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Sodium in PDB 4ohc: Crystal Structure of Orotate Phosphoribosyltransferase (Oprtase) From Burkholderia Cenocepacia

Enzymatic activity of Crystal Structure of Orotate Phosphoribosyltransferase (Oprtase) From Burkholderia Cenocepacia

All present enzymatic activity of Crystal Structure of Orotate Phosphoribosyltransferase (Oprtase) From Burkholderia Cenocepacia:
2.4.2.10;

Protein crystallography data

The structure of Crystal Structure of Orotate Phosphoribosyltransferase (Oprtase) From Burkholderia Cenocepacia, PDB code: 4ohc was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.85
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 76.310, 82.970, 83.100, 105.83, 104.27, 117.36
R / Rfree (%) 15.6 / 19.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Orotate Phosphoribosyltransferase (Oprtase) From Burkholderia Cenocepacia (pdb code 4ohc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Orotate Phosphoribosyltransferase (Oprtase) From Burkholderia Cenocepacia, PDB code: 4ohc:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4ohc

Go back to Sodium Binding Sites List in 4ohc
Sodium binding site 1 out of 4 in the Crystal Structure of Orotate Phosphoribosyltransferase (Oprtase) From Burkholderia Cenocepacia


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 Orotate Phosphoribosyltransferase (Oprtase) From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:27.6
occ:1.00
 O B:HOH549 2.3 43.1 1.0
O B:HOH430 2.3 28.2 1.0
O B:ASN113 2.3 30.7 1.0
O B:ILE116 2.4 25.4 1.0
O B:HOH482 2.4 30.1 1.0
O B:HOH495 2.4 32.5 1.0
C B:ASN113 3.3 31.9 1.0
C B:ILE116 3.6 24.6 1.0
OE2 B:GLU117 3.9 27.6 1.0
CB B:ASN113 4.0 35.2 1.0
N B:ILE116 4.0 25.3 1.0
OE1 B:GLU117 4.0 27.8 1.0
N B:ALA114 4.1 31.6 1.0
CA B:ALA114 4.1 30.8 1.0
C B:ALA114 4.2 29.1 1.0
CD B:GLU117 4.2 27.0 1.0
O B:HOH548 4.2 35.7 1.0
O E:HOH432 4.3 41.2 1.0
CA B:ILE116 4.3 24.5 1.0
O B:ALA114 4.3 28.9 1.0
CA B:ASN113 4.3 34.0 1.0
N B:GLU117 4.6 23.9 1.0
CB B:ILE116 4.6 24.7 1.0
N B:GLN115 4.7 28.0 1.0
CA B:GLU117 4.8 24.6 1.0
O B:HOH547 4.8 33.9 1.0

Sodium binding site 2 out of 4 in 4ohc

Go back to Sodium Binding Sites List in 4ohc
Sodium binding site 2 out of 4 in the Crystal Structure of Orotate Phosphoribosyltransferase (Oprtase) From Burkholderia Cenocepacia


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 Orotate Phosphoribosyltransferase (Oprtase) From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na303

b:33.4
occ:1.00
 O D:HOH557 2.2 25.6 1.0
O D:HOH580 2.2 36.0 1.0
O D:ILE116 2.3 26.1 1.0
O D:ASN113 2.4 33.8 1.0
O D:HOH562 2.5 44.6 1.0
C D:ASN113 3.5 35.3 1.0
C D:ILE116 3.5 24.7 1.0
OE2 D:GLU117 3.8 31.7 1.0
O D:HOH560 3.8 40.0 1.0
N D:ILE116 4.0 25.5 1.0
CD D:GLU117 4.1 29.9 1.0
OE1 D:GLU117 4.2 32.3 1.0
O D:HOH559 4.2 50.4 1.0
C D:ALA114 4.2 30.4 1.0
CB D:ASN113 4.2 40.3 1.0
CA D:ALA114 4.2 33.1 1.0
N D:ALA114 4.2 34.4 1.0
CA D:ILE116 4.3 24.6 1.0
O D:ALA114 4.4 29.7 1.0
CA D:ASN113 4.5 38.1 1.0
N D:GLU117 4.5 23.4 1.0
CB D:ILE116 4.7 25.6 1.0
CA D:GLU117 4.7 24.2 1.0
N D:GLN115 4.7 28.7 1.0
O D:HOH558 4.7 42.7 1.0
O A:HOH422 4.8 18.5 1.0
O D:HOH563 4.8 34.0 1.0
NZ A:LYS47 4.9 21.5 0.4

Sodium binding site 3 out of 4 in 4ohc

Go back to Sodium Binding Sites List in 4ohc
Sodium binding site 3 out of 4 in the Crystal Structure of Orotate Phosphoribosyltransferase (Oprtase) From Burkholderia Cenocepacia


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 Orotate Phosphoribosyltransferase (Oprtase) From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na303

b:27.4
occ:1.00
 O E:HOH442 2.2 31.7 1.0
O E:HOH590 2.3 40.9 1.0
O E:ASN113 2.3 32.2 1.0
O E:HOH441 2.3 28.6 1.0
O E:ILE116 2.4 24.1 1.0
O E:HOH536 2.5 34.9 1.0
C E:ASN113 3.4 32.7 1.0
C E:ILE116 3.6 23.4 1.0
OE2 E:GLU117 3.9 25.6 1.0
OE1 E:GLU117 4.0 25.6 1.0
N E:ILE116 4.1 24.3 1.0
CB E:ASN113 4.1 37.1 1.0
CD E:GLU117 4.1 24.8 1.0
CA E:ALA114 4.1 30.5 1.0
N E:ALA114 4.1 31.6 1.0
C E:ALA114 4.2 28.3 1.0
O E:ALA114 4.3 27.8 1.0
CA E:ILE116 4.3 23.5 1.0
O E:HOH541 4.4 35.7 1.0
O E:HOH534 4.4 35.6 1.0
CA E:ASN113 4.4 35.1 1.0
O E:HOH535 4.6 29.6 1.0
N E:GLU117 4.6 22.4 1.0
CB E:ILE116 4.6 23.9 1.0
N E:GLN115 4.8 27.0 1.0
CA E:GLU117 4.8 22.7 1.0
O B:HOH484 4.9 36.9 1.0
O E:HOH402 4.9 16.1 1.0

Sodium binding site 4 out of 4 in 4ohc

Go back to Sodium Binding Sites List in 4ohc
Sodium binding site 4 out of 4 in the Crystal Structure of Orotate Phosphoribosyltransferase (Oprtase) From Burkholderia Cenocepacia


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 Orotate Phosphoribosyltransferase (Oprtase) From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na302

b:30.1
occ:1.00
 O F:ASN113 2.3 34.6 1.0
O F:HOH534 2.3 35.0 1.0
O F:HOH531 2.3 40.0 1.0
O F:HOH602 2.4 46.9 1.0
O F:ILE116 2.4 26.5 1.0
O F:HOH532 2.4 29.8 1.0
C F:ASN113 3.4 35.8 1.0
C F:ILE116 3.6 25.6 1.0
O F:HOH536 3.8 54.4 1.0
OE2 F:GLU117 3.9 30.7 1.0
N F:ILE116 4.1 26.7 1.0
N F:ALA114 4.1 35.0 1.0
CA F:ALA114 4.1 33.7 1.0
OE1 F:GLU117 4.2 30.8 1.0
CB F:ASN113 4.2 40.4 1.0
CD F:GLU117 4.2 29.2 1.0
C F:ALA114 4.2 31.2 1.0
O F:HOH537 4.3 38.0 1.0
CA F:ILE116 4.4 25.7 1.0
CA F:ASN113 4.4 38.2 1.0
O F:ALA114 4.4 30.7 1.0
N F:GLU117 4.6 24.5 1.0
CB F:ILE116 4.7 26.3 1.0
N F:GLN115 4.8 29.6 1.0
CA F:GLU117 4.8 24.9 1.0
O F:HOH533 4.9 37.6 1.0
O C:HOH489 4.9 41.0 1.0
O F:HOH412 5.0 20.3 1.0

Reference:

C.M.Lukacs, J.Abendroth, T.E.Edwards, D.Lorimer. Crystal Structure of Orotate Phosphoribosyltransferase (Oprtase) From Burkholderia Cenocepacia To Be Published.
Page generated: Tue Dec 15 06:56:55 2020

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