1.0 S2 C:SF4301 3.7 117.8 1.0 SG C:CYS174 4.5 108.3 1.0 SG C:CYS96 4.5 108.8 1.0 CE C:LYS100 4.5 109.1 1.0 SG C:CYS99 4.7 109.6 1.0 NZ C:LYS100 5.0 111.6 1.0

P.Zecchin, L.Pecqueur, J.Oltmanns, C.Velours, V.Schunemann, M.Fontecave, B.Golinelli-Pimpaneau. Structure-Based Insights Into the Mechanism of [4FE-4S]-Dependent Sulfur Insertase Lare. Protein Sci. E4874 2023.
ISSN: ESSN 1469-896X
PubMed: 38100250
DOI: 10.1002/PRO.4874