Iron in PDB 4y0e: X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus

The structure of X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus, PDB code: 4y0e was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.40 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	103.900, 92.980, 136.980, 90.00, 96.11, 90.00
R / Rfree (%)	16 / 19.5

The binding sites of Iron atom in the X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus (pdb code 4y0e). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus, PDB code: 4y0e:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:33.8 occ:1.00 NE2 A:HIS262 2.0 29.9 1.0 NE2 A:HIS104 2.1 25.5 1.0 OD1 A:ASP106 2.2 36.3 1.0 O A:HOH671 2.2 41.0 1.0 O A:HOH670 2.3 31.5 1.0 CE1 A:HIS262 3.0 27.9 1.0 CD2 A:HIS262 3.0 27.7 1.0 CD2 A:HIS104 3.0 24.7 1.0 CE1 A:HIS104 3.1 28.0 1.0 CG A:ASP106 3.2 34.2 1.0 OD2 A:ASP106 3.6 33.5 1.0 NH1 A:ARG277 3.6 49.8 1.0 ND1 A:HIS262 4.0 23.3 1.0 CG A:HIS262 4.1 21.6 1.0 ND1 A:HIS104 4.1 22.8 1.0 CG A:HIS104 4.1 21.7 1.0 O1S A:EPE403 4.3 98.1 1.0 C10 A:EPE403 4.3 96.4 1.0 CB A:ASP106 4.6 27.2 1.0 CA A:ASP106 4.8 24.1 1.0 S A:EPE403 4.8 98.6 1.0 C6 A:EPE403 4.9 93.3 1.0 CB A:ALA100 4.9 40.8 1.0 CZ A:ARG277 5.0 50.0 1.0

Iron binding site 2 out of 8 in the X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:29.7 occ:1.00 NE2 B:HIS262 2.0 28.6 1.0 NE2 B:HIS104 2.1 20.5 1.0 OD1 B:ASP106 2.2 25.8 1.0 O B:HOH567 2.3 27.4 1.0 CE1 B:HIS262 2.8 27.3 1.0 CD2 B:HIS104 3.0 20.6 1.0 CD2 B:HIS262 3.0 24.2 1.0 CE1 B:HIS104 3.0 21.2 1.0 CG B:ASP106 3.2 28.1 1.0 OD2 B:ASP106 3.6 33.2 1.0 NH1 B:ARG277 3.8 43.2 1.0 ND1 B:HIS262 3.9 26.0 1.0 CG B:HIS262 4.1 20.1 1.0 ND1 B:HIS104 4.1 19.9 1.0 CG B:HIS104 4.1 17.3 1.0 O3S B:EPE403 4.2 96.3 1.0 C10 B:EPE403 4.4 95.7 1.0 CB B:ASP106 4.5 20.4 1.0 C6 B:EPE403 4.6 95.7 1.0 CA B:ASP106 4.8 20.0 1.0 S B:EPE403 4.8 96.7 1.0 CB B:ALA100 4.9 35.8 1.0

Iron binding site 3 out of 8 in the X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:23.1 occ:1.00 NE2 C:HIS262 1.9 24.0 1.0 NE2 C:HIS104 2.1 25.1 1.0 OD1 C:ASP106 2.2 25.7 1.0 O C:HOH794 2.2 22.5 1.0 CE1 C:HIS262 2.7 22.7 1.0 CD2 C:HIS262 3.0 22.2 1.0 CD2 C:HIS104 3.0 20.6 1.0 CE1 C:HIS104 3.0 26.0 1.0 CG C:ASP106 3.2 23.4 1.0 OD2 C:ASP106 3.5 23.9 1.0 NH1 C:ARG277 3.6 25.7 1.0 ND1 C:HIS262 3.9 22.8 1.0 CG C:HIS262 4.0 18.1 1.0 ND1 C:HIS104 4.1 20.4 1.0 CG C:HIS104 4.1 20.4 1.0 O3S C:EPE403 4.4 51.5 1.0 CB C:ASP106 4.5 12.7 1.0 C10 C:EPE403 4.6 56.6 1.0 CZ2 C:TRP255 4.6 19.1 1.0 CA C:ASP106 4.7 11.4 1.0 CZ C:ARG277 4.9 26.5 1.0 N C:ASP106 4.9 10.2 1.0

Iron binding site 4 out of 8 in the X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:25.5 occ:1.00 NE2 D:HIS262 2.0 21.7 1.0 NE2 D:HIS104 2.1 21.5 1.0 O D:HOH663 2.1 33.3 1.0 OD1 D:ASP106 2.2 27.4 1.0 O D:HOH559 2.3 22.9 1.0 CE1 D:HIS262 2.8 22.9 1.0 CD2 D:HIS104 2.9 21.4 1.0 CE1 D:HIS104 3.1 20.4 1.0 CD2 D:HIS262 3.1 20.7 1.0 CG D:ASP106 3.3 29.3 1.0 OD2 D:ASP106 3.7 34.3 1.0 NH1 D:ARG277 3.9 47.0 1.0 ND1 D:HIS262 4.0 18.6 1.0 CG D:HIS104 4.1 20.1 1.0 ND1 D:HIS104 4.1 24.5 1.0 CG D:HIS262 4.1 14.4 1.0 O1S D:EPE403 4.3 98.7 1.0 C10 D:EPE403 4.5 95.2 1.0 CB D:ASP106 4.6 20.8 1.0 C6 D:EPE403 4.8 89.7 1.0 CB D:ALA100 4.8 33.9 1.0 CA D:ASP106 4.8 17.7 1.0 S D:EPE403 4.9 98.3 1.0

Iron binding site 5 out of 8 in the X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe401 b:29.9 occ:1.00 O E:HOH706 2.0 33.1 1.0 NE2 E:HIS262 2.0 30.3 1.0 NE2 E:HIS104 2.2 23.8 1.0 OD1 E:ASP106 2.2 31.1 1.0 O E:HOH636 2.3 26.1 1.0 CE1 E:HIS262 2.8 30.1 1.0 O E:HOH670 2.9 53.4 1.0 CD2 E:HIS104 3.0 22.2 1.0 CD2 E:HIS262 3.1 25.6 1.0 CE1 E:HIS104 3.2 26.7 1.0 CG E:ASP106 3.2 31.6 1.0 OD2 E:ASP106 3.6 34.2 1.0 NH1 E:ARG277 3.6 49.1 1.0 ND1 E:HIS262 4.0 25.2 1.0 CG E:HIS262 4.1 22.9 1.0 CG E:HIS104 4.2 21.4 1.0 ND1 E:HIS104 4.2 22.4 1.0 O3S E:EPE403 4.4 87.5 1.0 C10 E:EPE403 4.5 85.6 1.0 CB E:ASP106 4.5 23.1 1.0 CA E:ASP106 4.8 20.8 1.0 CB E:ALA100 4.8 39.5 1.0 CZ E:ARG277 4.9 46.5 1.0 S E:EPE403 4.9 88.0 1.0 CZ2 E:TRP255 5.0 20.8 1.0

Iron binding site 6 out of 8 in the X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe401 b:26.7 occ:1.00 NE2 F:HIS262 1.9 27.1 1.0 NE2 F:HIS104 2.1 26.5 1.0 OD1 F:ASP106 2.1 26.4 1.0 O F:HOH560 2.2 26.9 1.0 CE1 F:HIS262 2.8 25.7 1.0 CD2 F:HIS262 3.0 24.3 1.0 CD2 F:HIS104 3.0 24.8 1.0 CE1 F:HIS104 3.1 26.6 1.0 CG F:ASP106 3.1 28.3 1.0 OD2 F:ASP106 3.5 33.3 1.0 NH1 F:ARG277 3.7 33.9 1.0 ND1 F:HIS262 3.9 23.0 1.0 CG F:HIS262 4.0 16.6 1.0 ND1 F:HIS104 4.1 23.1 1.0 CG F:HIS104 4.2 23.3 1.0 O1S F:EPE403 4.4 68.5 1.0 CB F:ASP106 4.5 17.8 1.0 C10 F:EPE403 4.6 71.1 1.0 CA F:ASP106 4.7 15.7 1.0 CZ2 F:TRP255 4.7 17.8 1.0 N F:ASP106 4.9 15.4 1.0 CZ F:ARG277 5.0 33.8 1.0

Iron binding site 7 out of 8 in the X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe401 b:38.7 occ:1.00 NE2 G:HIS262 2.0 35.9 1.0 OD1 G:ASP106 2.1 35.6 1.0 NE2 G:HIS104 2.1 29.1 1.0 O G:HOH600 2.4 38.7 1.0 CE1 G:HIS262 2.9 33.8 1.0 CE1 G:HIS104 3.0 26.2 1.0 CD2 G:HIS104 3.0 26.7 1.0 CD2 G:HIS262 3.1 29.4 1.0 CG G:ASP106 3.2 37.2 1.0 OD2 G:ASP106 3.6 40.2 1.0 NH1 G:ARG277 3.6 55.5 1.0 ND1 G:HIS262 4.0 27.1 1.0 ND1 G:HIS104 4.1 23.7 1.0 CG G:HIS262 4.1 27.2 1.0 CG G:HIS104 4.1 25.3 1.0 O3S G:EPE403 4.4 86.6 1.0 C10 G:EPE403 4.4 87.7 1.0 CB G:ASP106 4.5 31.3 1.0 CA G:ASP106 4.7 28.9 1.0 CZ2 G:TRP255 4.8 34.6 1.0 CZ G:ARG277 4.9 56.8 1.0 C6 G:EPE403 4.9 87.9 1.0 S G:EPE403 4.9 87.5 1.0 N G:ASP106 4.9 23.3 1.0

Iron binding site 8 out of 8 in the X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe401 b:30.7 occ:1.00 NE2 H:HIS262 1.9 28.4 1.0 NE2 H:HIS104 2.1 29.3 1.0 OD1 H:ASP106 2.2 30.0 1.0 O H:HOH699 2.2 42.0 1.0 O H:HOH546 2.4 26.1 1.0 CE1 H:HIS262 2.8 26.8 1.0 CD2 H:HIS262 3.0 24.8 1.0 CD2 H:HIS104 3.0 22.0 1.0 CE1 H:HIS104 3.1 27.7 1.0 CG H:ASP106 3.2 33.7 1.0 OD2 H:ASP106 3.6 35.9 1.0 NH1 H:ARG277 3.7 43.5 1.0 ND1 H:HIS262 3.9 24.0 1.0 CG H:HIS262 4.0 23.1 1.0 ND1 H:HIS104 4.1 25.4 1.0 CG H:HIS104 4.1 24.2 1.0 O2S H:EPE403 4.2 80.9 1.0 C10 H:EPE403 4.4 81.3 1.0 CB H:ASP106 4.5 22.5 1.0 CA H:ASP106 4.7 21.6 1.0 CZ2 H:TRP255 4.7 21.7 1.0 S H:EPE403 4.8 81.9 1.0 C6 H:EPE403 5.0 78.7 1.0 N H:ASP106 5.0 20.3 1.0 CZ H:ARG277 5.0 44.7 1.0

J.W.Fairman, J.Abendroth, D.Lorimer, T.E.Edwards, Ssgcid. X-Ray Crystal Structure of A Putative Dioxygenase From Mycobacterium Abscessus To Be Published.