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Sodium in PDB 6i3j: Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide

Enzymatic activity of Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide

All present enzymatic activity of Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide:
1.3.3.5;

Protein crystallography data

The structure of Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide, PDB code: 6i3j was solved by L.Svecova, T.Koval, T.Skalova, P.Kolenko, J.Duskova, L.H.Ostergaard, J.Dohnalek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.30 / 2.59
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 134.382, 203.846, 226.744, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 22.6

Other elements in 6i3j:

The structure of Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide also contains other interesting chemical elements:

Iron (Fe) 9 atoms
Chlorine (Cl) 1 atom
Copper (Cu) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide (pdb code 6i3j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide, PDB code: 6i3j:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 6i3j

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Sodium binding site 1 out of 8 in the Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na620

b:54.0
occ:1.00
 O6 A:NAG610 2.3 43.0 1.0
OE1 A:GLU525 3.1 54.5 1.0
C6 A:NAG610 3.3 42.0 1.0
CE2 A:TYR526 3.5 33.8 1.0
CB A:GLU525 3.5 43.4 1.0
O A:THR522 3.5 35.1 1.0
CD2 A:TYR526 3.8 33.9 1.0
CG2 A:THR522 3.9 33.1 1.0
CD A:GLU525 4.1 54.2 1.0
CZ A:TYR526 4.1 34.2 1.0
CG A:GLU525 4.4 47.6 1.0
C A:THR522 4.4 33.9 1.0
N2 A:NAG611 4.4 57.6 1.0
CA A:THR522 4.5 34.2 1.0
OH A:TYR526 4.5 35.3 1.0
C1 A:NAG611 4.6 55.5 1.0
CA A:GLU525 4.7 38.7 1.0
CG A:TYR526 4.7 33.0 1.0
CB A:THR522 4.7 33.4 1.0
C5 A:NAG610 4.7 41.3 1.0
C A:GLU525 4.8 36.9 1.0
N A:TYR526 4.8 35.8 1.0
C2 A:NAG611 4.9 61.0 1.0
C3 A:NAG611 4.9 69.0 1.0
CE1 A:TYR526 5.0 33.4 1.0

Sodium binding site 2 out of 8 in 6i3j

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Sodium binding site 2 out of 8 in the Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na621

b:36.5
occ:1.00
 O A:HOH967 2.3 34.2 1.0
O A:HOH925 2.5 34.2 1.0
OD2 A:ASP63 2.6 28.2 1.0
CG A:ASP63 3.5 28.6 1.0
CB A:ASP63 3.8 27.5 1.0
CD A:LYS21 3.8 29.3 1.0
CE A:MET65 3.8 29.7 1.0
O A:HOH883 3.8 29.2 1.0
CG A:PRO69 4.0 27.5 1.0
CB A:PRO69 4.0 27.1 1.0
NZ A:LYS21 4.0 29.1 1.0
CE A:LYS21 4.3 28.9 1.0
OD1 A:ASP63 4.6 27.9 1.0
CD A:PRO69 4.9 27.2 1.0
SD A:MET65 4.9 31.2 1.0

Sodium binding site 3 out of 8 in 6i3j

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Sodium binding site 3 out of 8 in the Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na622

b:40.6
occ:1.00
 O A:ASN86 2.9 28.5 1.0
OD1 A:ASN86 3.4 37.4 1.0
OE2 A:GLU88 3.5 31.6 0.5
CD A:PRO45 3.8 32.9 1.0
CG A:PRO45 4.0 32.3 1.0
CG A:ASN86 4.0 34.8 1.0
C A:ASN86 4.0 29.8 1.0
ND2 A:ASN86 4.4 36.1 1.0
CD A:GLU88 4.7 33.4 0.5
N A:ALA87 4.8 31.8 1.0
CA A:ALA87 4.8 34.5 1.0
CB A:ASN86 4.8 31.0 1.0
CA A:ASN86 4.9 28.5 1.0

Sodium binding site 4 out of 8 in 6i3j

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Sodium binding site 4 out of 8 in the Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na623

b:41.5
occ:1.00
 OD1 A:ASP285 2.6 38.6 1.0
O A:HOH905 2.9 38.7 1.0
OG A:SER284 3.1 36.2 1.0
CG A:ASP285 3.7 40.1 1.0
CB A:SER284 4.0 35.2 1.0
OD2 A:ASP285 4.2 44.2 1.0
N A:ASP285 4.4 42.4 1.0
C A:SER284 4.5 39.9 1.0
CA A:ASP285 4.7 39.0 1.0
CB A:ASP285 4.8 38.6 1.0
CA A:SER284 4.9 36.2 1.0
O A:SER284 4.9 40.5 1.0
O A:HOH707 5.0 27.4 1.0

Sodium binding site 5 out of 8 in 6i3j

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Sodium binding site 5 out of 8 in the Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na624

b:32.4
occ:1.00
 O A:HOH757 2.5 23.2 1.0
O A:ALA447 2.6 20.6 1.0
O A:HOH809 2.7 21.5 1.0
O A:LEU404 2.8 27.4 1.0
CA A:VAL405 3.6 26.1 1.0
C A:LEU404 3.7 26.4 1.0
C A:ALA447 3.8 25.1 1.0
CD2 A:PHE99 3.9 27.6 1.0
N A:ASP406 4.1 27.1 1.0
CB A:PHE99 4.1 25.6 1.0
N A:VAL405 4.1 26.9 1.0
C A:VAL405 4.2 26.0 1.0
CD1 A:LEU404 4.3 22.9 1.0
O A:HIS445 4.4 34.1 1.0
CD A:PRO448 4.4 26.9 1.0
CG A:LEU404 4.4 24.3 1.0
NE2 A:GLN126 4.5 26.6 1.0
CG A:PHE99 4.5 26.6 1.0
N A:PRO448 4.6 26.3 1.0
O A:HOH985 4.6 21.6 1.0
CB A:VAL405 4.7 26.6 1.0
OD2 A:ASP406 4.8 30.5 1.0
N A:ALA447 4.8 26.4 1.0
CE2 A:PHE99 4.8 26.4 1.0
CA A:ALA447 4.9 26.0 1.0
CG1 A:VAL405 4.9 28.7 1.0
CA A:LEU404 5.0 25.7 1.0
O A:HOH904 5.0 24.3 1.0

Sodium binding site 6 out of 8 in 6i3j

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Sodium binding site 6 out of 8 in the Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na618

b:53.5
occ:1.00
 O6 B:NAG609 2.3 61.1 1.0
O B:THR522 3.0 54.5 1.0
OE1 B:GLU525 3.0 72.0 1.0
CB B:GLU525 3.3 60.1 1.0
C6 B:NAG609 3.4 65.2 1.0
CE1 B:TYR526 3.6 41.2 1.0
CD1 B:TYR526 3.7 43.6 1.0
C B:THR522 4.0 55.4 1.0
CD B:GLU525 4.0 70.3 1.0
CG2 B:THR522 4.1 56.6 1.0
CA B:THR522 4.2 53.9 1.0
CZ B:TYR526 4.2 41.5 1.0
CG B:GLU525 4.3 66.4 1.0
C B:GLU525 4.3 53.8 1.0
CA B:GLU525 4.4 55.2 1.0
N B:TYR526 4.4 53.5 1.0
CG B:TYR526 4.5 43.5 1.0
C1 B:NAG610 4.5 74.9 1.0
OH B:TYR526 4.7 40.6 1.0
CB B:THR522 4.7 54.9 1.0
C5 B:NAG609 4.7 64.7 1.0
O B:GLU525 4.8 54.5 1.0
N B:GLU525 4.9 52.1 1.0
N2 B:NAG610 4.9 63.2 1.0
CE2 B:TYR526 4.9 40.7 1.0
C3 B:NAG610 5.0 78.5 1.0
C4 B:NAG609 5.0 66.2 1.0

Sodium binding site 7 out of 8 in 6i3j

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Sodium binding site 7 out of 8 in the Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na619

b:43.6
occ:1.00
 O B:HOH888 2.5 48.2 1.0
OD1 B:ASP285 2.5 56.0 1.0
OG B:SER284 3.3 47.2 1.0
CG B:ASP285 3.6 49.7 1.0
OD2 B:ASP285 4.0 44.2 1.0
CB B:SER284 4.1 46.4 1.0
O B:HOH904 4.4 43.0 1.0
O B:HOH811 4.5 45.0 1.0
N B:ASP285 4.5 46.8 1.0
OD2 B:ASP282 4.5 41.1 1.0
C B:SER284 4.7 47.2 1.0
O B:HOH890 4.8 41.6 1.0
CB B:ASP285 4.8 48.2 1.0
CA B:SER284 4.9 46.9 1.0
CA B:ASP285 5.0 46.6 1.0

Sodium binding site 8 out of 8 in 6i3j

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Sodium binding site 8 out of 8 in the Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Bilirubin Oxidase From Myrothecium Verrucaria in Complex with Ferricyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na620

b:45.0
occ:1.00
 OE2 B:GLU261 2.5 35.4 1.0
OD1 B:ASP338 2.7 40.3 1.0
O A:HOH806 2.9 38.0 1.0
O2 A:SIN617 3.3 32.9 1.0
CD B:GLU261 3.3 35.5 1.0
OE1 B:GLU261 3.3 36.0 1.0
CB A:ASN32 3.5 37.1 1.0
C1 A:SIN617 3.6 32.6 1.0
CG B:ASP338 3.6 38.1 1.0
CA B:ASP338 3.6 36.1 1.0
CB B:ASP338 3.7 37.0 1.0
C3 A:SIN619 4.0 72.1 1.0
O1 A:SIN617 4.0 31.2 1.0
C2 A:SIN617 4.1 33.0 1.0
CG1 A:VAL31 4.1 37.1 1.0
CA A:ASN32 4.2 34.9 1.0
N B:VAL339 4.3 35.6 1.0
C B:ASP338 4.3 37.2 1.0
O A:VAL31 4.3 31.9 1.0
C2 A:SIN619 4.6 76.5 1.0
CG A:ASN32 4.6 39.4 1.0
ND2 A:ASN32 4.6 38.2 1.0
C A:VAL31 4.7 34.5 1.0
N A:ASN32 4.7 33.7 1.0
CG B:GLU261 4.7 35.8 1.0
NH1 A:ARG527 4.8 35.8 1.0
OD2 B:ASP338 4.8 34.0 1.0
OD2 A:ASP533 4.8 47.6 1.0
N B:ASP338 4.8 34.6 1.0
O B:ARG337 4.9 36.2 1.0
O B:VAL339 4.9 38.4 1.0

Reference:

T.Koval, L.Svecova, L.H.Ostergaard, T.Skalova, J.Duskova, J.Hasek, P.Kolenko, K.Fejfarova, J.Stransky, M.Trundova, J.Dohnalek. Trp-His Covalent Adduct in Bilirubin Oxidase Is Crucial For Effective Bilirubin Binding But Has A Minor Role in Electron Transfer. Sci Rep V. 9 13700 2019.
ISSN: ESSN 2045-2322
PubMed: 31548583
DOI: 10.1038/S41598-019-50105-3
Page generated: Tue Oct 8 09:32:30 2024

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