Iron in PDB 6vjr: Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus

All present enzymatic activity of Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus:
5.3.3.3;

The structure of Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus, PDB code: 6vjr was solved by H.Demirci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.86 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.53, 72.954, 180.517, 90, 98.38, 90
R / Rfree (%)	15.8 / 17.5

Pages:

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

Binding sites:

The binding sites of Iron atom in the Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus (pdb code 6vjr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 20 binding sites of Iron where determined in the Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus, PDB code: 6vjr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in the Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:99.0 occ:0.71 FE1 A:SF4601 0.0 99.0 0.7 S4 A:SF4601 2.3 124.6 1.0 FE A:FE607 2.4 19.5 0.7 S3 A:SF4601 2.4 81.2 0.6 FE3 A:SF4601 3.1 123.8 1.0 O A:HOH724 3.1 128.8 0.4 FE2 A:SF4601 3.1 132.9 0.6 NE2 A:HIS295 3.3 19.0 1.0 CE1 A:TYR299 3.3 27.1 1.0 OE1 A:GLU449 3.3 31.1 1.0 OE2 A:GLU449 3.4 27.1 1.0 S2 A:SF4601 3.4 25.6 0.5 CZ A:TYR299 3.6 26.0 1.0 CE1 A:HIS295 3.6 21.1 1.0 OH A:TYR299 3.6 26.8 1.0 CD A:GLU449 3.7 28.5 1.0 FE4 A:SF4601 3.8 125.1 1.0 O A:HOH1081 3.9 27.9 0.4 CD1 A:TYR299 4.1 22.4 1.0 O A:HOH1081 4.4 38.0 0.6 CD2 A:HIS295 4.4 15.7 1.0 SG A:CYS301 4.4 20.1 0.9 O A:HOH761 4.4 89.0 1.0 CE2 A:TYR299 4.5 24.9 1.0 CE A:LYS302 4.7 18.8 1.0 NZ A:LYS302 4.7 30.1 1.0 ND1 A:HIS295 4.8 17.5 1.0 S1 A:SF4601 4.9 130.0 0.8 CG A:TYR299 4.9 17.6 1.0 CG A:GLU449 5.0 31.6 1.0

Iron binding site 2 out of 20 in the Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:132.9 occ:0.62 FE2 A:SF4601 0.0 132.9 0.6 S1 A:SF4601 2.0 130.0 0.8 O A:HOH724 2.1 128.8 0.4 FE4 A:SF4601 2.1 125.1 1.0 FE3 A:SF4601 2.3 123.8 1.0 S3 A:SF4601 2.4 81.2 0.6 SG A:CYS301 2.5 20.1 0.9 O A:HOH761 3.0 89.0 1.0 S4 A:SF4601 3.1 124.6 1.0 SG A:CYS301 3.1 28.9 0.1 FE1 A:SF4601 3.1 99.0 0.7 O A:HOH1042 3.2 34.6 1.0 CB A:CYS301 3.5 16.5 0.9 CB A:CYS301 3.5 17.9 0.1 S2 A:SF4601 3.6 25.6 0.5 SG A:CYS107 4.3 19.9 0.6 NZ A:LYS302 4.5 30.1 1.0 SG A:CYS103 4.5 18.1 0.6 CE A:LYS302 4.6 18.8 1.0 CZ A:PHE104 4.6 20.5 1.0 CA A:CYS103 4.8 21.5 0.6 CA A:CYS103 4.8 21.4 0.4 CB A:CYS103 4.9 23.4 0.6 O A:SER298 4.9 14.7 1.0 CB A:CYS103 4.9 23.4 0.4 CE2 A:PHE104 4.9 18.9 1.0 CE1 A:PHE104 4.9 21.6 1.0 CA A:CYS301 4.9 13.2 0.9 CA A:CYS301 5.0 14.5 0.1 SG A:CYS107 5.0 23.1 0.4

Iron binding site 3 out of 20 in the Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:123.8 occ:1.00 FE3 A:SF4601 0.0 123.8 1.0 O A:HOH724 2.1 128.8 0.4 S4 A:SF4601 2.3 124.6 1.0 FE2 A:SF4601 2.3 132.9 0.6 SG A:CYS103 2.4 18.1 0.6 S2 A:SF4601 2.4 25.6 0.5 S1 A:SF4601 2.6 130.0 0.8 FE4 A:SF4601 2.8 125.1 1.0 FE1 A:SF4601 3.1 99.0 0.7 O A:HOH1081 3.1 27.9 0.4 O A:HOH1081 3.2 38.0 0.6 CB A:CYS103 3.3 23.4 0.6 CB A:CYS103 3.3 23.4 0.4 CA A:CYS103 3.8 21.5 0.6 CA A:CYS103 3.8 21.4 0.4 S3 A:SF4601 3.9 81.2 0.6 SG A:CYS103 3.9 41.8 0.4 O A:HOH1042 4.0 34.6 1.0 N A:GLN105 4.3 19.9 1.0 N A:PHE104 4.4 20.2 1.0 C A:CYS103 4.4 23.5 0.6 C A:CYS103 4.4 23.4 0.4 CA A:GLN105 4.7 20.7 1.0 SG A:CYS301 4.7 20.1 0.9 NZ A:LYS302 4.7 30.1 1.0 OE1 A:GLU449 4.8 31.1 1.0 O A:HOH761 4.9 89.0 1.0 CG2 A:THR194 4.9 20.1 1.0 O A:HOH724 5.0 20.8 0.6 FE A:FE607 5.0 19.5 0.7 SG A:CYS301 5.0 28.9 0.1

Iron binding site 4 out of 20 in the Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:125.1 occ:1.00 FE4 A:SF4601 0.0 125.1 1.0 FE2 A:SF4601 2.1 132.9 0.6 SG A:CYS107 2.4 19.9 0.6 S2 A:SF4601 2.4 25.6 0.5 S1 A:SF4601 2.5 130.0 0.8 O A:HOH761 2.6 89.0 1.0 S3 A:SF4601 2.7 81.2 0.6 FE3 A:SF4601 2.8 123.8 1.0 CB A:CYS107 3.1 23.8 0.6 CB A:CYS107 3.1 23.1 0.4 SG A:CYS107 3.2 23.1 0.4 FE1 A:SF4601 3.8 99.0 0.7 O A:HOH724 3.9 128.8 0.4 CE1 A:PHE104 4.0 21.6 1.0 SG A:CYS301 4.1 20.1 0.9 N A:CYS107 4.2 20.7 0.6 N A:CYS107 4.2 20.1 0.4 CA A:CYS107 4.2 18.4 0.6 CA A:CYS107 4.2 19.0 0.4 CZ A:PHE104 4.3 20.5 1.0 CD1 A:PHE104 4.4 22.7 1.0 S4 A:SF4601 4.4 124.6 1.0 CB A:CYS301 4.5 16.5 0.9 CB A:CYS301 4.5 17.9 0.1 SG A:CYS301 4.5 28.9 0.1 N A:GLN105 4.6 19.9 1.0 SG A:CYS103 4.8 18.1 0.6 CE1 A:HIS295 4.9 21.1 1.0

Iron binding site 5 out of 20 in the Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe607 b:19.5 occ:0.72 OH A:TYR299 2.1 26.8 1.0 OE2 A:GLU449 2.1 27.1 1.0 NE2 A:HIS295 2.3 19.0 1.0 FE1 A:SF4601 2.4 99.0 0.7 CZ A:TYR299 3.0 26.0 1.0 CD2 A:HIS295 3.1 15.7 1.0 CD A:GLU449 3.2 28.5 1.0 CE1 A:HIS295 3.4 21.1 1.0 CE1 A:TYR299 3.5 27.1 1.0 OE1 A:GLU449 3.6 31.1 1.0 S4 A:SF4601 3.8 124.6 1.0 CE2 A:TYR299 3.9 24.9 1.0 CA A:GLY453 4.0 19.5 1.0 O A:HOH1081 4.2 27.9 0.4 CG A:HIS295 4.3 15.5 1.0 ND1 A:HIS295 4.4 17.5 1.0 C A:GLY453 4.4 13.7 1.0 S3 A:SF4601 4.4 81.2 0.6 CG A:GLU449 4.5 31.6 1.0 N A:ALA454 4.6 18.2 1.0 CD1 A:TYR299 4.7 22.4 1.0 S2 A:SF4601 4.8 25.6 0.5 FE3 A:SF4601 5.0 123.8 1.0 CG2 A:VAL108 5.0 24.2 1.0

Iron binding site 6 out of 20 in the Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:142.8 occ:0.61 FE1 B:SF4601 0.0 142.8 0.6 S4 B:SF4601 1.7 143.3 1.0 S3 B:SF4601 2.4 227.6 0.7 FE B:FE604 2.6 18.9 0.7 FE2 B:SF4601 2.7 225.9 1.0 FE3 B:SF4601 3.0 223.5 1.0 OE1 B:GLU449 3.1 37.7 1.0 S2 B:SF4601 3.3 223.4 1.0 CE1 B:TYR299 3.3 27.1 1.0 OE2 B:GLU449 3.5 32.9 1.0 FE4 B:SF4601 3.5 223.9 1.0 CD B:GLU449 3.6 33.3 1.0 NE2 B:HIS295 3.6 18.8 1.0 CZ B:TYR299 3.7 23.1 1.0 OH B:TYR299 3.8 25.6 1.0 O B:HOH904 3.9 74.5 1.0 CE1 B:HIS295 3.9 18.1 1.0 CD1 B:TYR299 4.0 17.2 1.0 SG B:CYS301 4.2 23.9 1.0 S1 B:SF4601 4.2 224.6 1.0 O B:HOH985 4.2 74.0 1.0 O B:HOH905 4.3 229.5 1.0 CE B:LYS302 4.5 19.9 1.0 NZ B:LYS302 4.5 36.1 1.0 CE2 B:TYR299 4.6 21.1 1.0 CD2 B:HIS295 4.7 17.4 1.0 CG B:TYR299 4.8 16.0 1.0 CG B:GLU449 4.9 25.4 1.0

Iron binding site 7 out of 20 in the Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:225.9 occ:1.00 FE2 B:SF4601 0.0 225.9 1.0 FE4 B:SF4601 1.8 223.9 1.0 S1 B:SF4601 1.8 224.6 1.0 S3 B:SF4601 2.0 227.6 0.7 FE3 B:SF4601 2.0 223.5 1.0 S4 B:SF4601 2.6 143.3 1.0 FE1 B:SF4601 2.7 142.8 0.6 SG B:CYS301 2.7 23.9 1.0 O B:HOH905 2.8 229.5 1.0 S2 B:SF4601 2.8 223.4 1.0 O B:HOH1052 3.5 33.5 1.0 CB B:CYS301 3.7 14.5 1.0 SG B:CYS107 4.3 28.9 1.0 SG B:CYS103 4.4 16.7 0.5 O B:HOH904 4.5 74.5 1.0 CB B:CYS107 4.7 23.2 1.0 NZ B:LYS302 4.7 36.1 1.0 CZ B:PHE104 4.8 21.6 1.0 CE B:LYS302 4.8 19.9 1.0 O B:SER298 4.8 15.5 1.0 CB B:CYS103 4.9 28.5 0.5 CB B:CYS103 4.9 28.9 0.5 CA B:CYS103 4.9 22.1 0.5 CA B:CYS103 4.9 21.8 0.5 CE1 B:PHE104 5.0 21.1 1.0 OE1 B:GLU449 5.0 37.7 1.0

Iron binding site 8 out of 20 in the Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:223.5 occ:1.00 FE3 B:SF4601 0.0 223.5 1.0 S2 B:SF4601 1.5 223.4 1.0 S1 B:SF4601 1.9 224.6 1.0 FE2 B:SF4601 2.0 225.9 1.0 FE4 B:SF4601 2.1 223.9 1.0 S4 B:SF4601 2.6 143.3 1.0 SG B:CYS103 2.6 16.7 0.5 FE1 B:SF4601 3.0 142.8 0.6 O B:HOH985 3.4 74.0 1.0 S3 B:SF4601 3.4 227.6 0.7 O B:HOH904 3.6 74.5 1.0 CB B:CYS103 3.6 28.5 0.5 CB B:CYS103 3.6 28.9 0.5 CA B:CYS103 4.0 22.1 0.5 CA B:CYS103 4.0 21.8 0.5 N B:GLN105 4.1 18.0 1.0 O B:HOH1052 4.4 33.5 1.0 N B:PHE104 4.4 20.1 1.0 O B:HOH905 4.4 229.5 1.0 CA B:GLN105 4.5 16.4 1.0 C B:CYS103 4.5 18.3 1.0 SG B:CYS103 4.6 47.8 0.5 SG B:CYS301 4.7 23.9 1.0 CB B:CYS107 4.9 23.2 1.0 OE1 B:GLU449 5.0 37.7 1.0 SG B:CYS107 5.0 28.9 1.0 CG2 B:THR194 5.0 21.2 1.0

Iron binding site 9 out of 20 in the Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:223.9 occ:1.00 FE4 B:SF4601 0.0 223.9 1.0 FE2 B:SF4601 1.8 225.9 1.0 S1 B:SF4601 1.9 224.6 1.0 S2 B:SF4601 1.9 223.4 1.0 FE3 B:SF4601 2.1 223.5 1.0 S3 B:SF4601 2.3 227.6 0.7 O B:HOH905 2.6 229.5 1.0 SG B:CYS107 2.9 28.9 1.0 CB B:CYS107 3.1 23.2 1.0 FE1 B:SF4601 3.5 142.8 0.6 S4 B:SF4601 3.9 143.3 1.0 SG B:CYS301 4.2 23.9 1.0 CE1 B:PHE104 4.2 21.1 1.0 N B:CYS107 4.2 22.4 1.0 CA B:CYS107 4.3 20.0 1.0 SG B:CYS103 4.5 16.7 0.5 N B:GLN105 4.5 18.0 1.0 CZ B:PHE104 4.5 21.6 1.0 CD1 B:PHE104 4.5 22.9 1.0 CB B:CYS301 4.7 14.5 1.0 CE1 B:HIS295 4.8 18.1 1.0 CA B:GLN105 4.9 16.4 1.0 O B:HOH1052 5.0 33.5 1.0 N B:PHE104 5.0 20.1 1.0

Iron binding site 10 out of 20 in the Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Oxygen Tolerant Archeal 4HYDROXYBUTYRYLCOA Dehydratase (4HBD) From N. Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe604 b:18.9 occ:0.68 OE2 B:GLU449 2.1 32.9 1.0 OH B:TYR299 2.1 25.6 1.0 NE2 B:HIS295 2.3 18.8 1.0 FE1 B:SF4601 2.6 142.8 0.6 CZ B:TYR299 3.0 23.1 1.0 CD2 B:HIS295 3.1 17.4 1.0 CD B:GLU449 3.1 33.3 1.0 CE1 B:HIS295 3.4 18.1 1.0 OE1 B:GLU449 3.5 37.7 1.0 CE1 B:TYR299 3.5 27.1 1.0 S4 B:SF4601 3.7 143.3 1.0 CE2 B:TYR299 3.9 21.1 1.0 CA B:GLY453 4.0 15.0 1.0 CG B:HIS295 4.3 16.2 1.0 C B:GLY453 4.4 12.9 1.0 ND1 B:HIS295 4.4 17.2 1.0 CG B:GLU449 4.4 25.4 1.0 S3 B:SF4601 4.5 227.6 0.7 N B:ALA454 4.6 18.3 1.0 CD1 B:TYR299 4.7 17.2 1.0 O B:HOH985 4.7 74.0 1.0 S2 B:SF4601 4.8 223.4 1.0 O B:GLY453 5.0 15.7 1.0 O B:HOH904 5.0 74.5 1.0 CD2 B:TYR299 5.0 20.6 1.0

H.Demirci, S.Wakatsuki. Structural Adaptation of Oxygen Tolerance in A Key Archaeal Carbon Fixation Enzyme To Be Published.