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Sodium in PDB 5cx7: Crystal Structure of Pduoc:Heme Complex

Protein crystallography data

The structure of Crystal Structure of Pduoc:Heme Complex, PDB code: 5cx7 was solved by S.Geremia, N.Hickey, D.Ortiz De Orue Lucana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.07 / 1.97
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.300, 130.120, 120.750, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18.6

Other elements in 5cx7:

The structure of Crystal Structure of Pduoc:Heme Complex also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 8 atoms
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Pduoc:Heme Complex (pdb code 5cx7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 18 binding sites of Sodium where determined in the Crystal Structure of Pduoc:Heme Complex, PDB code: 5cx7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 18 in 5cx7

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Sodium binding site 1 out of 18 in the Crystal Structure of Pduoc:Heme Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Pduoc:Heme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:45.1
occ:1.00
 OE2 A:GLU94 2.6 30.4 1.0
O C:HOH360 2.6 32.5 1.0
OG A:SER95 2.8 19.6 1.0
CL C:CL203 2.8 54.5 1.0
OE2 G:GLU94 3.1 28.4 1.0
NA G:NA205 3.2 46.5 1.0
NA A:NA206 3.3 54.8 1.0
CD A:GLU94 3.7 19.4 1.0
CB A:SER95 3.7 17.0 1.0
CG G:GLU94 3.8 18.6 1.0
CD G:GLU94 3.8 22.6 1.0
CA A:GLY92 4.1 12.5 1.0
CG A:GLU94 4.2 17.3 1.0
OG C:SER95 4.3 22.3 1.0
O A:GLY92 4.3 12.1 1.0
OG G:SER95 4.3 22.0 1.0
N A:SER95 4.4 13.3 1.0
O A:HOH323 4.5 13.2 1.0
C A:GLY92 4.5 11.7 1.0
OE1 A:GLU94 4.6 14.9 1.0
CA A:SER95 4.7 14.1 1.0
NA E:NA203 4.9 48.0 1.0
N A:GLY92 4.9 11.1 1.0
OH A:TYR91 5.0 18.4 1.0
OE1 G:GLU94 5.0 21.2 1.0

Sodium binding site 2 out of 18 in 5cx7

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Sodium binding site 2 out of 18 in the Crystal Structure of Pduoc:Heme Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Pduoc:Heme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:54.8
occ:1.00
 OE2 C:GLU94 2.6 29.7 1.0
CL C:CL203 2.7 54.5 1.0
OG C:SER95 2.7 22.3 1.0
OE2 A:GLU94 3.1 30.4 1.0
NA A:NA205 3.3 45.1 1.0
CD C:GLU94 3.6 24.6 1.0
CB C:SER95 3.6 16.0 1.0
NA E:NA203 3.7 48.0 1.0
CG A:GLU94 3.8 17.3 1.0
CD A:GLU94 3.8 19.4 1.0
CA C:GLY92 3.9 12.8 1.0
CG C:GLU94 4.2 19.3 1.0
O C:GLY92 4.2 11.5 1.0
OG E:SER95 4.3 19.7 1.0
N C:SER95 4.3 12.9 1.0
O C:HOH360 4.4 32.5 1.0
C C:GLY92 4.4 13.9 1.0
OG A:SER95 4.4 19.6 1.0
O E:HOH326 4.4 11.3 1.0
OE1 C:GLU94 4.5 22.3 1.0
CA C:SER95 4.6 14.7 1.0
NA G:NA205 4.7 46.5 1.0
N C:GLY92 4.7 11.9 1.0

Sodium binding site 3 out of 18 in 5cx7

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Sodium binding site 3 out of 18 in the Crystal Structure of Pduoc:Heme Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Pduoc:Heme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:46.7
occ:1.00
 O B:HOH332 2.4 39.6 1.0
CL D:CL204 2.4 46.7 1.0
OE2 B:GLU94 2.7 35.6 1.0
OG B:SER95 2.9 19.2 1.0
OE2 D:GLU94 3.0 39.7 1.0
NA D:NA203 3.1 41.6 1.0
NA H:NA203 3.6 49.8 1.0
CG D:GLU94 3.7 25.8 1.0
CD B:GLU94 3.8 26.0 1.0
CD D:GLU94 3.8 29.6 1.0
CB B:SER95 3.8 18.6 1.0
CA B:GLY92 4.0 15.1 1.0
O B:GLY92 4.3 15.3 1.0
CG B:GLU94 4.4 22.7 1.0
OG D:SER95 4.4 20.6 1.0
N B:SER95 4.4 15.9 1.0
OG H:SER95 4.4 23.2 1.0
C B:GLY92 4.5 14.8 1.0
O F:HOH350 4.5 47.3 1.0
O B:HOH317 4.5 17.9 1.0
OE1 B:GLU94 4.7 24.4 1.0
O F:HOH357 4.8 40.4 1.0
CA B:SER95 4.8 16.3 1.0
N B:GLY92 4.8 14.6 1.0
NA F:NA202 4.9 45.5 1.0
OE1 D:GLU94 4.9 25.2 1.0
OH H:TYR91 5.0 25.4 1.0
OH B:TYR91 5.0 23.0 1.0

Sodium binding site 4 out of 18 in 5cx7

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Sodium binding site 4 out of 18 in the Crystal Structure of Pduoc:Heme Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Pduoc:Heme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na203

b:41.6
occ:1.00
 OE2 D:GLU94 2.4 39.7 1.0
CL D:CL204 2.7 46.7 1.0
OG D:SER95 2.8 20.6 1.0
NA B:NA202 3.1 46.7 1.0
OE2 F:GLU94 3.3 37.3 1.0
CD D:GLU94 3.4 29.6 1.0
NA F:NA202 3.7 45.5 1.0
CB D:SER95 3.7 17.4 1.0
CG F:GLU94 3.9 18.0 1.0
CG D:GLU94 3.9 25.8 1.0
CA D:GLY92 4.0 14.7 1.0
CD F:GLU94 4.1 21.3 1.0
OG B:SER95 4.1 19.2 1.0
N D:SER95 4.2 15.1 1.0
O D:GLY92 4.2 12.7 1.0
OE1 D:GLU94 4.3 25.2 1.0
O D:HOH309 4.4 11.7 1.0
C D:GLY92 4.4 14.5 1.0
O B:HOH332 4.5 39.6 1.0
CA D:SER95 4.5 15.6 1.0
OG F:SER95 4.6 17.0 1.0
O F:HOH351 4.7 38.7 1.0
N D:GLY92 4.8 14.3 1.0
NA H:NA203 4.8 49.8 1.0

Sodium binding site 5 out of 18 in 5cx7

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Sodium binding site 5 out of 18 in the Crystal Structure of Pduoc:Heme Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Pduoc:Heme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na203

b:48.0
occ:1.00
 OE2 E:GLU94 2.3 32.7 1.0
CL C:CL203 2.8 54.5 1.0
OG E:SER95 2.8 19.7 1.0
OE2 C:GLU94 3.3 29.7 1.0
CD E:GLU94 3.3 21.7 1.0
NA G:NA205 3.4 46.5 1.0
CB E:SER95 3.7 14.9 1.0
NA A:NA206 3.7 54.8 1.0
CA E:GLY92 3.8 14.8 1.0
CG C:GLU94 3.9 19.3 1.0
CG E:GLU94 3.9 17.1 1.0
CD C:GLU94 4.0 24.6 1.0
O E:GLY92 4.1 13.2 1.0
N E:SER95 4.1 11.9 1.0
O E:HOH331 4.2 12.0 1.0
C E:GLY92 4.2 14.1 1.0
OE1 E:GLU94 4.2 20.9 1.0
OG G:SER95 4.3 22.0 1.0
CA E:SER95 4.5 12.6 1.0
N E:GLY92 4.6 15.0 1.0
OG C:SER95 4.7 22.3 1.0
NA A:NA205 4.9 45.1 1.0
OH G:TYR91 5.0 24.8 1.0

Sodium binding site 6 out of 18 in 5cx7

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Sodium binding site 6 out of 18 in the Crystal Structure of Pduoc:Heme Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Pduoc:Heme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na202

b:45.5
occ:1.00
 OE2 F:GLU94 2.4 37.3 1.0
O F:HOH351 2.5 38.7 1.0
OG F:SER95 3.0 17.0 1.0
CL D:CL204 3.0 46.7 1.0
OE2 H:GLU94 3.2 34.4 1.0
NA H:NA203 3.4 49.8 1.0
CD F:GLU94 3.5 21.3 1.0
NA D:NA203 3.7 41.6 1.0
CA F:GLY92 3.7 16.0 1.0
CB F:SER95 3.8 17.9 1.0
CG H:GLU94 3.8 21.8 1.0
CD H:GLU94 3.9 27.1 1.0
O F:GLY92 4.1 13.3 1.0
CG F:GLU94 4.1 18.0 1.0
C F:GLY92 4.2 14.3 1.0
O F:HOH310 4.2 14.8 1.0
N F:SER95 4.3 12.2 1.0
OE1 F:GLU94 4.3 24.4 1.0
O F:HOH350 4.4 47.3 1.0
OG D:SER95 4.5 20.6 1.0
N F:GLY92 4.5 15.8 1.0
OG H:SER95 4.6 23.2 1.0
CA F:SER95 4.7 14.5 1.0
O F:HOH357 4.7 40.4 1.0
NA B:NA202 4.9 46.7 1.0
OH D:TYR91 4.9 23.3 1.0

Sodium binding site 7 out of 18 in 5cx7

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Sodium binding site 7 out of 18 in the Crystal Structure of Pduoc:Heme Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Pduoc:Heme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na205

b:46.5
occ:1.00
 OE2 G:GLU94 2.5 28.4 1.0
CL C:CL203 2.7 54.5 1.0
OG G:SER95 2.8 22.0 1.0
NA A:NA205 3.2 45.1 1.0
OE2 E:GLU94 3.3 32.7 1.0
NA E:NA203 3.4 48.0 1.0
CD G:GLU94 3.6 22.6 1.0
CB G:SER95 3.7 19.7 1.0
CG E:GLU94 3.9 17.1 1.0
CD E:GLU94 4.0 21.7 1.0
CA G:GLY92 4.0 11.3 1.0
CG G:GLU94 4.1 18.6 1.0
OG A:SER95 4.2 19.6 1.0
O G:GLY92 4.3 11.8 1.0
N G:SER95 4.3 14.6 1.0
O G:HOH322 4.4 15.7 1.0
OG E:SER95 4.5 19.7 1.0
O C:HOH360 4.5 32.5 1.0
C G:GLY92 4.5 11.3 1.0
OE1 G:GLU94 4.5 21.2 1.0
CA G:SER95 4.6 15.9 1.0
NA A:NA206 4.7 54.8 1.0
N G:GLY92 4.8 13.0 1.0
OH A:TYR91 4.9 18.4 1.0

Sodium binding site 8 out of 18 in 5cx7

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Sodium binding site 8 out of 18 in the Crystal Structure of Pduoc:Heme Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Pduoc:Heme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na203

b:49.8
occ:1.00
 OE2 H:GLU94 2.4 34.4 1.0
O F:HOH350 2.4 47.3 1.0
CL D:CL204 2.8 46.7 1.0
OG H:SER95 2.9 23.2 1.0
OE2 B:GLU94 3.3 35.6 1.0
NA F:NA202 3.4 45.5 1.0
CD H:GLU94 3.4 27.1 1.0
NA B:NA202 3.6 46.7 1.0
CB H:SER95 3.8 19.2 1.0
CA H:GLY92 3.9 17.3 1.0
CG B:GLU94 4.0 22.7 1.0
CD B:GLU94 4.0 26.0 1.0
CG H:GLU94 4.0 21.8 1.0
O F:HOH351 4.1 38.7 1.0
O H:HOH321 4.3 13.6 1.0
O H:GLY92 4.3 13.4 1.0
N H:SER95 4.3 15.9 1.0
O B:HOH332 4.3 39.6 1.0
OG F:SER95 4.4 17.0 1.0
OE1 H:GLU94 4.4 27.4 1.0
C H:GLY92 4.4 15.2 1.0
O F:HOH357 4.5 40.4 1.0
OG B:SER95 4.6 19.2 1.0
CA H:SER95 4.7 17.2 1.0
N H:GLY92 4.7 18.1 1.0
NA D:NA203 4.8 41.6 1.0
OH F:TYR91 4.8 25.1 1.0
OH H:TYR91 4.9 25.4 1.0

Sodium binding site 9 out of 18 in 5cx7

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Sodium binding site 9 out of 18 in the Crystal Structure of Pduoc:Heme Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Pduoc:Heme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na204

b:37.8
occ:1.00
 NE2 H:HIS15 2.2 39.4 1.0
CE1 H:HIS15 2.8 34.4 1.0
CD2 H:HIS15 3.4 34.1 1.0
ND1 H:HIS15 4.0 38.2 1.0
CG H:HIS15 4.3 35.7 1.0
CG H:GLN19 4.9 26.0 1.0

Sodium binding site 10 out of 18 in 5cx7

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Sodium binding site 10 out of 18 in the Crystal Structure of Pduoc:Heme Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Pduoc:Heme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na206

b:51.4
occ:1.00
 O K:HOH345 2.5 32.6 1.0
OE2 I:GLU94 2.6 34.8 1.0
CL I:CL207 2.6 40.6 1.0
OG I:SER95 3.0 23.4 1.0
OE2 O:GLU94 3.1 26.5 1.0
NA I:NA208 3.2 46.0 1.0
NA M:NA204 3.4 47.3 1.0
CD I:GLU94 3.7 23.7 1.0
CG O:GLU94 3.8 19.9 1.0
CD O:GLU94 3.8 23.8 1.0
CB I:SER95 3.9 18.1 1.0
CA I:GLY92 4.0 15.0 1.0
CG I:GLU94 4.3 19.3 1.0
OG K:SER95 4.3 22.9 1.0
O I:GLY92 4.4 14.0 1.0
O I:HOH322 4.4 15.9 1.0
OG O:SER95 4.4 28.0 1.0
N I:SER95 4.5 14.5 1.0
C I:GLY92 4.5 15.4 1.0
OE1 I:GLU94 4.6 21.4 1.0
CA I:SER95 4.8 16.9 1.0
N I:GLY92 4.8 16.8 1.0
NA M:NA203 4.9 40.3 1.0
OH I:TYR91 4.9 29.9 1.0
OH K:TYR91 5.0 19.8 1.0

Reference:

D.Ortiz De Orue Lucana, N.Hickey, M.Hensel, J.P.Klare, S.Geremia, T.Tiufiakova, A.E.Torda. The Crystal Structure of the C-Terminal Domain of the Salmonella Enterica Pduo Protein: An Old Fold with A New Heme-Binding Mode. Front Microbiol V. 7 1010 2016.
ISSN: ESSN 1664-302X
PubMed: 27446048
DOI: 10.3389/FMICB.2016.01010
Page generated: Mon Oct 7 20:28:03 2024

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