Iron in PDB 4jc0: Crystal Structure of Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77

The structure of Crystal Structure of Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77, PDB code: 4jc0 was solved by F.Forouhar, M.Hussain, J.Seetharaman, Y.Fang, C.X.Chen, K.Cunningham, K.Conover, L.-C.Ma, R.Xiao, T.B.Acton, G.T.Montelione, L.Tong, J.F.Hunt, Northeast Structural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.46 / 3.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.721, 86.948, 172.795, 90.00, 90.00, 90.00
R / Rfree (%)	24.5 / 29.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77 (pdb code 4jc0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Crystal Structure of Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77, PDB code: 4jc0:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the Crystal Structure of Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77


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 Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:84.9 occ:1.00 FE6 A:FS5501 0.0 84.9 1.0 S5 A:FS5501 2.2 40.9 1.0 S6 A:FS5501 2.2 62.2 1.0 S8 A:FS5501 2.2 56.7 1.0 SG A:CYS79 2.3 91.5 1.0 FE7 A:FS5501 2.6 71.3 1.0 FE5 A:FS5501 2.7 90.8 1.0 FE8 A:FS5501 2.7 91.1 1.0 ND2 A:ASN13 3.3 94.4 1.0 CB A:CYS79 3.5 91.5 1.0 S7 A:FS5501 3.7 56.0 1.0 CG A:ASN13 4.5 94.4 1.0 SG A:CYS10 4.6 74.6 1.0 SG A:CYS46 4.6 93.8 1.0 N A:ALA47 4.6 1.0 1.0 S9 A:FS5501 4.6 52.3 0.8 CA A:CYS46 4.6 0.9 1.0 NZ A:LYS161 4.7 77.9 1.0 O A:THR45 4.7 87.7 1.0 CE A:LYS161 4.7 77.9 1.0 CA A:CYS79 4.9 90.3 1.0

Iron binding site 2 out of 16 in the Crystal Structure of Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77


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 Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:71.3 occ:1.00 FE7 A:FS5501 0.0 71.3 1.0 SG A:CYS10 2.2 74.6 1.0 S7 A:FS5501 2.2 56.0 1.0 S6 A:FS5501 2.2 62.2 1.0 S8 A:FS5501 2.2 56.7 1.0 FE6 A:FS5501 2.6 84.9 1.0 FE5 A:FS5501 2.7 90.8 1.0 FE8 A:FS5501 2.7 91.1 1.0 CB A:CYS10 3.3 74.6 1.0 S5 A:FS5501 3.7 40.9 1.0 CE A:LYS12 4.0 85.5 1.0 NZ A:LYS12 4.0 85.5 1.0 ND2 A:ASN13 4.2 94.4 1.0 CA A:CYS10 4.5 65.5 1.0 N A:CYS10 4.5 65.5 1.0 C A:GLY9 4.6 63.0 1.0 O A:GLY9 4.6 63.0 1.0 S9 A:FS5501 4.7 52.3 0.8 SG A:CYS46 4.7 93.8 1.0 SG A:CYS79 4.8 91.5 1.0 CB A:LYS12 4.9 85.5 1.0 CB A:ASN13 4.9 94.4 1.0 CG A:ASN13 4.9 94.4 1.0 CD A:LYS12 4.9 85.5 1.0 N A:ASN13 5.0 0.5 1.0

Iron binding site 3 out of 16 in the Crystal Structure of Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77


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 Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:91.1 occ:1.00 FE8 A:FS5501 0.0 91.1 1.0 S9 A:FS5501 2.2 52.3 0.8 S7 A:FS5501 2.2 56.0 1.0 S8 A:FS5501 2.2 56.7 1.0 S5 A:FS5501 2.2 40.9 1.0 FE7 A:FS5501 2.7 71.3 1.0 FE6 A:FS5501 2.7 84.9 1.0 FE5 A:FS5501 2.8 90.8 1.0 S10 A:FS5501 3.5 2.8 0.6 S6 A:FS5501 3.9 62.2 1.0 O A:PHE48 4.3 0.4 1.0 S11 A:FS5501 4.4 46.2 0.6 SG A:CYS79 4.5 91.5 1.0 NZ A:LYS12 4.6 85.5 1.0 SG A:CYS46 4.8 93.8 1.0 SG A:CYS10 4.8 74.6 1.0 NE2 A:GLN192 4.8 80.8 1.0 CD1 A:ILE157 4.9 91.8 1.0

Iron binding site 4 out of 16 in the Crystal Structure of Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77


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 Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:90.8 occ:1.00 FE5 A:FS5501 0.0 90.8 1.0 S5 A:FS5501 2.2 40.9 1.0 S7 A:FS5501 2.2 56.0 1.0 S6 A:FS5501 2.2 62.2 1.0 SG A:CYS46 2.2 93.8 1.0 FE7 A:FS5501 2.7 71.3 1.0 FE6 A:FS5501 2.7 84.9 1.0 FE8 A:FS5501 2.8 91.1 1.0 CB A:CYS46 3.4 93.8 1.0 CA A:CYS46 3.8 0.9 1.0 S8 A:FS5501 3.8 56.7 1.0 N A:ALA47 4.0 1.0 1.0 O A:GLY9 4.1 63.0 1.0 CG1 A:ILE49 4.2 0.8 1.0 C A:CYS46 4.3 0.9 1.0 O A:PHE48 4.4 0.4 1.0 C A:GLY9 4.4 63.0 1.0 SG A:CYS10 4.4 74.6 1.0 SG A:CYS79 4.6 91.5 1.0 N A:PHE48 4.6 0.4 1.0 CA A:GLY9 4.6 63.0 1.0 CB A:CYS10 4.6 74.6 1.0 ND2 A:ASN13 4.7 94.4 1.0 S9 A:FS5501 4.8 52.3 0.8 C A:PHE48 4.9 0.4 1.0

Iron binding site 5 out of 16 in the Crystal Structure of Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77


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 Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:0.2 occ:1.00 FE4 A:FS5501 0.0 0.2 1.0 S13 A:FS5501 2.1 28.7 0.8 S3 A:FS5501 2.1 48.8 1.0 S4 A:FS5501 2.2 52.7 1.0 S1 A:FS5501 2.2 30.8 1.0 FE2 A:FS5501 2.5 79.8 1.0 FE9 A:FS5501 2.5 62.0 1.0 FE1 A:FS5501 2.6 47.2 1.0 S12 A:FS5501 3.3 74.0 0.6 S2 A:FS5501 3.8 69.3 1.0 O A:GLN192 4.1 80.2 1.0 SG A:CYS155 4.2 94.2 1.0 SG A:CYS152 4.4 73.7 1.0 SG A:CYS148 4.5 65.2 1.0 CB A:CYS155 4.7 94.2 1.0 S11 A:FS5501 4.8 46.2 0.6 C A:GLN192 4.9 80.2 1.0

Iron binding site 6 out of 16 in the Crystal Structure of Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77


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 Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:62.0 occ:1.00 FE9 A:FS5501 0.0 62.0 1.0 S4 A:FS5501 2.2 52.7 1.0 SG A:CYS148 2.2 65.2 1.0 S2 A:FS5501 2.2 69.3 1.0 S1 A:FS5501 2.2 30.8 1.0 FE1 A:FS5501 2.5 47.2 1.0 FE2 A:FS5501 2.5 79.8 1.0 FE4 A:FS5501 2.5 0.2 1.0 CB A:CYS148 3.0 65.2 1.0 S3 A:FS5501 3.6 48.8 1.0 CB A:ARG150 4.4 74.6 1.0 CA A:CYS148 4.4 69.1 1.0 S13 A:FS5501 4.5 28.7 0.8 CB A:GLN192 4.5 80.8 1.0 O A:GLN192 4.6 80.2 1.0 SG A:CYS155 4.6 94.2 1.0 SG A:CYS152 4.6 73.7 1.0 CB A:ASP193 4.7 99.1 1.0 CG A:ARG150 4.8 74.6 1.0 C A:GLN192 4.8 80.2 1.0 C A:CYS148 4.9 69.1 1.0 N A:ARG150 5.0 56.2 1.0 S12 A:FS5501 5.0 74.0 0.6

Iron binding site 7 out of 16 in the Crystal Structure of Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77


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 Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:79.8 occ:1.00 FE2 A:FS5501 0.0 79.8 1.0 S3 A:FS5501 2.2 48.8 1.0 S4 A:FS5501 2.2 52.7 1.0 S2 A:FS5501 2.2 69.3 1.0 SG A:CYS155 2.2 94.2 1.0 FE9 A:FS5501 2.5 62.0 1.0 FE4 A:FS5501 2.5 0.2 1.0 FE1 A:FS5501 2.5 47.2 1.0 CB A:CYS155 2.8 94.2 1.0 S1 A:FS5501 3.7 30.8 1.0 CB A:CYS152 4.2 73.7 1.0 S13 A:FS5501 4.3 28.7 0.8 SG A:CYS152 4.3 73.7 1.0 CA A:CYS155 4.3 89.4 1.0 CB A:ILE157 4.4 91.8 1.0 CD A:PRO158 4.5 0.3 1.0 SG A:CYS148 4.5 65.2 1.0 CG1 A:ILE157 4.6 91.8 1.0 CG A:PRO158 4.8 0.3 1.0 CB A:CYS148 4.8 65.2 1.0 C A:CYS155 5.0 89.4 1.0

Iron binding site 8 out of 16 in the Crystal Structure of Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77


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 Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:47.2 occ:1.00 FE1 A:FS5501 0.0 47.2 1.0 S2 A:FS5501 2.2 69.3 1.0 SG A:CYS152 2.2 73.7 1.0 S3 A:FS5501 2.2 48.8 1.0 S1 A:FS5501 2.2 30.8 1.0 FE9 A:FS5501 2.5 62.0 1.0 FE2 A:FS5501 2.5 79.8 1.0 FE4 A:FS5501 2.6 0.2 1.0 CB A:CYS152 3.1 73.7 1.0 S4 A:FS5501 3.7 52.7 1.0 CB A:ARG150 4.1 74.6 1.0 SG A:CYS148 4.1 65.2 1.0 CB A:CYS155 4.3 94.2 1.0 O A:ARG150 4.3 56.2 1.0 CA A:CYS152 4.5 88.0 1.0 SG A:CYS155 4.5 94.2 1.0 CD2 A:HIS229 4.6 94.0 1.0 S13 A:FS5501 4.6 28.7 0.8 N A:CYS152 4.6 88.0 1.0 C A:ARG150 4.7 56.2 1.0 CA A:ARG150 4.9 56.2 1.0 CG A:ARG150 5.0 74.6 1.0

Iron binding site 9 out of 16 in the Crystal Structure of Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77


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 Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:84.2 occ:1.00 FE6 B:FS5501 0.0 84.2 1.0 S8 B:FS5501 2.1 60.2 1.0 S5 B:FS5501 2.2 68.7 1.0 S6 B:FS5501 2.2 78.5 1.0 SG B:CYS79 2.3 93.3 1.0 FE7 B:FS5501 2.6 93.0 1.0 FE8 B:FS5501 2.7 89.5 1.0 FE5 B:FS5501 2.8 83.5 1.0 CB B:CYS79 3.4 93.3 1.0 ND2 B:ASN13 3.4 96.7 1.0 S7 B:FS5501 3.7 82.5 1.0 CG B:ASN13 4.2 96.7 1.0 CE B:LYS161 4.2 77.8 1.0 NZ B:LYS161 4.3 77.8 1.0 N B:ALA47 4.3 0.8 1.0 CA B:CYS46 4.3 0.3 1.0 SG B:CYS46 4.4 89.5 1.0 OD1 B:ASN13 4.5 96.7 1.0 O B:THR45 4.5 94.0 1.0 S9 B:FS5501 4.6 59.6 0.8 SG B:CYS10 4.7 82.9 1.0 CA B:CYS79 4.8 95.9 1.0 CB B:CYS46 4.8 89.5 1.0 C B:CYS46 4.9 0.3 1.0 CE1 B:PHE160 5.0 0.9 1.0

Iron binding site 10 out of 16 in the Crystal Structure of Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77


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 Thermotoga Maritima Holo Rimo in Complex with Pentasulfide, Northeast Structural Genomics Consortium Target VR77 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:93.0 occ:1.00 FE7 B:FS5501 0.0 93.0 1.0 SG B:CYS10 2.2 82.9 1.0 S7 B:FS5501 2.2 82.5 1.0 S8 B:FS5501 2.2 60.2 1.0 S6 B:FS5501 2.2 78.5 1.0 FE6 B:FS5501 2.6 84.2 1.0 FE5 B:FS5501 2.6 83.5 1.0 FE8 B:FS5501 2.7 89.5 1.0 CB B:CYS10 3.2 82.9 1.0 S5 B:FS5501 3.6 68.7 1.0 ND2 B:ASN13 4.0 96.7 1.0 CE B:LYS12 4.2 87.1 1.0 NZ B:LYS12 4.3 87.1 1.0 CG B:ASN13 4.3 96.7 1.0 N B:CYS10 4.3 61.2 1.0 C B:GLY9 4.3 66.1 1.0 O B:GLY9 4.3 66.1 1.0 CA B:CYS10 4.3 61.2 1.0 CB B:ASN13 4.6 96.7 1.0 NZ B:LYS161 4.7 77.8 1.0 S9 B:FS5501 4.7 59.6 0.8 SG B:CYS79 4.7 93.3 1.0 SG B:CYS46 4.8 89.5 1.0 OD1 B:ASN13 4.8 96.7 1.0 N B:ASN13 4.8 1.0 1.0 CB B:LYS12 4.9 87.1 1.0 C B:CYS10 5.0 61.2 1.0 CA B:GLY9 5.0 66.1 1.0

F.Forouhar, S.Arragain, M.Atta, S.Gambarelli, J.M.Mouesca, M.Hussain, R.Xiao, S.Kieffer-Jaquinod, J.Seetharaman, T.B.Acton, G.T.Montelione, E.Mulliez, J.F.Hunt, M.Fontecave. Two Fe-S Clusters Catalyze Sulfur Insertion By Radical-Sam Methylthiotransferases. Nat.Chem.Biol. V. 9 333 2013.
ISSN: ISSN 1552-4450
PubMed: 23542644
DOI: 10.1038/NCHEMBIO.1229