Iron in PDB 8ys5: Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form

All present enzymatic activity of Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form:
1.2.7.3;

The structure of Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form (pdb code 8ys5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form, PDB code: 8ys5:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in the Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:36.6 occ:1.00 FE1 D:SF4201 0.0 36.6 1.0 SG D:CYS19 2.3 34.4 1.0 S3 D:SF4201 2.3 22.5 1.0 S2 D:SF4201 2.3 30.7 1.0 S4 D:SF4201 2.3 41.2 1.0 FE2 D:SF4201 2.7 28.8 1.0 FE4 D:SF4201 2.7 51.1 1.0 FE3 D:SF4201 2.7 41.5 1.0 CB D:CYS19 3.2 21.2 1.0 CA D:CYS19 3.5 20.3 1.0 N D:LYS20 3.8 30.1 1.0 S1 D:SF4201 3.9 31.2 1.0 CB D:ALA70 4.1 19.3 1.0 N D:GLY21 4.1 20.1 1.0 C D:CYS19 4.2 24.5 1.0 CB D:ALA48 4.4 22.0 1.0 N D:CYS19 4.8 25.9 1.0 SG D:CYS25 4.8 24.0 0.8 SG D:CYS66 4.8 17.9 0.5 CA D:GLY21 4.8 20.4 1.0 SG D:CYS22 4.9 30.5 0.5 CA D:LYS20 5.0 36.0 1.0

Iron binding site 2 out of 24 in the Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:28.8 occ:1.00 FE2 D:SF4201 0.0 28.8 1.0 SG D:CYS25 2.3 24.0 0.8 S1 D:SF4201 2.3 31.2 1.0 S3 D:SF4201 2.3 22.5 1.0 S4 D:SF4201 2.3 41.2 1.0 CB D:CYS25 2.7 14.9 1.0 FE1 D:SF4201 2.7 36.6 1.0 FE4 D:SF4201 2.7 51.1 1.0 FE3 D:SF4201 2.7 41.5 1.0 S2 D:SF4201 3.9 30.7 1.0 CA D:CYS25 3.9 14.7 1.0 N D:CYS25 3.9 22.8 0.7 CB D:ALA48 4.1 22.0 1.0 CE D:MET36 4.5 29.8 1.0 SG D:CYS19 4.5 34.4 1.0 SG D:CYS22 4.7 30.5 0.5 SG D:CYS66 4.8 17.9 0.5 C D:CYS25 4.8 24.6 1.0 N D:VAL26 4.9 33.1 1.0 CB D:CYS66 5.0 19.1 1.0

Iron binding site 3 out of 24 in the Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:41.5 occ:1.00 FE3 D:SF4201 0.0 41.5 1.0 SG D:CYS66 2.3 17.9 0.5 S2 D:SF4201 2.3 30.7 1.0 S1 D:SF4201 2.3 31.2 1.0 S4 D:SF4201 2.3 41.2 1.0 FE4 D:SF4201 2.7 51.1 1.0 FE1 D:SF4201 2.7 36.6 1.0 FE2 D:SF4201 2.7 28.8 1.0 CB D:CYS66 3.1 19.1 1.0 CB D:ALA70 3.8 19.3 1.0 S3 D:SF4201 3.9 22.5 1.0 CA D:CYS66 3.9 15.9 1.0 CB D:CYS25 4.4 14.9 1.0 CD D:PRO67 4.5 19.2 1.0 C D:CYS66 4.6 18.9 1.0 CG2 D:ILE71 4.6 24.1 1.0 N D:ALA70 4.6 22.3 1.0 CA D:ALA70 4.7 10.8 1.0 SG D:CYS22 4.7 30.5 0.5 N D:ILE71 4.7 26.7 1.0 N D:PRO67 4.8 26.4 1.0 SG D:CYS25 4.8 24.0 0.8 CB D:ILE71 4.9 18.2 1.0 C D:ALA70 4.9 16.0 1.0 SG D:CYS19 4.9 34.4 1.0 N D:ASP68 4.9 21.9 0.6

Iron binding site 4 out of 24 in the Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:51.1 occ:1.00 FE4 D:SF4201 0.0 51.1 1.0 SG D:CYS22 2.3 30.5 0.5 S3 D:SF4201 2.3 22.5 1.0 S1 D:SF4201 2.3 31.2 1.0 S2 D:SF4201 2.3 30.7 1.0 FE3 D:SF4201 2.7 41.5 1.0 FE2 D:SF4201 2.7 28.8 1.0 FE1 D:SF4201 2.7 36.6 1.0 N D:CYS22 3.7 21.7 1.0 CB D:CYS22 3.7 15.5 1.0 S4 D:SF4201 3.9 41.2 1.0 CA D:CYS22 4.2 20.4 1.0 CD D:PRO67 4.3 19.2 1.0 N D:ASP23 4.4 28.0 1.0 OD2 D:ASP68 4.5 33.3 1.0 N D:GLY21 4.5 20.1 1.0 SG D:CYS66 4.6 17.9 0.5 C D:CYS22 4.6 28.7 1.0 SG D:CYS19 4.7 34.4 1.0 CB D:CYS25 4.7 14.9 1.0 N D:CYS25 4.7 22.8 0.7 SG D:CYS25 4.7 24.0 0.8 C D:GLY21 4.8 27.9 1.0 N D:ILE24 4.8 22.8 1.0 CA D:GLY21 4.9 20.4 1.0

Iron binding site 5 out of 24 in the Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe202 b:39.7 occ:1.00 FE1 D:SF4202 0.0 39.7 1.0 SG D:CYS59 2.3 37.9 0.5 S2 D:SF4202 2.3 36.2 1.0 S4 D:SF4202 2.3 60.0 1.0 S3 D:SF4202 2.3 39.5 1.0 FE3 D:SF4202 2.7 51.6 1.0 FE2 D:SF4202 2.7 57.8 1.0 FE4 D:SF4202 2.7 50.9 1.0 O D:CYS59 2.8 36.2 1.0 O D:ILE57 3.4 36.7 1.0 CB D:CYS59 3.6 31.5 1.0 C D:CYS59 3.7 31.9 1.0 S1 D:SF4202 3.9 64.6 1.0 CA D:CYS59 4.0 32.8 1.0 N D:CYS59 4.0 41.2 1.0 C D:ILE57 4.3 41.9 1.0 N D:ILE57 4.4 37.0 1.0 CD D:PRO30 4.5 34.3 1.0 SG D:CYS56 4.6 35.9 0.5 SG D:CYS62 4.6 30.2 0.7 CB D:ILE57 4.7 30.2 1.0 SG D:CYS29 4.7 40.3 0.7 CA D:ILE57 4.7 37.5 1.0 N D:VAL60 4.8 25.5 1.0

Iron binding site 6 out of 24 in the Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe202 b:57.8 occ:1.00 FE2 D:SF4202 0.0 57.8 1.0 SG D:CYS56 2.3 35.9 0.5 S3 D:SF4202 2.3 39.5 1.0 S4 D:SF4202 2.3 60.0 1.0 S1 D:SF4202 2.3 64.6 1.0 FE1 D:SF4202 2.7 39.7 1.0 FE4 D:SF4202 2.7 50.9 1.0 FE3 D:SF4202 2.7 51.6 1.0 CB D:CYS56 3.6 39.6 1.0 O D:ILE57 3.6 36.7 1.0 N D:ILE57 3.8 37.0 1.0 S2 D:SF4202 3.9 36.2 1.0 CA D:CYS56 4.0 39.9 1.0 CG1 D:VAL12 4.4 33.2 0.7 C D:CYS56 4.4 39.1 1.0 C D:ILE57 4.6 41.9 1.0 SG D:CYS59 4.8 37.9 0.5 SG D:CYS62 4.8 30.2 0.7 CB D:VAL12 4.8 24.8 1.0 CA D:ILE57 4.8 37.5 1.0 SG D:CYS29 4.8 40.3 0.7 O D:CYS59 4.9 36.2 1.0 CB D:VAL33 4.9 22.8 1.0 CG2 D:VAL33 4.9 34.0 1.0

Iron binding site 7 out of 24 in the Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe202 b:51.6 occ:1.00 FE3 D:SF4202 0.0 51.6 1.0 SG D:CYS29 2.3 40.3 0.7 S2 D:SF4202 2.3 36.2 1.0 S4 D:SF4202 2.3 60.0 1.0 S1 D:SF4202 2.3 64.6 1.0 FE1 D:SF4202 2.7 39.7 1.0 FE4 D:SF4202 2.7 50.9 1.0 FE2 D:SF4202 2.7 57.8 1.0 CB D:CYS29 3.4 23.5 1.0 S3 D:SF4202 3.9 39.5 1.0 CA D:CYS29 3.9 21.6 1.0 CB D:VAL33 4.3 22.8 1.0 SG D:CYS59 4.5 37.9 0.5 CD1 D:LEU34 4.5 16.4 1.0 C D:CYS29 4.6 29.1 1.0 CG2 D:VAL33 4.7 34.0 1.0 CD D:PRO30 4.8 34.3 1.0 N D:PRO30 4.8 29.9 1.0 SG D:CYS62 4.8 30.2 0.7 N D:ALA31 4.8 26.9 1.0 CB D:ALA31 4.8 34.0 0.5 SG D:CYS56 4.9 35.9 0.5 N D:VAL33 4.9 35.4 1.0 CG D:LEU34 4.9 20.3 1.0 CG1 D:VAL33 5.0 24.5 1.0

Iron binding site 8 out of 24 in the Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe202 b:50.9 occ:1.00 FE4 D:SF4202 0.0 50.9 1.0 SG D:CYS62 2.3 30.2 0.7 S3 D:SF4202 2.3 39.5 1.0 S2 D:SF4202 2.3 36.2 1.0 S1 D:SF4202 2.3 64.6 1.0 FE1 D:SF4202 2.7 39.7 1.0 FE3 D:SF4202 2.7 51.6 1.0 FE2 D:SF4202 2.7 57.8 1.0 CB D:CYS62 3.2 27.0 1.0 O D:CYS59 3.8 36.2 1.0 S4 D:SF4202 3.9 60.0 1.0 N D:CYS62 4.4 18.6 1.0 CA D:CYS62 4.4 21.0 1.0 CG2 D:VAL73 4.7 29.6 1.0 CD1 D:LEU34 4.7 16.4 1.0 SG D:CYS29 4.7 40.3 0.7 SG D:CYS56 4.7 35.9 0.5 SG D:CYS59 4.9 37.9 0.5 C D:CYS59 4.9 31.9 1.0

Iron binding site 9 out of 24 in the Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:18.6 occ:1.00 FE1 C:SF4301 0.0 18.6 1.0 SG C:CYS19 2.3 37.6 1.0 S4 C:SF4301 2.3 37.0 1.0 S3 C:SF4301 2.3 28.7 1.0 S2 C:SF4301 2.3 37.0 1.0 FE4 C:SF4301 2.7 42.3 1.0 FE2 C:SF4301 2.7 50.5 1.0 FE3 C:SF4301 2.7 38.7 1.0 CB C:CYS19 3.3 29.5 1.0 S1 C:SF4301 3.9 27.3 1.0 O C:TRP18 3.9 22.4 0.0 N C:CYS19 4.2 27.8 1.0 C C:TRP18 4.2 24.9 0.5 CA C:CYS19 4.2 33.5 1.0 CB C:ILE204 4.5 9.1 1.0 CG1 C:ILE204 4.5 7.4 1.0 CB C:CYS22 4.5 23.2 1.0 CB B:VAL43 4.6 27.9 1.0 CG1 B:VAL43 4.7 26.1 1.0 SG C:CYS22 4.8 38.9 1.0 SG C:CYS53 4.8 27.6 1.0 SG C:CYS202 4.8 17.5 1.0 CG2 B:VAL43 4.9 22.8 1.0

Iron binding site 10 out of 24 in the Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:50.5 occ:1.00 FE2 C:SF4301 0.0 50.5 1.0 SG C:CYS22 2.3 38.9 1.0 S4 C:SF4301 2.3 37.0 1.0 S3 C:SF4301 2.3 28.7 1.0 S1 C:SF4301 2.3 27.3 1.0 FE4 C:SF4301 2.7 42.3 1.0 FE3 C:SF4301 2.7 38.7 1.0 FE1 C:SF4301 2.7 18.6 1.0 CB C:CYS22 2.8 23.2 1.0 S2 C:SF4301 3.9 37.0 1.0 CA C:CYS22 4.1 18.1 1.0 OD2 C:ASP24 4.5 15.0 1.0 O C:ASN201 4.6 26.5 1.0 SG C:CYS53 4.6 27.6 1.0 SG C:CYS202 4.7 17.5 1.0 CB C:TRP18 4.7 13.2 1.0 SG C:CYS19 4.7 37.6 1.0 CD1 C:TRP18 4.8 19.8 1.0 CB C:CYS19 4.9 29.5 1.0 CB C:CYS202 5.0 16.5 1.0 C C:CYS22 5.0 17.9 1.0 CA C:CYS202 5.0 12.6 1.0

W.Lan, Y.Gao, H.Bi. Cryo-Em Structure of the Helicobacter Pylori Oordabc Complex in the Apo-Form To Be Published.