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Sodium in PDB 3nyu: X-Ray Crystal Structure of the Wbpe (Wlbe) Aminotransferase From Pseudomonas Aeruginosa As the Plp Internal Aldimine Adduct with Lysine 185

Protein crystallography data

The structure of X-Ray Crystal Structure of the Wbpe (Wlbe) Aminotransferase From Pseudomonas Aeruginosa As the Plp Internal Aldimine Adduct with Lysine 185, PDB code: 3nyu was solved by H.M.Holden, J.B.Thoden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 47.628, 54.068, 150.903, 84.26, 82.43, 64.93
R / Rfree (%) 18.1 / 21.9

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Crystal Structure of the Wbpe (Wlbe) Aminotransferase From Pseudomonas Aeruginosa As the Plp Internal Aldimine Adduct with Lysine 185 (pdb code 3nyu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Crystal Structure of the Wbpe (Wlbe) Aminotransferase From Pseudomonas Aeruginosa As the Plp Internal Aldimine Adduct with Lysine 185, PDB code: 3nyu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3nyu

Go back to Sodium Binding Sites List in 3nyu
Sodium binding site 1 out of 2 in the X-Ray Crystal Structure of the Wbpe (Wlbe) Aminotransferase From Pseudomonas Aeruginosa As the Plp Internal Aldimine Adduct with Lysine 185


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of the Wbpe (Wlbe) Aminotransferase From Pseudomonas Aeruginosa As the Plp Internal Aldimine Adduct with Lysine 185 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na368

b:4.9
occ:1.00
O A:HOH1038 2.0 6.3 1.0
O B:HOH1035 2.1 6.4 1.0
O A:HOH383 2.1 6.9 1.0
O A:HOH1039 2.1 7.2 1.0
O B:HOH1036 2.1 6.0 1.0
O B:HOH1037 2.1 6.9 1.0
OD2 A:ASP231 4.0 8.0 1.0
O A:HOH408 4.0 8.5 1.0
O B:HOH388 4.0 7.6 1.0
OD2 B:ASP231 4.0 6.6 1.0
O A:ASP192 4.1 8.3 1.0
O B:ASP192 4.1 7.3 1.0
OD1 A:ASP231 4.2 6.5 1.0
OD1 B:ASP231 4.2 8.1 1.0
O B:HOH378 4.2 6.2 1.0
O A:HOH426 4.2 6.6 1.0
CG A:ASP231 4.4 7.8 1.0
CG B:ASP231 4.4 6.5 1.0
O A:ARG229 4.7 6.5 1.0
O A:ALA57 4.7 5.6 1.0
CB B:ASP192 4.7 6.5 1.0
CB A:ASP192 4.7 5.6 1.0
O B:ALA57 4.7 5.2 1.0
O B:ARG229 4.8 6.1 1.0
C A:ASP192 4.9 7.2 1.0
C B:ASP192 4.9 6.2 1.0
CB B:ALA57 4.9 4.2 1.0

Sodium binding site 2 out of 2 in 3nyu

Go back to Sodium Binding Sites List in 3nyu
Sodium binding site 2 out of 2 in the X-Ray Crystal Structure of the Wbpe (Wlbe) Aminotransferase From Pseudomonas Aeruginosa As the Plp Internal Aldimine Adduct with Lysine 185


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Crystal Structure of the Wbpe (Wlbe) Aminotransferase From Pseudomonas Aeruginosa As the Plp Internal Aldimine Adduct with Lysine 185 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na368

b:11.1
occ:1.00
O D:HOH1042 2.0 11.9 1.0
O C:HOH1043 2.0 13.3 1.0
O C:HOH1044 2.1 12.7 1.0
O C:HOH409 2.1 10.6 1.0
O C:HOH1040 2.1 13.0 1.0
O D:HOH1041 2.1 13.7 1.0
OD2 C:ASP231 4.0 13.4 1.0
O D:HOH374 4.0 14.2 1.0
O C:HOH436 4.0 15.0 1.0
OD2 D:ASP231 4.0 15.6 1.0
O D:ASP192 4.1 11.9 1.0
OD1 C:ASP231 4.2 13.3 1.0
OD1 D:ASP231 4.2 13.5 1.0
O C:ASP192 4.2 12.3 1.0
O D:HOH397 4.2 12.1 1.0
O C:HOH403 4.2 11.4 1.0
CG C:ASP231 4.3 7.9 1.0
CG D:ASP231 4.4 15.9 1.0
O D:ALA57 4.6 13.0 1.0
CB D:ASP192 4.7 11.7 1.0
O D:ARG229 4.7 13.9 1.0
O C:ALA57 4.7 11.1 1.0
CB C:ASP192 4.7 13.0 1.0
O C:ARG229 4.8 10.0 1.0
CB C:ALA57 4.9 10.6 1.0
C D:ASP192 4.9 11.0 1.0
CB D:ALA57 4.9 11.1 1.0
C C:ASP192 5.0 12.6 1.0

Reference:

G.T.Dow, M.Gilbert, J.B.Thoden, H.M.Holden. Structural Investigation on Wlarg From Campylobacter Jejuni: A Sugar Aminotransferase. Protein Sci. V. 26 586 2017.
ISSN: ISSN 0961-8368
PubMed: 28028852
DOI: 10.1002/PRO.3109
Page generated: Tue Dec 15 06:19:33 2020

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