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Sodium in PDB 5loq: Structure of Coproheme Bound Hemq From Listeria Monocytogenes

Protein crystallography data

The structure of Structure of Coproheme Bound Hemq From Listeria Monocytogenes, PDB code: 5loq was solved by D.Puehringer, G.Mlynek, S.Hofbauer, K.Djinovic-Carugo, C.Obinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.00 / 1.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.687, 129.369, 77.916, 90.00, 105.52, 90.00
R / Rfree (%) 18.4 / 21.5

Other elements in 5loq:

The structure of Structure of Coproheme Bound Hemq From Listeria Monocytogenes also contains other interesting chemical elements:

Iron (Fe) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Coproheme Bound Hemq From Listeria Monocytogenes (pdb code 5loq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of Coproheme Bound Hemq From Listeria Monocytogenes, PDB code: 5loq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5loq

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Sodium binding site 1 out of 5 in the Structure of Coproheme Bound Hemq From Listeria Monocytogenes


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 Bound Hemq From Listeria Monocytogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:25.2
occ:1.00
O A:GLY65 2.2 29.0 1.0
O A:ILE63 2.3 28.3 1.0
O A:ALA68 2.3 23.6 1.0
OE1 B:GLU86 2.4 45.2 1.0
O A:HOH401 2.4 30.9 1.0
HA A:ASP69 2.9 30.0 1.0
C A:GLY65 3.3 29.5 1.0
H A:GLY65 3.4 36.8 1.0
N A:GLY65 3.4 30.6 1.0
C A:ILE63 3.4 26.6 1.0
CD B:GLU86 3.4 42.4 1.0
C A:ALA68 3.4 22.6 1.0
HA A:LEU64 3.4 31.5 1.0
OD1 A:ASP69 3.5 43.1 1.0
C A:LEU64 3.6 27.9 1.0
CA A:ASP69 3.8 24.9 1.0
O A:HOH507 3.8 35.0 1.0
OE2 B:GLU86 3.8 43.7 1.0
CA A:LEU64 3.8 26.2 1.0
H A:ALA68 3.8 26.9 1.0
CA A:GLY65 3.9 30.7 1.0
HG22 A:ILE63 4.0 29.7 1.0
N A:ASP69 4.0 22.2 1.0
N A:LEU64 4.0 25.4 1.0
HB A:ILE63 4.1 31.6 1.0
O A:LEU64 4.1 26.9 1.0
CG A:ASP69 4.2 35.9 1.0
O A:HOH466 4.2 31.8 1.0
HA A:GLN66 4.3 33.0 1.0
O B:HOH499 4.3 34.0 1.0
N A:GLN66 4.5 29.0 1.0
HA2 A:GLY65 4.5 36.9 1.0
CA A:ILE63 4.5 26.7 1.0
N A:ALA68 4.6 22.4 1.0
H A:ILE63 4.6 32.6 1.0
CB A:ASP69 4.6 29.6 1.0
HG2 B:GLU86 4.6 43.6 1.0
CA A:ALA68 4.6 23.3 1.0
CG B:GLU86 4.7 36.3 1.0
HA3 A:GLY65 4.7 36.9 1.0
CB A:ILE63 4.7 26.2 1.0
HD21 B:ASN83 4.7 42.0 1.0
C A:ASP69 4.7 26.1 1.0
CG2 A:ILE63 4.7 24.7 1.0
CA A:GLN66 4.8 27.4 1.0
H A:ASP69 4.8 26.8 1.0
H A:LEU64 4.9 30.5 1.0
O A:ASP69 4.9 27.3 1.0
N A:ILE63 4.9 27.1 1.0
HB3 A:ASP69 5.0 35.6 1.0

Sodium binding site 2 out of 5 in 5loq

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Sodium binding site 2 out of 5 in the Structure of Coproheme Bound Hemq From Listeria Monocytogenes


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 Bound Hemq From Listeria Monocytogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:26.9
occ:1.00
O B:GLY65 2.3 24.7 1.0
OE1 E:GLU86 2.3 39.0 1.0
O B:ILE63 2.3 25.8 1.0
O B:HOH410 2.3 31.6 1.0
O B:ALA68 2.4 26.8 1.0
HA B:ASP69 3.0 31.1 1.0
H B:GLY65 3.3 31.7 1.0
CD E:GLU86 3.3 37.9 1.0
N B:GLY65 3.4 26.4 1.0
C B:GLY65 3.4 24.3 1.0
C B:ILE63 3.4 24.7 1.0
C B:ALA68 3.5 25.5 1.0
HA B:LEU64 3.5 32.2 1.0
C B:LEU64 3.6 26.6 1.0
O B:HOH464 3.7 32.9 1.0
OE2 E:GLU86 3.9 37.6 1.0
CA B:ASP69 3.9 25.9 1.0
H B:ALA68 3.9 29.9 1.0
O E:HOH439 3.9 37.7 1.0
CA B:LEU64 3.9 26.8 1.0
OD1 B:ASP69 4.0 33.2 1.0
CA B:GLY65 4.0 25.2 1.0
HG22 B:ILE63 4.0 27.6 1.0
N B:ASP69 4.0 25.4 1.0
N B:LEU64 4.1 25.7 1.0
HB B:ILE63 4.1 28.3 1.0
O B:LEU64 4.2 26.0 1.0
HA B:GLN66 4.3 26.5 1.0
O E:HOH496 4.3 25.8 1.0
HG2 E:GLU86 4.4 43.0 1.0
O B:HOH450 4.4 29.3 1.0
N B:GLN66 4.5 21.9 1.0
CA B:ILE63 4.5 23.9 1.0
HA2 B:GLY65 4.5 30.3 1.0
CG B:ASP69 4.5 31.6 1.0
CG E:GLU86 4.5 35.8 1.0
H B:ILE63 4.5 29.5 1.0
N B:ALA68 4.6 24.9 1.0
CB B:ILE63 4.6 23.5 1.0
HA3 B:GLY65 4.7 30.3 1.0
CA B:ALA68 4.7 24.6 1.0
CG2 B:ILE63 4.8 22.9 1.0
CA B:GLN66 4.8 22.0 1.0
C B:ASP69 4.8 23.8 1.0
CB B:ASP69 4.8 29.1 1.0
H B:ASP69 4.8 30.5 1.0
HD21 E:ASN83 4.9 39.2 1.0
O B:ASP69 4.9 23.0 1.0
H B:LEU64 4.9 30.9 1.0
N B:ILE63 4.9 24.5 1.0
HG3 E:GLU86 5.0 43.0 1.0

Sodium binding site 3 out of 5 in 5loq

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Sodium binding site 3 out of 5 in the Structure of Coproheme Bound Hemq From Listeria Monocytogenes


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 Bound Hemq From Listeria Monocytogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:26.4
occ:1.00
O C:GLY65 2.2 24.3 1.0
O C:ALA68 2.3 25.0 1.0
O C:ILE63 2.4 23.5 1.0
O C:HOH406 2.4 30.8 1.0
OE1 A:GLU86 2.5 35.4 1.0
HA C:ASP69 2.9 29.2 1.0
C C:GLY65 3.4 22.6 1.0
C C:ALA68 3.4 24.1 1.0
CD A:GLU86 3.4 35.9 1.0
C C:ILE63 3.4 23.8 1.0
HA C:LEU64 3.5 32.6 1.0
N C:GLY65 3.5 24.2 1.0
H C:GLY65 3.5 29.1 1.0
C C:LEU64 3.6 25.2 1.0
O C:HOH459 3.7 31.0 1.0
CA C:ASP69 3.8 24.3 1.0
H C:ALA68 3.8 27.2 1.0
O A:HOH458 3.9 45.6 1.0
OE2 A:GLU86 3.9 37.2 1.0
CA C:LEU64 3.9 27.1 1.0
N C:ASP69 4.0 24.1 1.0
OD1 C:ASP69 4.0 33.0 1.0
CA C:GLY65 4.0 23.0 1.0
HG22 C:ILE63 4.0 26.7 1.0
N C:LEU64 4.1 24.8 1.0
O C:LEU64 4.2 25.0 1.0
HB C:ILE63 4.2 28.0 1.0
HA C:GLN66 4.3 27.3 1.0
O A:HOH514 4.3 27.8 1.0
O C:HOH438 4.3 25.8 1.0
N C:GLN66 4.5 22.2 1.0
HG2 A:GLU86 4.5 40.5 1.0
CG C:ASP69 4.5 30.3 1.0
N C:ALA68 4.5 22.6 1.0
CA C:ILE63 4.5 24.5 1.0
H C:ILE63 4.6 33.0 1.0
HA2 C:GLY65 4.6 27.7 1.0
CG A:GLU86 4.6 33.7 1.0
CA C:ALA68 4.6 23.3 1.0
C C:ASP69 4.7 24.0 1.0
CB C:ASP69 4.7 26.6 1.0
HA3 C:GLY65 4.7 27.7 1.0
CB C:ILE63 4.7 23.3 1.0
H C:ASP69 4.8 28.9 1.0
CA C:GLN66 4.8 22.7 1.0
CG2 C:ILE63 4.8 22.2 1.0
O C:ASP69 4.9 24.6 1.0
H C:LEU64 4.9 29.8 1.0
HD21 A:ASN83 4.9 36.4 1.0
N C:ILE63 4.9 27.4 1.0

Sodium binding site 4 out of 5 in 5loq

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Sodium binding site 4 out of 5 in the Structure of Coproheme Bound Hemq From Listeria Monocytogenes


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 Bound Hemq From Listeria Monocytogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:23.9
occ:1.00
O D:GLY65 2.2 25.9 1.0
O D:ILE63 2.3 22.6 1.0
O D:ALA68 2.3 22.8 1.0
OE1 C:GLU86 2.4 41.0 1.0
O D:HOH424 2.4 33.4 1.0
HA D:ASP69 2.9 29.6 1.0
C D:GLY65 3.3 24.8 1.0
CD C:GLU86 3.4 37.6 1.0
C D:ILE63 3.4 23.4 1.0
C D:ALA68 3.4 23.0 1.0
N D:GLY65 3.4 23.7 1.0
HA D:LEU64 3.4 28.7 1.0
H D:GLY65 3.5 28.5 1.0
C D:LEU64 3.6 23.2 1.0
O D:HOH489 3.7 34.2 1.0
CA D:ASP69 3.8 24.6 1.0
OE2 C:GLU86 3.8 37.5 1.0
CA D:LEU64 3.9 23.9 1.0
O C:HOH435 3.9 43.2 1.0
H D:ALA68 3.9 28.9 1.0
CA D:GLY65 4.0 23.4 1.0
HG22 D:ILE63 4.0 31.6 1.0
N D:ASP69 4.0 23.3 1.0
N D:LEU64 4.1 23.3 1.0
OD1 D:ASP69 4.1 34.3 1.0
HB D:ILE63 4.1 30.4 1.0
O D:LEU64 4.2 24.3 1.0
HA D:GLN66 4.3 28.2 1.0
O D:HOH527 4.3 24.7 1.0
O C:HOH493 4.3 27.9 1.0
N D:GLN66 4.5 24.4 1.0
HA2 D:GLY65 4.5 28.1 1.0
CA D:ILE63 4.5 23.5 1.0
CG D:ASP69 4.5 32.2 1.0
H D:ILE63 4.5 29.5 1.0
N D:ALA68 4.6 24.0 1.0
HG2 C:GLU86 4.6 40.3 1.0
CB D:ILE63 4.6 25.3 1.0
CA D:ALA68 4.6 23.8 1.0
CG C:GLU86 4.7 33.5 1.0
HA3 D:GLY65 4.7 28.1 1.0
CB D:ASP69 4.7 28.7 1.0
C D:ASP69 4.7 22.6 1.0
CG2 D:ILE63 4.7 26.3 1.0
H D:ASP69 4.8 28.0 1.0
CA D:GLN66 4.8 23.5 1.0
O D:ASP69 4.8 23.0 1.0
N D:ILE63 4.9 24.5 1.0
H D:LEU64 4.9 28.0 1.0
HD21 C:ASN83 4.9 38.6 1.0

Sodium binding site 5 out of 5 in 5loq

Go back to Sodium Binding Sites List in 5loq
Sodium binding site 5 out of 5 in the Structure of Coproheme Bound Hemq From Listeria Monocytogenes


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 Bound Hemq From Listeria Monocytogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na301

b:19.6
occ:1.00
O E:GLY65 2.2 28.3 1.0
O E:HOH415 2.2 34.0 1.0
O E:ILE63 2.3 22.5 1.0
O E:ALA68 2.3 23.6 1.0
OE1 D:GLU86 2.5 41.8 1.0
HA E:ASP69 2.9 26.9 1.0
C E:GLY65 3.3 23.8 1.0
C E:ILE63 3.4 22.3 1.0
C E:ALA68 3.4 21.6 1.0
N E:GLY65 3.4 24.8 1.0
H E:GLY65 3.5 29.8 1.0
CD D:GLU86 3.5 39.4 1.0
HA E:LEU64 3.5 28.2 1.0
C E:LEU64 3.6 23.5 1.0
O E:HOH501 3.6 30.4 1.0
CA E:ASP69 3.8 22.4 1.0
H E:ALA68 3.8 26.2 1.0
OD1 E:ASP69 3.9 34.7 1.0
CA E:LEU64 3.9 23.4 1.0
O D:HOH479 3.9 44.9 1.0
CA E:GLY65 4.0 23.3 1.0
HG22 E:ILE63 4.0 29.4 1.0
OE2 D:GLU86 4.0 39.4 1.0
N E:ASP69 4.0 23.0 1.0
N E:LEU64 4.1 22.4 1.0
HB E:ILE63 4.1 28.4 1.0
O E:LEU64 4.2 24.0 1.0
O E:HOH468 4.3 27.5 1.0
HA E:GLN66 4.3 29.5 1.0
O D:HOH529 4.3 30.3 1.0
N E:GLN66 4.4 23.2 1.0
H E:ILE63 4.4 30.2 1.0
CG E:ASP69 4.5 30.8 1.0
CA E:ILE63 4.5 23.8 1.0
HG2 D:GLU86 4.5 43.2 1.0
HA2 E:GLY65 4.5 28.1 1.0
N E:ALA68 4.5 21.8 1.0
CA E:ALA68 4.6 22.0 1.0
HA3 E:GLY65 4.7 28.1 1.0
CB E:ILE63 4.7 23.6 1.0
CG D:GLU86 4.7 36.0 1.0
C E:ASP69 4.7 21.7 1.0
CB E:ASP69 4.7 26.6 1.0
HD21 D:ASN83 4.7 38.1 1.0
CG2 E:ILE63 4.7 24.4 1.0
CA E:GLN66 4.8 24.5 1.0
O E:ASP69 4.8 22.7 1.0
H E:ASP69 4.8 27.7 1.0
N E:ILE63 4.8 25.2 1.0
H E:LEU64 4.9 26.9 1.0

Reference:

S.Hofbauer, G.Mlynek, L.Milazzo, D.Puhringer, D.Maresch, I.Schaffner, P.G.Furtmuller, G.Smulevich, K.Djinovic-Carugo, C.Obinger. Hydrogen Peroxide-Mediated Conversion of Coproheme to Heme B By Hemq-Lessons From the First Crystal Structure and Kinetic Studies. Febs J. V. 283 4386 2016.
ISSN: ISSN 1742-4658
PubMed: 27758026
DOI: 10.1111/FEBS.13930
Page generated: Mon Oct 7 22:22:38 2024

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