Iron in PDB 6icm: Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd

All present enzymatic activity of Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd:
1.14.13.178;

The structure of Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd, PDB code: 6icm was solved by J.H.Kim, B.H.Kim, S.Y.Kang, H.K.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.46 / 2.96
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	118.265, 118.265, 455.692, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 26.1

Pages:

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

Binding sites:

The binding sites of Iron atom in the Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd (pdb code 6icm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 11 binding sites of Iron where determined in the Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd, PDB code: 6icm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 11 in the Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe400 b:42.9 occ:1.00 FE1 A:FES400 0.0 42.9 1.0 S2 A:FES400 2.2 39.7 1.0 S1 A:FES400 2.2 40.5 1.0 SG A:CYS81 2.3 47.6 1.0 SG A:CYS62 2.3 49.8 1.0 FE2 A:FES400 2.8 43.8 1.0 CB A:CYS62 3.2 39.0 1.0 CB A:CYS81 3.2 41.0 1.0 CB A:HIS64 4.0 44.0 1.0 CB A:TYR83 4.2 39.0 1.0 ND1 A:HIS84 4.4 45.2 1.0 N A:HIS84 4.4 47.6 1.0 ND1 A:HIS64 4.5 46.6 1.0 CB A:ALA67 4.6 41.4 1.0 CA A:CYS62 4.6 43.5 1.0 CA A:CYS81 4.7 40.2 1.0 N A:ARG65 4.7 48.6 1.0 N A:TYR83 4.7 43.5 1.0 CG A:HIS64 4.8 46.7 1.0 CA A:TYR83 4.9 43.7 1.0 CB A:TRP86 4.9 44.2 1.0 N A:HIS64 5.0 50.3 1.0 CG A:TRP86 5.0 48.3 1.0

Iron binding site 2 out of 11 in the Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe400 b:43.8 occ:1.00 FE2 A:FES400 0.0 43.8 1.0 ND1 A:HIS84 2.0 45.2 1.0 ND1 A:HIS64 2.1 46.6 1.0 S1 A:FES400 2.2 40.5 1.0 S2 A:FES400 2.2 39.7 1.0 FE1 A:FES400 2.8 42.9 1.0 CE1 A:HIS84 2.9 39.8 1.0 CG A:HIS84 3.0 41.5 1.0 CG A:HIS64 3.0 46.7 1.0 CE1 A:HIS64 3.1 46.2 1.0 CB A:HIS64 3.3 44.0 1.0 CB A:HIS84 3.3 44.4 1.0 N A:HIS84 3.8 47.6 1.0 NE2 A:HIS84 4.0 43.7 1.0 CD2 A:HIS84 4.0 44.1 1.0 CB A:TYR83 4.1 39.0 1.0 CA A:HIS84 4.1 48.6 1.0 CD2 A:HIS64 4.2 48.4 1.0 NE2 A:HIS64 4.2 53.6 1.0 N A:ARG65 4.3 48.6 1.0 CB A:ARG65 4.4 38.1 1.0 CG A:TYR83 4.5 42.7 1.0 SG A:CYS62 4.5 49.8 1.0 CA A:HIS64 4.6 46.1 1.0 C A:TYR83 4.6 44.5 1.0 CG A:ARG65 4.7 37.5 1.0 SG A:CYS81 4.7 47.6 1.0 CD2 A:TYR83 4.7 38.8 1.0 NE1 A:TRP86 4.8 43.3 1.0 C A:HIS64 4.8 44.4 1.0 CD1 A:TRP86 4.8 46.4 1.0 C A:HIS84 4.9 46.3 1.0 CA A:TYR83 4.9 43.7 1.0 CA A:ARG65 5.0 44.7 1.0

Iron binding site 3 out of 11 in the Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:95.1 occ:1.00 OD2 A:ASP289 2.2 63.7 1.0 NE2 A:HIS178 2.5 59.4 1.0 O A:HOH501 2.5 49.5 1.0 OD1 A:ASP289 2.6 58.6 1.0 NE2 A:HIS173 2.7 62.7 1.0 CG A:ASP289 2.8 63.1 1.0 CD2 A:HIS178 3.4 64.6 1.0 CE1 A:HIS178 3.4 60.4 1.0 CD2 A:HIS173 3.5 61.4 1.0 CE1 A:HIS173 3.7 66.3 1.0 ND2 A:ASN167 3.8 46.8 1.0 OD1 A:ASN167 3.8 61.2 1.0 CG1 A:VAL285 4.1 50.3 1.0 CG A:ASN167 4.1 54.1 1.0 O A:ASN167 4.2 57.4 1.0 CB A:ASP289 4.3 57.8 1.0 ND1 A:HIS178 4.5 59.8 1.0 CG A:HIS178 4.5 63.9 1.0 CG A:HIS173 4.7 60.9 1.0 ND1 A:HIS173 4.8 66.1 1.0 C A:ASN167 5.0 56.2 1.0

Iron binding site 4 out of 11 in the Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe400 b:52.4 occ:1.00 FE1 B:FES400 0.0 52.4 1.0 S2 B:FES400 2.2 51.9 1.0 S1 B:FES400 2.2 54.6 1.0 SG B:CYS81 2.3 59.5 1.0 SG B:CYS62 2.5 65.8 1.0 FE2 B:FES400 3.0 61.6 1.0 CB B:CYS81 3.1 56.3 1.0 CB B:CYS62 3.3 60.6 1.0 CB B:HIS64 4.1 58.2 1.0 ND1 B:HIS64 4.2 65.7 1.0 CA B:CYS81 4.6 50.1 1.0 CB B:TYR83 4.6 54.2 1.0 CB B:ALA67 4.6 50.7 1.0 CG B:HIS64 4.7 64.4 1.0 N B:ARG65 4.7 63.0 1.0 N B:HIS84 4.7 62.4 1.0 CA B:CYS62 4.8 57.5 1.0 CB B:TRP86 4.8 61.5 1.0 CG B:TRP86 4.8 61.6 1.0 ND1 B:HIS84 4.9 63.7 1.0 N B:HIS64 4.9 60.8 1.0 N B:ALA67 5.0 59.3 1.0

Iron binding site 5 out of 11 in the Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe400 b:61.6 occ:1.00 FE2 B:FES400 0.0 61.6 1.0 ND1 B:HIS64 2.0 65.7 1.0 ND1 B:HIS84 2.1 63.7 1.0 S1 B:FES400 2.2 54.6 1.0 S2 B:FES400 2.2 51.9 1.0 CE1 B:HIS64 2.8 67.3 1.0 FE1 B:FES400 3.0 52.4 1.0 CG B:HIS84 3.1 60.9 1.0 CG B:HIS64 3.1 64.4 1.0 CE1 B:HIS84 3.1 64.2 1.0 CB B:HIS84 3.4 58.3 1.0 CB B:HIS64 3.6 58.2 1.0 N B:HIS84 3.8 62.4 1.0 NE2 B:HIS64 3.9 64.2 1.0 CB B:ARG65 4.0 58.2 1.0 N B:ARG65 4.0 63.0 1.0 CB B:TYR83 4.1 54.2 1.0 CD2 B:HIS64 4.1 64.9 1.0 CA B:HIS84 4.1 59.7 1.0 NE2 B:HIS84 4.2 66.2 1.0 CD2 B:HIS84 4.2 64.4 1.0 CG B:ARG65 4.3 58.1 1.0 CG B:TYR83 4.3 51.5 1.0 CD2 B:TYR83 4.5 50.6 1.0 SG B:CYS81 4.5 59.5 1.0 CA B:ARG65 4.6 58.8 1.0 C B:TYR83 4.7 64.1 1.0 C B:HIS64 4.7 61.0 1.0 CA B:HIS64 4.8 58.1 1.0 SG B:CYS62 4.8 65.8 1.0 NE1 B:TRP86 4.9 65.0 1.0 C B:HIS84 4.9 58.9 1.0 CA B:TYR83 5.0 58.6 1.0 CD1 B:TRP86 5.0 64.3 1.0

Iron binding site 6 out of 11 in the Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:0.3 occ:1.00 OD2 B:ASP289 2.3 58.7 1.0 O B:HOH501 2.4 40.0 1.0 OD1 B:ASP289 2.5 48.6 1.0 CG B:ASP289 2.7 49.9 1.0 NE2 B:HIS173 2.7 51.0 1.0 NE2 B:HIS178 2.9 52.1 1.0 OD1 B:ASN167 3.0 54.5 1.0 ND2 B:ASN167 3.5 46.0 1.0 CG B:ASN167 3.6 45.4 1.0 CE1 B:HIS173 3.6 54.9 1.0 CD2 B:HIS173 3.6 51.4 1.0 CE1 B:HIS178 3.6 49.5 1.0 CD2 B:HIS178 3.9 52.8 1.0 O B:ASN167 4.0 52.0 1.0 CB B:ASP289 4.1 46.4 1.0 C B:ASN167 4.7 50.8 1.0 ND1 B:HIS173 4.7 56.6 1.0 CG B:HIS173 4.7 54.2 1.0 ND1 B:HIS178 4.8 53.5 1.0 CG B:HIS178 5.0 53.7 1.0 CB B:ASN167 5.0 43.7 1.0

Iron binding site 7 out of 11 in the Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe400 b:55.4 occ:1.00 FE1 C:FES400 0.0 55.4 1.0 ND1 C:HIS64 2.1 53.8 1.0 S1 C:FES400 2.2 51.6 1.0 S2 C:FES400 2.2 53.5 1.0 ND1 C:HIS84 2.2 54.0 1.0 FE2 C:FES400 2.8 52.1 1.0 CG C:HIS64 3.0 53.5 1.0 CG C:HIS84 3.0 53.4 1.0 CE1 C:HIS64 3.1 54.7 1.0 CB C:HIS84 3.2 53.3 1.0 CE1 C:HIS84 3.3 58.1 1.0 CB C:HIS64 3.3 55.7 1.0 N C:HIS84 3.6 64.3 1.0 CA C:HIS84 4.0 58.2 1.0 CB C:TYR83 4.1 58.1 1.0 CD2 C:HIS64 4.2 55.4 1.0 NE2 C:HIS64 4.2 53.3 1.0 CD2 C:HIS84 4.2 57.5 1.0 N C:ARG65 4.3 59.3 1.0 NE2 C:HIS84 4.3 60.9 1.0 CB C:ARG65 4.4 53.7 1.0 SG C:CYS81 4.5 65.0 1.0 CG C:TYR83 4.6 51.5 1.0 CA C:HIS64 4.6 54.4 1.0 CG C:ARG65 4.6 51.1 1.0 NE1 C:TRP86 4.7 55.1 1.0 C C:TYR83 4.7 64.5 1.0 C C:HIS84 4.7 57.0 1.0 SG C:CYS62 4.7 62.9 1.0 CD1 C:TRP86 4.8 55.0 1.0 C C:HIS64 4.8 57.8 1.0 CE2 C:TRP86 4.8 53.4 1.0 CD2 C:TYR83 4.9 51.1 1.0 CA C:TYR83 4.9 60.7 1.0 CG C:TRP86 5.0 54.1 1.0 CA C:ARG65 5.0 54.0 1.0

Iron binding site 8 out of 11 in the Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe400 b:52.1 occ:1.00 FE2 C:FES400 0.0 52.1 1.0 S2 C:FES400 2.2 53.5 1.0 S1 C:FES400 2.2 51.6 1.0 SG C:CYS81 2.2 65.0 1.0 SG C:CYS62 2.6 62.9 1.0 FE1 C:FES400 2.8 55.4 1.0 CB C:CYS81 3.1 58.6 1.0 CB C:CYS62 3.3 51.3 1.0 CB C:HIS64 4.0 55.7 1.0 CB C:TYR83 4.3 58.1 1.0 ND1 C:HIS64 4.5 53.8 1.0 N C:HIS84 4.5 64.3 1.0 CB C:ALA67 4.5 52.4 1.0 CA C:CYS81 4.5 55.4 1.0 N C:ARG65 4.6 59.3 1.0 ND1 C:HIS84 4.6 54.0 1.0 CG C:HIS64 4.7 53.5 1.0 CA C:CYS62 4.7 48.0 1.0 N C:TYR83 4.8 56.0 1.0 N C:HIS64 4.8 54.1 1.0 OH C:TYR88 4.9 58.1 1.0 C C:CYS81 4.9 58.3 1.0 CA C:HIS64 5.0 54.4 1.0

Iron binding site 9 out of 11 in the Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:0.3 occ:1.00 OD2 C:ASP289 2.3 71.0 1.0 OD1 C:ASP289 2.4 66.5 1.0 O C:HOH501 2.4 62.5 1.0 CE1 C:HIS173 2.5 79.0 1.0 CG C:ASP289 2.6 67.6 1.0 NE2 C:HIS178 2.7 65.5 1.0 NE2 C:HIS173 3.1 72.4 1.0 CD2 C:HIS178 3.5 65.0 1.0 ND1 C:HIS173 3.6 76.2 1.0 OD1 C:ASN167 3.7 61.8 1.0 ND2 C:ASN167 3.7 58.5 1.0 CE1 C:HIS178 3.7 63.8 1.0 CG C:ASN167 4.0 60.8 1.0 CB C:ASP289 4.2 62.3 1.0 O C:ASN167 4.3 65.2 1.0 CD2 C:HIS173 4.4 71.9 1.0 CD1 C:ILE177 4.6 67.5 1.0 CG C:HIS173 4.6 74.4 1.0 CG C:HIS178 4.7 65.9 1.0 ND1 C:HIS178 4.8 62.2 1.0 O C:VAL285 4.9 59.9 1.0

Iron binding site 10 out of 11 in the Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Pseudomonas Putida CBB5 Ndma with Ferredoxin Domain of Ndmd within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe601 b:73.2 occ:1.00 FE1 D:FES601 0.0 73.2 1.0 SG D:CYS537 2.2 71.0 1.0 S2 D:FES601 2.2 67.9 1.0 S1 D:FES601 2.2 60.4 1.0 SG D:CYS542 2.3 60.1 1.0 O D:CYS537 2.6 77.8 1.0 FE2 D:FES601 3.0 64.1 1.0 N D:GLY543 3.4 64.0 1.0 CB D:CYS542 3.5 62.3 1.0 C D:CYS537 3.5 73.5 1.0 N D:CYS542 3.6 47.5 1.0 CB D:CYS537 3.6 69.6 1.0 N D:CYS537 3.7 63.7 1.0 CA D:CYS537 3.9 65.4 1.0 O D:GLN539 3.9 67.8 1.0 CA D:CYS542 3.9 51.7 1.0 N D:THR544 4.0 59.1 1.0 C D:CYS542 4.1 60.2 1.0 OG1 D:THR544 4.1 67.4 1.0 CA D:GLY543 4.3 55.4 1.0 N D:SER536 4.4 69.1 1.0 C D:SER536 4.5 69.4 1.0 N D:VAL541 4.5 60.5 1.0 C D:GLY543 4.6 64.7 1.0 N D:CYS545 4.6 61.3 1.0 SG D:CYS545 4.7 53.9 1.0 C D:VAL541 4.7 55.5 1.0 SG D:CYS575 4.7 64.5 1.0 N D:GLU538 4.7 72.3 1.0 CA D:SER536 4.8 67.0 1.0 CB D:SER536 4.8 69.3 1.0 CA D:THR544 5.0 64.5 1.0

J.H.Kim, B.H.Kim, S.Brooks, S.Y.Kang, R.M.Summers, H.K.Song. Structural and Mechanistic Insights Into Caffeine Degradation By the Bacterial N-Demethylase Complex. J.Mol.Biol. V. 431 3647 2019.
ISSN: ESSN 1089-8638
PubMed: 31412262
DOI: 10.1016/J.JMB.2019.08.004