Sodium in PDB 6fxj: Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III

The structure of Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III, PDB code: 6fxj was solved by S.Hofbauer, V.Pfanzagl, G.Mlynek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.89 / 1.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.870, 129.110, 77.920, 90.00, 105.96, 90.00
R / Rfree (%)	18.6 / 21.4

The structure of Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III also contains other interesting chemical elements:

Iron	(Fe)	5 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III (pdb code 6fxj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III, PDB code: 6fxj:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:25.0 occ:1.00 OE2 B:GLU86 2.2 25.0 0.4 O A:GLY65 2.3 25.0 1.0 O A:ILE63 2.4 22.4 1.0 O A:ALA68 2.4 22.6 1.0 HA A:ASP69 2.7 27.6 1.0 OD1 A:ASP69 2.8 34.3 1.0 O B:HOH491 3.1 34.4 1.0 CD B:GLU86 3.1 25.3 0.4 H A:GLY65 3.3 28.9 1.0 OE1 B:GLU86 3.4 25.0 0.4 C A:GLY65 3.4 23.7 1.0 N A:GLY65 3.4 24.0 1.0 C A:ALA68 3.5 21.6 1.0 C A:ILE63 3.5 21.8 1.0 CA A:ASP69 3.6 22.9 1.0 HA A:LEU64 3.6 25.6 1.0 OE2 B:GLU86 3.7 24.1 0.6 C A:LEU64 3.7 23.6 1.0 HD21 B:ASN83 3.8 37.1 1.0 CG A:ASP69 3.9 32.6 1.0 N A:ASP69 3.9 20.9 1.0 CA A:GLY65 4.0 22.5 1.0 CA A:LEU64 4.0 21.3 1.0 H A:ALA68 4.1 23.1 1.0 N A:LEU64 4.2 21.4 1.0 HB A:ILE63 4.2 26.7 1.0 CB A:ASP69 4.2 26.4 1.0 O A:LEU64 4.3 23.7 1.0 HG22 A:ILE63 4.3 25.6 1.0 HD22 B:ASN83 4.3 37.1 1.0 CD B:GLU86 4.3 25.8 0.6 HA A:GLN66 4.4 29.3 1.0 ND2 B:ASN83 4.4 30.8 1.0 HB3 A:ASP69 4.4 31.8 1.0 O A:HOH493 4.5 28.7 1.0 HA2 A:GLY65 4.5 27.1 1.0 N A:GLN66 4.5 23.7 1.0 CG B:GLU86 4.5 25.6 0.4 OE1 B:GLU86 4.5 25.6 0.6 H A:ILE63 4.6 28.5 0.7 CA A:ILE63 4.6 23.3 1.0 H A:ILE63 4.6 28.5 0.3 C A:ASP69 4.7 21.1 1.0 HG2 B:GLU86 4.7 30.8 0.4 HA3 A:GLY65 4.7 27.1 1.0 O B:HOH519 4.7 33.3 1.0 H A:ASP69 4.7 25.2 1.0 CB A:ILE63 4.8 22.2 1.0 CA A:ALA68 4.8 21.4 1.0 N A:ALA68 4.8 19.5 1.0 O A:ASP69 4.8 22.7 1.0 HG3 B:GLU86 4.8 30.8 0.4 CA A:GLN66 4.9 24.3 1.0 N A:ILE63 4.9 23.7 1.0 HB3 B:GLU86 5.0 31.4 0.6 OD2 A:ASP69 5.0 32.5 1.0 CG2 A:ILE63 5.0 21.3 1.0

Sodium binding site 2 out of 7 in the Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:22.1 occ:1.00 O C:GLY65 2.2 21.3 1.0 O C:ALA68 2.3 20.0 1.0 OE2 A:GLU86 2.4 50.2 1.0 O C:ILE63 2.4 20.7 1.0 O C:HOH401 2.7 35.3 1.0 HA C:ASP69 2.8 27.6 1.0 OD1 C:ASP69 2.8 31.4 1.0 C C:GLY65 3.3 22.0 1.0 C C:ALA68 3.4 20.0 1.0 H C:GLY65 3.4 24.4 1.0 N C:GLY65 3.4 20.4 1.0 CD A:GLU86 3.5 48.0 1.0 C C:ILE63 3.6 20.7 1.0 CA C:ASP69 3.6 23.0 1.0 C C:LEU64 3.7 20.9 1.0 HA C:LEU64 3.7 26.6 1.0 O C:HOH513 3.7 42.7 1.0 CG C:ASP69 3.9 28.3 1.0 N C:ASP69 3.9 20.7 1.0 H C:ALA68 3.9 25.3 1.0 CA C:GLY65 4.0 20.6 1.0 OE1 A:GLU86 4.0 47.8 1.0 CA C:LEU64 4.1 22.1 1.0 HG22 C:ILE63 4.2 24.2 1.0 O C:LEU64 4.2 20.6 1.0 N C:LEU64 4.2 20.8 1.0 O C:HOH493 4.2 27.9 1.0 HB C:ILE63 4.3 24.0 1.0 CB C:ASP69 4.3 24.9 1.0 HA C:GLN66 4.3 24.5 1.0 O A:HOH521 4.4 33.5 1.0 N C:GLN66 4.5 21.1 1.0 HA2 C:GLY65 4.5 24.8 1.0 OD1 A:ASN83 4.6 29.0 1.0 HB3 C:ASP69 4.6 30.0 1.0 N C:ALA68 4.6 21.0 1.0 H C:ILE63 4.6 33.7 1.0 HG2 A:GLU86 4.6 51.0 1.0 CA C:ALA68 4.6 21.0 1.0 CA C:ILE63 4.7 20.8 1.0 HA3 C:GLY65 4.7 24.8 1.0 H C:ASP69 4.7 25.0 1.0 C C:ASP69 4.7 23.5 1.0 CG A:GLU86 4.8 42.4 1.0 CB C:ILE63 4.8 20.4 1.0 CA C:GLN66 4.8 20.3 1.0 OD2 C:ASP69 4.9 27.0 1.0 O C:ASP69 4.9 25.0 1.0 O A:HOH473 4.9 42.0 1.0 CG2 C:ILE63 4.9 20.2 1.0 N C:ILE63 5.0 28.0 1.0

Sodium binding site 3 out of 7 in the Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:27.0 occ:1.00 O B:GLY65 2.3 21.2 1.0 O B:ILE63 2.3 21.2 1.0 O B:ALA68 2.5 23.3 1.0 HA B:ASP69 2.8 28.2 1.0 OD1 B:ASP69 3.1 38.6 1.0 OE1 E:GLU86 3.2 38.4 1.0 H B:GLY65 3.3 24.7 1.0 C B:GLY65 3.4 20.3 1.0 N B:GLY65 3.4 20.5 1.0 C B:ILE63 3.5 20.2 1.0 C B:ALA68 3.5 22.3 1.0 C B:LEU64 3.7 21.7 1.0 HA B:LEU64 3.7 26.5 1.0 O B:HOH476 3.7 40.9 1.0 CD E:GLU86 3.7 39.1 1.0 CA B:ASP69 3.7 23.4 1.0 OE2 E:GLU86 3.9 39.3 1.0 HD21 E:ASN83 3.9 31.7 1.0 CA B:GLY65 4.0 20.5 1.0 N B:ASP69 4.0 22.3 1.0 CA B:LEU64 4.0 22.0 1.0 H B:ALA68 4.1 26.4 1.0 CG B:ASP69 4.1 33.7 1.0 HG22 B:ILE63 4.2 23.3 1.0 N B:LEU64 4.2 20.4 1.0 HB B:ILE63 4.2 24.2 1.0 O B:LEU64 4.2 20.4 1.0 HD22 E:ASN83 4.3 31.7 1.0 HG2 E:GLU86 4.3 41.7 1.0 HA B:GLN66 4.4 25.3 1.0 ND2 E:ASN83 4.4 26.4 1.0 CB B:ASP69 4.5 27.3 1.0 H B:ILE63 4.5 25.6 0.4 HA2 B:GLY65 4.5 24.7 1.0 N B:GLN66 4.5 19.5 1.0 H B:ILE63 4.6 25.6 0.6 CA B:ILE63 4.6 20.8 1.0 O E:HOH525 4.6 28.8 1.0 CG E:GLU86 4.6 34.7 1.0 HA3 B:GLY65 4.7 24.7 1.0 C B:ASP69 4.7 22.5 1.0 O B:HOH480 4.7 26.4 1.0 CB B:ILE63 4.7 20.1 1.0 N B:ALA68 4.8 22.0 1.0 HB3 B:ASP69 4.8 32.9 1.0 H B:ASP69 4.8 26.9 1.0 O B:ASP69 4.8 21.6 1.0 CA B:ALA68 4.8 20.8 1.0 CA B:GLN66 4.9 21.0 1.0 N B:ILE63 4.9 21.3 1.0 CG2 B:ILE63 4.9 19.8 1.0

Sodium binding site 4 out of 7 in the Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III within 5.0Å range: probe atom residue distance (Å) B Occ C:Na305 b:36.8 occ:1.00 O C:HOH569 1.9 51.4 1.0 HG1 C:THR50 2.0 40.7 1.0 HH21 C:ARG76 2.3 31.8 1.0 OG1 C:THR50 2.7 33.9 1.0 O C:HOH507 3.0 23.7 1.0 HA C:MET47 3.1 46.0 1.0 NH2 C:ARG76 3.1 26.4 1.0 HG2 C:MET47 3.3 43.7 1.0 HE C:ARG76 3.3 32.5 1.0 HB C:THR50 3.3 43.0 1.0 HG21 C:THR50 3.5 44.4 1.0 CB C:THR50 3.5 35.8 1.0 HH22 C:ARG76 3.5 31.8 1.0 HG22 C:VAL85 3.8 40.1 1.0 NE C:ARG76 3.9 27.0 1.0 CZ C:ARG76 3.9 26.2 1.0 CA C:MET47 4.0 38.2 1.0 CG2 C:THR50 4.0 36.9 1.0 O C:ASP46 4.1 41.4 1.0 CG C:MET47 4.2 36.3 1.0 O C:HOH514 4.4 34.7 1.0 HE3 C:MET47 4.4 52.3 1.0 HG21 C:VAL85 4.4 40.1 1.0 N C:MET47 4.5 39.8 1.0 HG23 C:THR50 4.5 44.4 1.0 H C:THR50 4.5 46.1 1.0 CG2 C:VAL85 4.5 33.3 1.0 C C:ASP46 4.5 39.8 1.0 HH12 C:ARG88 4.5 68.6 1.0 CB C:MET47 4.6 37.2 1.0 HG3 C:MET47 4.6 43.7 1.0 O C:HOH435 4.6 44.2 1.0 O C:HOH536 4.6 42.6 1.0 HB3 C:ASP46 4.7 49.3 1.0 HB3 C:MET47 4.7 44.7 1.0 HH11 C:ARG88 4.7 68.6 1.0 HG22 C:THR50 4.8 44.4 1.0 HG23 C:VAL85 4.8 40.1 1.0 NH1 C:ARG88 4.8 57.1 1.0 O C:HOH427 4.9 36.0 1.0 CA C:THR50 4.9 38.0 1.0 O C:MET47 5.0 36.5 1.0 C C:MET47 5.0 36.7 1.0 O C:HOH576 5.0 46.4 1.0 H C:MET47 5.0 47.9 1.0

Sodium binding site 5 out of 7 in the Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:21.4 occ:1.00 O D:GLY65 2.3 22.2 1.0 O D:ALA68 2.3 20.8 1.0 O D:ILE63 2.4 19.3 1.0 O D:HOH408 2.6 34.2 1.0 HA D:ASP69 2.8 25.6 1.0 OD1 D:ASP69 3.2 30.4 1.0 C D:ALA68 3.4 22.1 1.0 C D:GLY65 3.4 21.4 1.0 O C:HOH542 3.5 45.7 1.0 H D:GLY65 3.5 27.9 1.0 C D:ILE63 3.5 19.3 1.0 OE1 C:GLU86 3.5 46.4 1.0 N D:GLY65 3.5 23.2 1.0 HA D:LEU64 3.6 23.6 1.0 CA D:ASP69 3.6 21.3 1.0 CD C:GLU86 3.7 44.9 1.0 OE2 C:GLU86 3.7 46.2 1.0 C D:LEU64 3.8 20.5 1.0 N D:ASP69 3.9 19.5 1.0 H D:ALA68 3.9 24.8 1.0 CA D:LEU64 4.0 19.6 1.0 CA D:GLY65 4.1 22.6 1.0 CG D:ASP69 4.1 28.1 1.0 HG22 D:ILE63 4.2 23.9 1.0 HB D:ILE63 4.2 24.6 1.0 N D:LEU64 4.2 19.4 1.0 HA D:GLN66 4.3 22.9 1.0 O D:LEU64 4.3 20.0 1.0 HG2 C:GLU86 4.3 46.8 1.0 O C:HOH539 4.4 26.3 1.0 CB D:ASP69 4.4 24.0 1.0 O D:HOH507 4.5 25.1 1.0 OD1 C:ASN83 4.5 31.4 1.0 H D:ILE63 4.5 23.4 1.0 N D:GLN66 4.5 19.8 1.0 CA D:ILE63 4.6 20.2 1.0 HA2 D:GLY65 4.6 27.2 1.0 N D:ALA68 4.6 20.6 1.0 CG C:GLU86 4.6 38.9 1.0 CA D:ALA68 4.7 22.0 1.0 C D:ASP69 4.7 19.7 1.0 H D:ASP69 4.7 23.5 1.0 CB D:ILE63 4.7 20.4 1.0 HA3 D:GLY65 4.8 27.2 1.0 HB3 D:ASP69 4.8 28.9 1.0 O D:ASP69 4.8 20.6 1.0 CA D:GLN66 4.8 19.0 1.0 CG2 D:ILE63 4.9 19.9 1.0 N D:ILE63 4.9 19.5 1.0

Sodium binding site 6 out of 7 in the Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III within 5.0Å range: probe atom residue distance (Å) B Occ D:Na306 b:56.4 occ:1.00 O D:HOH599 3.8 56.8 1.0 O D:HOH418 4.1 32.3 1.0 CD1 D:TYR125 4.2 30.0 1.0 CE1 D:TYR125 4.2 29.3 1.0 CG D:TYR125 4.3 27.8 1.0 CZ D:TYR125 4.4 29.5 1.0 HD1 D:TYR125 4.5 36.1 1.0 HH D:TYR135 4.5 34.3 1.0 CD2 D:TYR125 4.5 27.9 1.0 HE1 D:TYR125 4.5 35.3 1.0 CE2 D:TYR125 4.5 28.8 1.0 OH D:TYR135 4.7 28.5 1.0 HB3 D:TYR125 4.7 34.2 1.0 HD2 D:TYR125 5.0 33.5 1.0

Sodium binding site 7 out of 7 in the Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Coproheme Decarboxylase From Listeria Monocytogenes in Complex with Iron Coproporphyrin III within 5.0Å range: probe atom residue distance (Å) B Occ E:Na301 b:20.4 occ:1.00 O E:ILE63 2.3 19.1 1.0 O E:GLY65 2.3 18.6 1.0 O E:ALA68 2.4 21.7 1.0 O E:HOH408 2.6 36.4 1.0 HA E:ASP69 2.8 27.5 1.0 O E:HOH540 3.2 32.6 1.0 C E:ILE63 3.4 18.7 1.0 C E:GLY65 3.4 18.8 1.0 OD1 E:ASP69 3.4 35.2 1.0 H E:GLY65 3.5 24.0 1.0 C E:ALA68 3.5 23.4 1.0 N E:GLY65 3.5 19.9 1.0 HA E:LEU64 3.6 24.5 1.0 CA E:ASP69 3.7 22.8 1.0 C E:LEU64 3.7 21.1 1.0 OE2 D:GLU86 3.8 40.5 1.0 CD D:GLU86 3.9 40.5 1.0 OE1 D:GLU86 3.9 40.8 1.0 N E:ASP69 4.0 22.5 1.0 CA E:LEU64 4.0 20.4 1.0 H E:ALA68 4.0 24.1 1.0 CA E:GLY65 4.1 19.3 1.0 HB E:ILE63 4.1 21.9 1.0 N E:LEU64 4.1 19.7 1.0 HG22 E:ILE63 4.1 21.7 1.0 CG E:ASP69 4.2 31.7 1.0 O E:LEU64 4.3 21.1 1.0 HG2 D:GLU86 4.3 48.5 1.0 HA E:GLN66 4.4 25.6 1.0 H E:ILE63 4.5 25.8 0.7 CA E:ILE63 4.5 18.7 1.0 O D:HOH583 4.5 25.7 1.0 OD1 D:ASN83 4.5 30.5 1.0 O E:HOH483 4.5 26.4 1.0 H E:ILE63 4.5 25.8 0.3 CB E:ASP69 4.5 26.8 1.0 N E:GLN66 4.6 18.5 1.0 HA2 E:GLY65 4.6 23.3 1.0 C E:ASP69 4.6 20.5 1.0 CB E:ILE63 4.6 18.6 1.0 N E:ALA68 4.7 20.0 1.0 CG D:GLU86 4.7 40.3 1.0 CA E:ALA68 4.7 20.9 1.0 O E:ASP69 4.7 21.1 1.0 H E:ASP69 4.7 27.1 1.0 HA3 E:GLY65 4.8 23.3 1.0 N E:ILE63 4.8 21.4 1.0 CG2 E:ILE63 4.9 18.5 1.0 HB3 E:ASP69 4.9 32.2 1.0 CA E:GLN66 4.9 21.3 1.0 H E:LEU64 4.9 23.7 1.0

L.Milazzo, T.Gabler, D.Puhringer, Z.Jandova, D.Maresch, H.Michlits, V.Pfanzagl, K.Djinovic-Carugo, C.Oostenbrink, P.G.Furtmuller, C.Obinger, G.Smulevich, S.Hofbauer. Redox Cofactor Rotates During Its Stepwise Decarboxylation: Molecular Mechanism of Conversion of Coproheme to Hemeb. Acs Catalysis V. 9 6766 2019.
ISSN: ESSN 2155-5435
PubMed: 31423350
DOI: 10.1021/ACSCATAL.9B00963