Iron in PDB 9gyb: Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli

All present enzymatic activity of Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli:
1.2.7.4;

The structure of Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli, PDB code: 9gyb was solved by C.Cavazza, U.Contaldo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.71 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	92.45, 200.573, 116.37, 90, 111.21, 90
R / Rfree (%)	22.7 / 28.8

The structure of Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Nickel	(Ni)	6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli (pdb code 9gyb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 60 binding sites of Iron where determined in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli, PDB code: 9gyb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 60 in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli


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 the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:96.1 occ:1.00 FE1 A:SF4701 0.0 96.1 1.0 SG A:CYS58 2.3 75.0 1.0 S4 A:SF4701 2.3 64.7 1.0 S3 A:SF4701 2.3 81.4 1.0 S2 A:SF4701 2.3 88.0 1.0 FE2 A:SF4701 2.7 90.0 1.0 FE3 A:SF4701 2.8 94.7 1.0 FE4 A:SF4701 2.8 91.9 1.0 CB A:CYS58 3.4 55.4 1.0 N A:VAL71 4.0 51.9 1.0 S1 A:SF4701 4.0 75.1 1.0 SG A:CYS50 4.0 71.8 1.0 N A:CYS58 4.2 57.5 1.0 CA A:GLY70 4.2 59.9 1.0 CB A:CYS50 4.4 67.3 1.0 CA A:CYS58 4.4 60.4 1.0 CA A:GLY56 4.4 61.8 1.0 SG A:CYS53 4.5 75.8 1.0 N A:GLY56 4.5 62.0 1.0 C A:GLY70 4.6 59.9 1.0 N A:CYS72 4.7 63.2 1.0 SG A:CYS72 4.9 78.4 1.0 CB A:VAL71 4.9 56.6 1.0 CA A:VAL71 4.9 50.2 1.0 CG2 A:VAL71 5.0 57.5 1.0

Iron binding site 2 out of 60 in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli


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 the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:90.0 occ:1.00 FE2 A:SF4701 0.0 90.0 1.0 SG A:CYS53 2.2 75.8 1.0 S3 A:SF4701 2.3 81.4 1.0 S4 A:SF4701 2.3 64.7 1.0 S1 A:SF4701 2.3 75.1 1.0 CB A:CYS53 2.7 59.7 1.0 FE4 A:SF4701 2.7 91.9 1.0 FE3 A:SF4701 2.7 94.7 1.0 FE1 A:SF4701 2.7 96.1 1.0 N A:CYS53 3.6 62.1 1.0 CA A:CYS53 3.6 63.5 1.0 S2 A:SF4701 3.9 88.0 1.0 SG A:CYS50 4.3 71.8 1.0 C A:CYS53 4.3 63.6 1.0 CG2 A:VAL203 4.5 46.1 1.0 SG A:CYS58 4.7 75.0 1.0 CB A:CYS72 4.7 62.0 1.0 C A:ILE52 4.7 59.2 1.0 N A:GLY56 4.7 62.0 1.0 O A:CYS53 4.8 80.1 1.0 SG A:CYS72 4.8 78.4 1.0 CB A:VAL203 4.8 48.7 1.0 CB A:ILE52 4.8 47.2 1.0 N A:ILE52 4.9 66.9 1.0 N A:LEU54 4.9 53.4 1.0 N A:LYS55 5.0 64.7 1.0

Iron binding site 3 out of 60 in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli


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 the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:94.7 occ:1.00 FE3 A:SF4701 0.0 94.7 1.0 SG A:CYS50 2.2 71.8 1.0 S2 A:SF4701 2.3 88.0 1.0 S1 A:SF4701 2.3 75.1 1.0 S4 A:SF4701 2.3 64.7 1.0 FE4 A:SF4701 2.7 91.9 1.0 FE2 A:SF4701 2.7 90.0 1.0 FE1 A:SF4701 2.8 96.1 1.0 CB A:CYS50 3.1 67.3 1.0 NH2 A:ARG82 3.4 54.9 1.0 S3 A:SF4701 3.8 81.4 1.0 CB A:ILE52 4.3 47.2 1.0 CD1 A:ILE52 4.3 55.3 1.0 N A:ILE52 4.5 66.9 1.0 SG A:CYS72 4.5 78.4 1.0 CA A:CYS50 4.5 76.6 1.0 CZ A:ARG82 4.6 51.0 1.0 N A:ARG51 4.6 65.0 1.0 N A:CYS53 4.8 62.1 1.0 C A:CYS50 4.8 84.5 1.0 CB A:CYS53 4.9 59.7 1.0 CG1 A:ILE52 4.9 49.9 1.0 SG A:CYS58 4.9 75.0 1.0 CA A:ILE52 4.9 57.4 1.0 SG A:CYS53 5.0 75.8 1.0

Iron binding site 4 out of 60 in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli


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 the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:91.9 occ:1.00 FE4 A:SF4701 0.0 91.9 1.0 S3 A:SF4701 2.2 81.4 1.0 SG A:CYS72 2.2 78.4 1.0 S2 A:SF4701 2.3 88.0 1.0 S1 A:SF4701 2.3 75.1 1.0 FE3 A:SF4701 2.7 94.7 1.0 FE2 A:SF4701 2.7 90.0 1.0 FE1 A:SF4701 2.8 96.1 1.0 CB A:CYS72 2.8 62.0 1.0 N A:CYS72 3.4 63.2 1.0 CA A:CYS72 3.7 60.0 1.0 S4 A:SF4701 3.9 64.7 1.0 N A:VAL71 4.3 51.9 1.0 NH2 A:ARG82 4.5 54.9 1.0 SG A:CYS53 4.5 75.8 1.0 CA A:GLY70 4.5 59.9 1.0 C A:GLY70 4.6 59.9 1.0 C A:VAL71 4.6 53.2 1.0 C A:CYS72 4.6 62.0 1.0 SG A:CYS58 4.7 75.0 1.0 N A:GLY73 4.7 59.5 1.0 SG A:CYS50 4.9 71.8 1.0 CB A:ALA74 4.9 60.9 1.0 CA A:VAL71 5.0 50.2 1.0

Iron binding site 5 out of 60 in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli


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 the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:90.2 occ:0.48 FE1 A:RQM702 0.0 90.2 0.5 S2 A:RQM702 2.3 87.1 0.5 SG A:CYS338 2.3 78.1 1.0 S4 A:RQM702 2.3 78.2 0.5 S3 A:RQM702 2.3 83.9 0.5 FE3 A:RQM702 2.7 95.5 0.5 FE4 A:RQM702 2.8 76.7 0.5 NZ A:LYS568 2.9 84.5 1.0 NI A:RQM702 3.2 97.6 0.5 FE2 A:RQM702 3.3 72.2 0.5 CB A:CYS338 3.5 77.0 1.0 S1 A:RQM702 3.8 80.5 0.5 CE A:LYS568 4.0 80.2 1.0 CE A:MET565 4.3 67.3 1.0 CB A:CYS451 4.4 86.7 1.0 NE2 A:HIS265 4.4 82.9 1.0 OG A:SER566 4.7 67.0 1.0 SG A:CYS451 4.8 79.8 1.0 CA A:CYS338 4.8 70.8 1.0 CB A:SER566 4.9 58.2 1.0 CD1 A:TYR317 5.0 71.8 1.0 SG A:CYS481 5.0 78.8 1.0 CD A:LYS568 5.0 72.1 1.0

Iron binding site 6 out of 60 in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli


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 the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:72.2 occ:0.48 FE2 A:RQM702 0.0 72.2 0.5 SG A:CYS531 2.3 96.6 1.0 S3 A:RQM702 2.3 83.9 0.5 NI A:RQM702 2.6 97.6 0.5 NZ A:LYS568 2.7 84.5 1.0 NE2 A:HIS265 2.8 82.9 1.0 CE1 A:HIS265 2.9 86.5 1.0 SG A:CYS300 2.9 76.7 1.0 FE1 A:RQM702 3.3 90.2 0.5 CE A:LYS568 3.6 80.2 1.0 S1 A:RQM702 3.6 80.5 0.5 FE4 A:RQM702 3.7 76.7 0.5 S4 A:RQM702 3.8 78.2 0.5 CB A:CYS531 3.8 62.8 1.0 CD2 A:HIS265 4.1 69.5 1.0 ND1 A:HIS265 4.2 87.3 1.0 CB A:CYS300 4.2 78.2 1.0 FE3 A:RQM702 4.3 95.5 0.5 SG A:CYS338 4.7 78.1 1.0 CG A:HIS265 4.8 72.5 1.0 N A:CYS531 4.8 57.1 1.0 CA A:CYS531 4.9 61.0 1.0 CD A:LYS568 5.0 72.1 1.0 S2 A:RQM702 5.0 87.1 0.5

Iron binding site 7 out of 60 in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli


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 the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:95.5 occ:0.48 FE3 A:RQM702 0.0 95.5 0.5 CB A:CYS451 2.1 86.7 1.0 S4 A:RQM702 2.3 78.2 0.5 S2 A:RQM702 2.3 87.1 0.5 S1 A:RQM702 2.3 80.5 0.5 NI A:RQM702 2.4 97.6 0.5 FE1 A:RQM702 2.7 90.2 0.5 CA A:CYS451 2.7 80.3 1.0 FE4 A:RQM702 2.7 76.7 0.5 SG A:CYS451 3.0 79.8 1.0 N A:CYS451 3.5 73.5 1.0 O A:GLY450 3.7 65.5 1.0 C A:GLY450 3.9 62.5 1.0 S3 A:RQM702 3.9 83.9 0.5 SG A:CYS481 4.0 78.8 1.0 C A:CYS451 4.0 75.0 1.0 FE2 A:RQM702 4.3 72.2 0.5 CE A:MET565 4.3 67.3 1.0 CB A:CYS481 4.3 62.7 1.0 N A:ASN452 4.3 77.4 1.0 OG A:SER566 4.5 67.0 1.0 SG A:CYS338 4.8 78.1 1.0 NZ A:LYS568 4.9 84.5 1.0 O A:CYS451 5.0 73.4 1.0

Iron binding site 8 out of 60 in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli


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 the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:76.7 occ:0.48 FE4 A:RQM702 0.0 76.7 0.5 S2 A:RQM702 2.3 87.1 0.5 S3 A:RQM702 2.3 83.9 0.5 SG A:CYS481 2.3 78.8 1.0 S1 A:RQM702 2.3 80.5 0.5 FE3 A:RQM702 2.7 95.5 0.5 FE1 A:RQM702 2.8 90.2 0.5 NI A:RQM702 3.6 97.6 0.5 CB A:CYS481 3.7 62.7 1.0 FE2 A:RQM702 3.7 72.2 0.5 SG A:CYS299 3.9 79.8 1.0 S4 A:RQM702 4.2 78.2 0.5 CB A:TYR317 4.2 72.0 1.0 CB A:CYS299 4.3 69.0 1.0 N A:CYS481 4.4 64.0 1.0 CB A:CYS451 4.5 86.7 1.0 SG A:CYS338 4.5 78.1 1.0 CA A:CYS481 4.6 62.0 1.0 CB A:CYS338 4.7 77.0 1.0 CA A:CYS451 4.7 80.3 1.0 CA A:CYS299 4.8 69.8 1.0 CD1 A:TYR317 4.8 71.8 1.0 CG A:TYR317 4.8 71.8 1.0 SG A:CYS300 4.9 76.7 1.0 CA A:TYR317 5.0 72.7 1.0 N A:TYR317 5.0 76.2 1.0

Iron binding site 9 out of 60 in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli


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 the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe701 b:108.1 occ:1.00 FE1 B:SF4701 0.0 108.1 1.0 SG A:CYS41 2.2 81.6 1.0 S2 B:SF4701 2.3 80.5 1.0 S3 B:SF4701 2.3 79.9 1.0 S4 B:SF4701 2.3 92.3 1.0 FE2 B:SF4701 2.7 115.7 1.0 FE3 B:SF4701 2.7 111.9 1.0 FE4 B:SF4701 2.7 107.8 1.0 CB A:CYS41 3.0 76.3 1.0 S1 B:SF4701 3.9 93.7 1.0 CB A:PHE43 4.4 78.5 1.0 CA A:CYS41 4.5 70.2 1.0 N A:GLY44 4.5 71.3 1.0 SG B:CYS41 4.7 79.2 1.0 SG A:CYS49 4.8 84.2 1.0 SG B:CYS49 4.9 106.8 1.0

Iron binding site 10 out of 60 in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli


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 the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe701 b:115.7 occ:1.00 FE2 B:SF4701 0.0 115.7 1.0 SG B:CYS41 2.2 79.2 1.0 S3 B:SF4701 2.2 79.9 1.0 S1 B:SF4701 2.3 93.7 1.0 S4 B:SF4701 2.3 92.3 1.0 FE1 B:SF4701 2.7 108.1 1.0 FE4 B:SF4701 2.7 107.8 1.0 FE3 B:SF4701 2.7 111.9 1.0 CB B:CYS41 3.1 63.4 1.0 S2 B:SF4701 3.9 80.5 1.0 N B:GLY44 4.3 65.2 1.0 CB B:PHE43 4.3 73.5 1.0 SG A:CYS49 4.5 84.2 1.0 CA B:CYS41 4.5 59.2 1.0 SG A:CYS41 4.6 81.6 1.0 SG B:CYS49 4.8 106.8 1.0 CB B:CYS49 4.8 83.0 1.0 CA B:GLY44 4.9 71.2 1.0

U.Contaldo, B.Guigliarelli, J.Perard, T.Pichon, A.Le Goff, C.Cavazza. Insights Into the Role of the D-Cluster in [Nife]-Codh From Rhodospirillum Rubrum. Chemistry 03648 2025.
ISSN: ISSN 0947-6539
PubMed: 39912726
DOI: 10.1002/CHEM.202403648