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Sodium in PDB 6wye: Crystal Structure of Neisseria Gonorrhoeae Serine Acetyltransferase (Cyse)

Enzymatic activity of Crystal Structure of Neisseria Gonorrhoeae Serine Acetyltransferase (Cyse)

All present enzymatic activity of Crystal Structure of Neisseria Gonorrhoeae Serine Acetyltransferase (Cyse):
2.3.1.30;

Protein crystallography data

The structure of Crystal Structure of Neisseria Gonorrhoeae Serine Acetyltransferase (Cyse), PDB code: 6wye was solved by J.L.Hicks, K.E.Oldham, E.L.Summers, E.J.Prentice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.11 / 2.01
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 77.897, 93.867, 102.019, 90, 91.29, 90
R / Rfree (%) 18.3 / 22.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Neisseria Gonorrhoeae Serine Acetyltransferase (Cyse) (pdb code 6wye). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Neisseria Gonorrhoeae Serine Acetyltransferase (Cyse), PDB code: 6wye:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6wye

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Sodium binding site 1 out of 6 in the Crystal Structure of Neisseria Gonorrhoeae Serine Acetyltransferase (Cyse)


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 Neisseria Gonorrhoeae Serine Acetyltransferase (Cyse) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:43.1
occ:1.00
 O A:TYR93 2.3 35.4 1.0
O A:ASP96 2.3 33.5 1.0
O C:HOH469 2.4 37.5 1.0
O A:CYS99 2.5 37.0 1.0
C A:ASP96 3.3 32.5 1.0
C A:TYR93 3.4 36.8 1.0
C A:CYS99 3.6 38.0 1.0
CA A:PRO97 3.9 34.0 1.0
N A:PRO97 4.0 33.3 1.0
N A:ASP96 4.1 34.7 1.0
O A:ILE92 4.1 34.3 1.0
CA A:TYR93 4.1 34.2 1.0
N A:CYS99 4.1 34.6 1.0
CA A:CYS99 4.2 34.0 1.0
CB A:CYS99 4.2 32.3 1.0
O A:GLU94 4.3 40.4 1.0
CA A:ASP96 4.3 33.1 1.0
C A:PRO97 4.3 37.1 1.0
O C:HOH468 4.3 48.9 1.0
C A:GLU94 4.4 40.4 1.0
N A:GLU94 4.5 37.9 1.0
O A:PRO97 4.6 36.4 1.0
N A:ASP100 4.7 38.7 1.0
CA A:GLU94 4.7 42.0 1.0
N A:ARG95 4.7 38.1 1.0
C A:ARG95 4.8 36.8 1.0
CB A:ASP96 4.9 30.3 1.0
CG A:TYR93 5.0 40.7 1.0
N A:ALA98 5.0 30.5 1.0
C A:ILE92 5.0 31.5 1.0

Sodium binding site 2 out of 6 in 6wye

Go back to Sodium Binding Sites List in 6wye
Sodium binding site 2 out of 6 in the Crystal Structure of Neisseria Gonorrhoeae Serine Acetyltransferase (Cyse)


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 Neisseria Gonorrhoeae Serine Acetyltransferase (Cyse) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:44.0
occ:1.00
 O B:CYS99 2.4 38.2 1.0
O B:TYR93 2.4 36.7 1.0
O B:ASP96 2.5 30.8 1.0
O B:HOH441 2.5 53.4 1.0
O B:HOH403 2.5 43.0 1.0
C B:ASP96 3.3 31.8 1.0
C B:CYS99 3.5 39.0 1.0
C B:TYR93 3.6 37.9 1.0
CA B:PRO97 3.8 34.5 1.0
N B:PRO97 3.9 33.6 1.0
N B:CYS99 4.1 33.1 1.0
CA B:CYS99 4.2 35.5 1.0
C B:PRO97 4.2 37.0 1.0
CA B:TYR93 4.2 38.3 1.0
N B:ASP96 4.2 36.8 1.0
OD1 B:ASP100 4.2 61.2 1.0
O B:ILE92 4.3 36.3 1.0
CB B:CYS99 4.3 35.3 1.0
O B:GLU94 4.3 40.1 1.0
CA B:ASP96 4.4 33.4 1.0
O B:PRO97 4.4 34.2 1.0
C B:GLU94 4.5 42.1 1.0
N B:ASP100 4.5 42.6 1.0
N B:GLU94 4.6 38.7 1.0
CG B:ASP100 4.8 59.9 1.0
CA B:ASP100 4.8 47.6 1.0
CA B:GLU94 4.9 41.0 1.0
N B:ALA98 4.9 36.2 1.0
N B:ARG95 4.9 40.1 1.0
CG B:TYR93 5.0 46.3 1.0

Sodium binding site 3 out of 6 in 6wye

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Sodium binding site 3 out of 6 in the Crystal Structure of Neisseria Gonorrhoeae Serine Acetyltransferase (Cyse)


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 Neisseria Gonorrhoeae Serine Acetyltransferase (Cyse) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:41.3
occ:1.00
 O C:TYR93 2.4 31.9 1.0
O C:CYS99 2.4 39.3 1.0
O C:HOH481 2.4 44.0 1.0
O C:ASP96 2.5 28.8 1.0
O C:HOH440 2.7 45.3 1.0
C C:ASP96 3.4 31.1 1.0
C C:TYR93 3.5 33.9 1.0
C C:CYS99 3.5 37.9 1.0
CA C:PRO97 3.8 32.9 1.0
N C:PRO97 4.0 32.8 1.0
N C:CYS99 4.1 33.3 1.0
N C:ASP96 4.2 30.3 1.0
CA C:TYR93 4.2 34.3 1.0
CA C:CYS99 4.2 35.1 1.0
O C:ILE92 4.2 34.9 1.0
C C:PRO97 4.3 32.5 1.0
CB C:CYS99 4.3 34.8 1.0
O C:GLU94 4.3 36.2 1.0
CA C:ASP96 4.4 30.6 1.0
C C:GLU94 4.4 35.7 1.0
O C:PRO97 4.5 31.7 1.0
OD1 C:ASP100 4.6 55.1 1.0
N C:GLU94 4.6 31.8 1.0
N C:ASP100 4.6 37.4 1.0
CA C:GLU94 4.8 34.9 1.0
N C:ARG95 4.9 34.0 1.0
CG C:TYR93 4.9 40.1 1.0
N C:ALA98 5.0 32.2 1.0
CA C:ASP100 5.0 42.7 1.0
C C:ARG95 5.0 33.6 1.0
SG C:CYS99 5.0 34.2 1.0

Sodium binding site 4 out of 6 in 6wye

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Sodium binding site 4 out of 6 in the Crystal Structure of Neisseria Gonorrhoeae Serine Acetyltransferase (Cyse)


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 Neisseria Gonorrhoeae Serine Acetyltransferase (Cyse) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:42.9
occ:1.00
 O D:CYS99 2.4 36.8 1.0
O D:TYR93 2.4 37.2 1.0
O D:ASP96 2.4 34.7 1.0
O D:HOH480 2.5 49.0 1.0
O D:HOH429 2.7 51.0 1.0
C D:ASP96 3.4 34.6 1.0
C D:CYS99 3.5 37.5 1.0
C D:TYR93 3.5 38.6 1.0
CA D:PRO97 3.9 34.6 1.0
N D:PRO97 4.0 36.2 1.0
N D:CYS99 4.1 35.6 1.0
CA D:TYR93 4.1 39.0 1.0
CA D:CYS99 4.1 35.5 1.0
N D:ASP96 4.2 32.1 1.0
CB D:CYS99 4.2 34.7 1.0
O D:ILE92 4.2 37.9 1.0
C D:PRO97 4.3 37.1 1.0
CA D:ASP96 4.3 34.8 1.0
O D:GLU94 4.4 40.9 1.0
C D:GLU94 4.5 40.4 1.0
N D:GLU94 4.6 37.4 1.0
O D:PRO97 4.6 36.0 1.0
N D:ASP100 4.6 42.4 1.0
CA D:GLU94 4.8 40.1 1.0
SG D:CYS99 4.9 36.7 1.0
CG D:TYR93 4.9 45.6 1.0
N D:ARG95 4.9 37.7 1.0
CA D:ASP100 4.9 45.8 1.0
CB D:ASP96 4.9 35.6 1.0
N D:ALA98 5.0 37.7 1.0

Sodium binding site 5 out of 6 in 6wye

Go back to Sodium Binding Sites List in 6wye
Sodium binding site 5 out of 6 in the Crystal Structure of Neisseria Gonorrhoeae Serine Acetyltransferase (Cyse)


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 Neisseria Gonorrhoeae Serine Acetyltransferase (Cyse) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na301

b:42.5
occ:1.00
 O E:ASP96 2.4 31.8 1.0
O E:CYS99 2.4 38.1 1.0
O E:TYR93 2.4 34.7 1.0
O E:HOH421 2.6 40.6 1.0
C E:ASP96 3.3 31.7 1.0
C E:CYS99 3.5 39.2 1.0
C E:TYR93 3.5 37.8 1.0
CA E:PRO97 3.8 35.7 1.0
N E:PRO97 3.9 34.4 1.0
N E:CYS99 4.1 32.5 1.0
O E:ILE92 4.1 32.1 1.0
CA E:TYR93 4.1 37.8 1.0
CA E:CYS99 4.1 34.7 1.0
N E:ASP96 4.2 33.8 1.0
CB E:CYS99 4.2 32.6 1.0
C E:PRO97 4.3 39.0 1.0
CA E:ASP96 4.3 32.2 1.0
O E:GLU94 4.4 38.8 1.0
C E:GLU94 4.5 38.5 1.0
O E:PRO97 4.5 35.6 1.0
N E:GLU94 4.6 39.1 1.0
N E:ASP100 4.6 41.6 1.0
CA E:GLU94 4.9 39.2 1.0
N E:ARG95 4.9 35.6 1.0
CG E:TYR93 4.9 43.6 1.0
CA E:ASP100 4.9 42.2 1.0
N E:ALA98 4.9 37.1 1.0
C E:ARG95 4.9 32.6 1.0
SG E:CYS99 4.9 37.5 1.0
CB E:ASP96 4.9 31.5 1.0
CD1 E:TYR93 5.0 44.2 1.0

Sodium binding site 6 out of 6 in 6wye

Go back to Sodium Binding Sites List in 6wye
Sodium binding site 6 out of 6 in the Crystal Structure of Neisseria Gonorrhoeae Serine Acetyltransferase (Cyse)


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 Neisseria Gonorrhoeae Serine Acetyltransferase (Cyse) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na301

b:45.9
occ:1.00
 O F:HOH460 2.4 43.7 1.0
O F:TYR93 2.4 38.6 1.0
O F:ASP96 2.5 37.2 1.0
O F:CYS99 2.5 46.2 1.0
O F:HOH470 2.6 55.6 1.0
C F:ASP96 3.4 37.7 1.0
C F:TYR93 3.5 38.4 1.0
C F:CYS99 3.7 45.2 1.0
CA F:PRO97 3.9 37.5 1.0
N F:PRO97 4.0 37.0 1.0
O F:ILE92 4.2 34.9 1.0
N F:ASP96 4.2 37.4 1.0
N F:CYS99 4.2 40.6 1.0
CA F:TYR93 4.2 41.7 1.0
O F:GLU94 4.3 43.5 1.0
CA F:CYS99 4.3 41.3 1.0
C F:PRO97 4.3 40.5 1.0
CB F:CYS99 4.3 39.7 1.0
CA F:ASP96 4.4 38.4 1.0
C F:GLU94 4.4 42.0 1.0
N F:GLU94 4.6 37.1 1.0
O F:PRO97 4.6 38.4 1.0
N F:ASP100 4.8 45.8 1.0
CA F:GLU94 4.8 40.4 1.0
N F:ARG95 4.9 39.2 1.0
C F:ARG95 4.9 40.8 1.0

Reference:

J.L.Hicks, K.E.Oldham, E.L.Summers, E.J.Prentice. Crystal Structure of Neisseria Gonorrhoeae Serine Acetyltransferase (Cyse) To Be Published.
Page generated: Tue Oct 8 14:43:34 2024

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