Iron in PDB 8pmk: Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound

The structure of Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound also contains other interesting chemical elements:

Potassium

(K)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound (pdb code 8pmk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 18 binding sites of Iron where determined in the Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound, PDB code: 8pmk:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 18 in the Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound


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 Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:120.9 occ:1.00 ND1 A:HIS166 2.0 77.5 1.0 OE1 A:GLU235 2.1 96.3 1.0 ND1 A:HIS189 2.1 82.0 1.0 O9 A:BYN601 2.2 103.2 1.0 OE2 A:GLU235 2.6 99.0 1.0 CD A:GLU235 2.6 95.6 1.0 CE1 A:HIS166 2.7 79.3 1.0 O10 A:BYN601 2.8 80.2 1.0 CG A:HIS189 3.0 80.2 1.0 P1 A:BYN601 3.0 90.5 1.0 CB A:HIS189 3.1 79.8 1.0 CG A:HIS166 3.2 77.8 1.0 CE1 A:HIS189 3.3 77.9 1.0 O8 A:BYN601 3.5 93.3 1.0 CB A:HIS166 3.8 80.8 1.0 NE2 A:HIS166 3.9 78.9 1.0 O A:ILE167 4.0 83.4 1.0 K A:K605 4.1 103.1 1.0 CG A:GLU235 4.1 86.9 1.0 CD2 A:HIS189 4.2 77.2 1.0 CD2 A:HIS166 4.2 80.0 1.0 NE2 A:HIS189 4.3 79.4 1.0 CA A:HIS166 4.3 82.9 1.0 N A:ILE167 4.3 86.0 1.0 O7 A:BYN601 4.4 94.0 1.0 CA A:HIS189 4.5 73.9 1.0 CZ A:PHE161 4.6 88.9 1.0 C A:ILE167 4.6 79.5 1.0 C A:HIS166 4.7 88.5 1.0 O A:ALA222 4.8 94.5 1.0 CB A:GLU235 5.0 82.4 1.0

Iron binding site 2 out of 18 in the Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound


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 Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:128.4 occ:1.00 OD2 A:ASP436 2.2 90.8 1.0 O A:ASP476 2.6 80.7 1.0 O A:THR478 2.6 72.8 1.0 OG F:SER465 2.6 140.3 1.0 O A:ARG430 2.6 77.7 1.0 CG A:ASP436 3.4 83.8 1.0 C A:ASP476 3.6 61.2 1.0 N A:THR478 3.7 48.8 1.0 CB F:SER465 3.7 142.9 1.0 C A:THR478 3.8 64.1 1.0 C A:ARG430 3.9 64.3 1.0 C A:ALA477 4.0 56.1 1.0 CA A:ALA477 4.1 52.8 1.0 OD1 A:ASP436 4.2 85.2 1.0 N A:ALA477 4.3 45.1 1.0 CG A:ASP476 4.3 74.3 1.0 CB A:ASP436 4.3 72.6 1.0 CA A:THR478 4.3 55.4 1.0 OD1 A:ASP476 4.4 78.8 1.0 CB A:ASP476 4.5 65.8 1.0 OG1 A:THR478 4.5 64.0 1.0 CA A:VAL431 4.6 60.0 1.0 OD2 A:ASP476 4.6 79.2 1.0 CA A:ASP476 4.7 50.1 1.0 N A:VAL431 4.7 61.6 1.0 CB A:ARG430 4.7 54.4 1.0 O A:ALA477 4.8 70.5 1.0 CA A:ARG430 4.8 56.6 1.0 N A:VAL479 4.9 71.5 1.0 N A:ASN432 4.9 70.3 1.0 N F:SER465 5.0 140.9 1.0 CA F:SER465 5.0 143.3 1.0

Iron binding site 3 out of 18 in the Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound


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 Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe604 b:124.3 occ:1.00 O A:ILE366 2.3 83.9 1.0 OG1 A:THR342 2.3 101.7 1.0 OE2 A:GLU346 2.6 84.3 1.0 O A:THR342 3.5 92.7 1.0 CB A:THR342 3.5 91.9 1.0 C A:ILE366 3.5 61.8 1.0 CD A:GLU346 3.8 81.8 1.0 C A:THR342 4.0 83.9 1.0 O A:ALA338 4.1 105.4 1.0 OD1 A:ASN339 4.2 95.5 1.0 CB A:ILE366 4.3 53.6 1.0 CA A:ILE366 4.3 48.8 1.0 CA A:THR342 4.4 83.7 1.0 N A:PRO367 4.5 63.5 1.0 CA A:PRO367 4.5 73.6 1.0 CG2 A:THR342 4.5 90.0 1.0 OE1 A:GLU346 4.6 85.1 1.0 N A:ILE366 4.6 52.1 1.0 C A:PRO367 4.6 77.1 1.0 O A:PRO367 4.6 85.3 1.0 CG A:GLU346 4.8 77.5 1.0 OG A:SER343 4.8 77.9 1.0 C A:ALA338 4.8 98.5 1.0 N A:SER343 4.8 76.4 1.0 CE1 A:HIS365 4.8 62.9 1.0 CG2 A:ILE366 4.9 54.7 1.0 CA A:ASN339 4.9 86.6 1.0 NH2 A:ARG96 5.0 87.5 1.0

Iron binding site 4 out of 18 in the Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound


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 Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe602 b:120.9 occ:1.00 ND1 B:HIS166 2.0 77.5 1.0 OE1 B:GLU235 2.1 96.3 1.0 ND1 B:HIS189 2.1 82.0 1.0 O9 B:BYN601 2.2 103.2 1.0 OE2 B:GLU235 2.6 99.0 1.0 CD B:GLU235 2.6 95.6 1.0 CE1 B:HIS166 2.7 79.3 1.0 O10 B:BYN601 2.8 80.2 1.0 CG B:HIS189 2.9 80.2 1.0 P1 B:BYN601 3.0 90.5 1.0 CB B:HIS189 3.1 79.8 1.0 CG B:HIS166 3.2 77.8 1.0 CE1 B:HIS189 3.3 77.9 1.0 O8 B:BYN601 3.5 93.3 1.0 CB B:HIS166 3.8 80.8 1.0 NE2 B:HIS166 3.9 78.9 1.0 O B:ILE167 4.0 83.4 1.0 K B:K605 4.1 103.1 1.0 CG B:GLU235 4.1 86.9 1.0 CD2 B:HIS189 4.2 77.2 1.0 CD2 B:HIS166 4.2 80.0 1.0 NE2 B:HIS189 4.3 79.4 1.0 CA B:HIS166 4.3 82.9 1.0 N B:ILE167 4.3 86.0 1.0 O7 B:BYN601 4.4 94.0 1.0 CA B:HIS189 4.5 73.9 1.0 CZ B:PHE161 4.6 88.9 1.0 C B:ILE167 4.6 79.5 1.0 C B:HIS166 4.7 88.5 1.0 O B:ALA222 4.8 94.5 1.0 CB B:GLU235 5.0 82.4 1.0

Iron binding site 5 out of 18 in the Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound


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 Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe603 b:128.4 occ:1.00 OD2 B:ASP436 2.2 90.8 1.0 O B:ASP476 2.6 80.7 1.0 O B:THR478 2.6 72.8 1.0 O B:ARG430 2.6 77.7 1.0 OG C:SER465 2.7 140.3 1.0 CG B:ASP436 3.4 83.8 1.0 C B:ASP476 3.6 61.2 1.0 N B:THR478 3.7 48.8 1.0 C B:THR478 3.8 64.1 1.0 CB C:SER465 3.8 142.9 1.0 C B:ARG430 3.9 64.3 1.0 C B:ALA477 4.0 56.1 1.0 CA B:ALA477 4.1 52.8 1.0 OD1 B:ASP436 4.2 85.2 1.0 N B:ALA477 4.3 45.1 1.0 CG B:ASP476 4.3 74.3 1.0 CB B:ASP436 4.3 72.6 1.0 CA B:THR478 4.3 55.4 1.0 OD1 B:ASP476 4.4 78.8 1.0 CB B:ASP476 4.5 65.8 1.0 OG1 B:THR478 4.5 64.0 1.0 CA B:VAL431 4.6 60.0 1.0 OD2 B:ASP476 4.6 79.2 1.0 CA B:ASP476 4.7 50.1 1.0 N B:VAL431 4.7 61.6 1.0 CB B:ARG430 4.7 54.4 1.0 O B:ALA477 4.8 70.5 1.0 CA B:ARG430 4.8 56.6 1.0 N B:VAL479 4.9 71.5 1.0 N B:ASN432 4.9 70.3 1.0 N C:SER465 5.0 140.9 1.0

Iron binding site 6 out of 18 in the Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound


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 Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe604 b:124.3 occ:1.00 O B:ILE366 2.3 83.9 1.0 OG1 B:THR342 2.3 101.7 1.0 OE2 B:GLU346 2.6 84.3 1.0 O B:THR342 3.5 92.7 1.0 CB B:THR342 3.5 91.9 1.0 C B:ILE366 3.5 61.8 1.0 CD B:GLU346 3.8 81.8 1.0 C B:THR342 4.0 83.9 1.0 O B:ALA338 4.1 105.4 1.0 OD1 B:ASN339 4.2 95.5 1.0 CB B:ILE366 4.3 53.6 1.0 CA B:ILE366 4.4 48.8 1.0 CA B:THR342 4.4 83.7 1.0 N B:PRO367 4.5 63.5 1.0 CA B:PRO367 4.5 73.6 1.0 CG2 B:THR342 4.5 90.0 1.0 OE1 B:GLU346 4.6 85.1 1.0 N B:ILE366 4.6 52.1 1.0 C B:PRO367 4.6 77.1 1.0 O B:PRO367 4.6 85.3 1.0 CG B:GLU346 4.8 77.5 1.0 OG B:SER343 4.8 77.9 1.0 C B:ALA338 4.8 98.5 1.0 N B:SER343 4.8 76.4 1.0 CE1 B:HIS365 4.8 62.9 1.0 CG2 B:ILE366 4.9 54.7 1.0 CA B:ASN339 4.9 86.6 1.0 NH2 B:ARG96 5.0 87.5 1.0

Iron binding site 7 out of 18 in the Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound


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 Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe602 b:120.9 occ:1.00 ND1 C:HIS166 2.0 77.5 1.0 OE1 C:GLU235 2.1 96.3 1.0 ND1 C:HIS189 2.1 82.0 1.0 O9 C:BYN601 2.2 103.2 1.0 OE2 C:GLU235 2.6 99.0 1.0 CD C:GLU235 2.6 95.6 1.0 CE1 C:HIS166 2.7 79.3 1.0 O10 C:BYN601 2.8 80.2 1.0 P1 C:BYN601 3.0 90.5 1.0 CG C:HIS189 3.0 80.2 1.0 CB C:HIS189 3.1 79.8 1.0 CG C:HIS166 3.2 77.8 1.0 CE1 C:HIS189 3.3 77.9 1.0 O8 C:BYN601 3.5 93.3 1.0 CB C:HIS166 3.8 80.8 1.0 NE2 C:HIS166 3.9 78.9 1.0 O C:ILE167 4.0 83.4 1.0 K C:K605 4.1 103.1 1.0 CG C:GLU235 4.1 86.9 1.0 CD2 C:HIS189 4.2 77.2 1.0 CD2 C:HIS166 4.2 80.0 1.0 NE2 C:HIS189 4.3 79.4 1.0 CA C:HIS166 4.3 82.9 1.0 N C:ILE167 4.3 86.0 1.0 O7 C:BYN601 4.4 94.0 1.0 CA C:HIS189 4.5 73.9 1.0 CZ C:PHE161 4.6 88.9 1.0 C C:ILE167 4.6 79.5 1.0 C C:HIS166 4.7 88.5 1.0 O C:ALA222 4.8 94.5 1.0 CB C:GLU235 5.0 82.4 1.0

Iron binding site 8 out of 18 in the Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound


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 Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe603 b:128.4 occ:1.00 OD2 C:ASP436 2.2 90.8 1.0 O C:ASP476 2.6 80.7 1.0 O C:THR478 2.6 72.8 1.0 O C:ARG430 2.6 77.7 1.0 OG B:SER465 2.7 140.3 1.0 CG C:ASP436 3.4 83.8 1.0 C C:ASP476 3.6 61.2 1.0 N C:THR478 3.7 48.8 1.0 C C:THR478 3.8 64.1 1.0 CB B:SER465 3.8 142.9 1.0 C C:ARG430 3.9 64.3 1.0 C C:ALA477 4.0 56.1 1.0 CA C:ALA477 4.1 52.8 1.0 OD1 C:ASP436 4.2 85.2 1.0 N C:ALA477 4.3 45.1 1.0 CG C:ASP476 4.3 74.3 1.0 CB C:ASP436 4.3 72.6 1.0 CA C:THR478 4.3 55.4 1.0 OD1 C:ASP476 4.4 78.8 1.0 CB C:ASP476 4.5 65.8 1.0 OG1 C:THR478 4.5 64.0 1.0 CA C:VAL431 4.6 60.0 1.0 OD2 C:ASP476 4.6 79.2 1.0 CA C:ASP476 4.7 50.1 1.0 N C:VAL431 4.7 61.6 1.0 CB C:ARG430 4.7 54.4 1.0 O C:ALA477 4.8 70.5 1.0 CA C:ARG430 4.8 56.6 1.0 N C:VAL479 4.9 71.5 1.0 N C:ASN432 4.9 70.3 1.0

Iron binding site 9 out of 18 in the Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound


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 Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe604 b:124.3 occ:1.00 O C:ILE366 2.3 83.9 1.0 OG1 C:THR342 2.3 101.7 1.0 OE2 C:GLU346 2.6 84.3 1.0 O C:THR342 3.5 92.7 1.0 CB C:THR342 3.5 91.9 1.0 C C:ILE366 3.5 61.8 1.0 CD C:GLU346 3.8 81.8 1.0 C C:THR342 4.0 83.9 1.0 O C:ALA338 4.1 105.4 1.0 OD1 C:ASN339 4.2 95.5 1.0 CB C:ILE366 4.3 53.6 1.0 CA C:ILE366 4.4 48.8 1.0 CA C:THR342 4.4 83.7 1.0 N C:PRO367 4.5 63.5 1.0 CA C:PRO367 4.5 73.6 1.0 CG2 C:THR342 4.5 90.0 1.0 OE1 C:GLU346 4.6 85.1 1.0 N C:ILE366 4.6 52.1 1.0 C C:PRO367 4.6 77.1 1.0 O C:PRO367 4.6 85.3 1.0 CG C:GLU346 4.8 77.5 1.0 OG C:SER343 4.8 77.9 1.0 C C:ALA338 4.8 98.5 1.0 N C:SER343 4.8 76.4 1.0 CE1 C:HIS365 4.8 62.9 1.0 CG2 C:ILE366 4.9 54.7 1.0 CA C:ASN339 4.9 86.6 1.0 NH2 C:ARG96 5.0 87.5 1.0

Iron binding site 10 out of 18 in the Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound


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 Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe602 b:120.9 occ:1.00 ND1 D:HIS166 2.0 77.5 1.0 OE1 D:GLU235 2.1 96.3 1.0 ND1 D:HIS189 2.1 82.0 1.0 O9 D:BYN601 2.2 103.2 1.0 OE2 D:GLU235 2.6 99.0 1.0 CD D:GLU235 2.6 95.6 1.0 CE1 D:HIS166 2.7 79.3 1.0 O10 D:BYN601 2.8 80.2 1.0 CG D:HIS189 3.0 80.2 1.0 P1 D:BYN601 3.0 90.5 1.0 CB D:HIS189 3.1 79.8 1.0 CG D:HIS166 3.2 77.8 1.0 CE1 D:HIS189 3.3 77.9 1.0 O8 D:BYN601 3.5 93.3 1.0 CB D:HIS166 3.8 80.8 1.0 NE2 D:HIS166 3.9 78.9 1.0 O D:ILE167 4.0 83.4 1.0 K D:K605 4.1 103.1 1.0 CG D:GLU235 4.1 86.9 1.0 CD2 D:HIS189 4.2 77.2 1.0 CD2 D:HIS166 4.2 80.0 1.0 NE2 D:HIS189 4.3 79.4 1.0 CA D:HIS166 4.3 82.9 1.0 N D:ILE167 4.3 86.0 1.0 O7 D:BYN601 4.4 94.0 1.0 CA D:HIS189 4.5 73.9 1.0 CZ D:PHE161 4.6 88.9 1.0 C D:ILE167 4.6 79.5 1.0 C D:HIS166 4.7 88.5 1.0 O D:ALA222 4.8 94.5 1.0 CB D:GLU235 5.0 82.4 1.0

K.Kayastha, U.Ermler. Active Pcd Complex with Prfmn Bound To Be Published.