Atomistry » Sodium » PDB 6hz1-6ic1 » 6i3j
Atomistry »
  Sodium »
    PDB 6hz1-6ic1 »
      6i3j »

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

Go back to Sodium Binding Sites List in 6i3j
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

Go back to Sodium Binding Sites List in 6i3j
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

Go back to Sodium Binding Sites List in 6i3j
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

Go back to Sodium Binding Sites List in 6i3j
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

Go back to Sodium Binding Sites List in 6i3j
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

Go back to Sodium Binding Sites List in 6i3j
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

Go back to Sodium Binding Sites List in 6i3j
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

Go back to Sodium Binding Sites List in 6i3j
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

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy