Sodium in PDB 3pvz: Udp-N-Acetylglucosamine 4,6-Dehydratase From Vibrio Fischeri

The structure of Udp-N-Acetylglucosamine 4,6-Dehydratase From Vibrio Fischeri, PDB code: 3pvz was solved by J.Osipiuk, N.Marshall, C.Tesar, L.Pearson, K.Buck, A.Joachimiak, Midwestcenter For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.00 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	69.920, 74.837, 88.789, 102.71, 95.15, 100.35
R / Rfree (%)	18.7 / 23.3

The binding sites of Sodium atom in the Udp-N-Acetylglucosamine 4,6-Dehydratase From Vibrio Fischeri (pdb code 3pvz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Udp-N-Acetylglucosamine 4,6-Dehydratase From Vibrio Fischeri, PDB code: 3pvz:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Udp-N-Acetylglucosamine 4,6-Dehydratase From Vibrio Fischeri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Udp-N-Acetylglucosamine 4,6-Dehydratase From Vibrio Fischeri within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:42.3 occ:1.00 O A:HOH487 2.2 25.5 1.0 OE1 A:GLN109 2.3 30.5 1.0 O A:HOH485 2.4 24.4 1.0 O D:HOH482 2.4 24.2 1.0 OE1 D:GLN109 2.5 32.8 1.0 O D:HOH498 2.5 28.2 1.0 CD A:GLN109 3.3 28.4 1.0 CD D:GLN109 3.4 30.4 1.0 NE2 D:GLN109 3.6 27.4 1.0 NE2 A:GLN109 3.7 22.1 1.0 NH2 A:ARG34 4.3 30.0 1.0 O A:HOH486 4.3 18.0 1.0 NH1 D:ARG34 4.3 26.1 1.0 O D:HOH401 4.4 25.7 1.0 NH2 D:ARG34 4.5 22.0 1.0 NH1 A:ARG34 4.5 26.9 1.0 CG A:GLN109 4.6 26.6 1.0 O A:ALA152 4.7 30.7 1.0 O D:ALA152 4.7 36.9 1.0 CG D:GLN109 4.8 29.9 1.0 CZ D:ARG34 4.9 24.0 1.0 CZ A:ARG34 4.9 26.4 1.0

Sodium binding site 2 out of 3 in the Udp-N-Acetylglucosamine 4,6-Dehydratase From Vibrio Fischeri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Udp-N-Acetylglucosamine 4,6-Dehydratase From Vibrio Fischeri within 5.0Å range: probe atom residue distance (Å) B Occ A:Na607 b:41.0 occ:1.00 O A:HOH504 2.2 39.0 1.0 O A:HOH460 2.3 24.9 1.0 O D:HOH450 2.4 15.7 1.0 O A:GLN32 2.5 27.1 1.0 O D:ALA106 2.6 23.4 1.0 C D:ALA106 3.6 24.4 1.0 C A:GLN32 3.7 26.4 1.0 CB A:GLN32 4.1 27.5 1.0 O D:LYS105 4.3 31.7 1.0 NE2 A:GLN58 4.3 21.4 1.0 N D:ASP107 4.4 23.9 1.0 O A:HOH467 4.4 23.2 1.0 CA D:ASP107 4.4 25.3 1.0 OD2 A:ASP111 4.5 19.6 1.0 CA A:GLN32 4.5 27.1 1.0 O D:ASP107 4.5 26.9 1.0 CA D:ALA106 4.5 27.4 1.0 OE1 A:GLN58 4.6 33.7 1.0 OE1 A:GLN32 4.6 35.6 1.0 N A:SER33 4.7 25.2 1.0 CA A:SER33 4.8 25.7 1.0 CD A:GLN58 4.9 28.3 1.0 OD1 A:ASP111 5.0 22.1 1.0 CG A:ASP111 5.0 29.9 1.0

Sodium binding site 3 out of 3 in the Udp-N-Acetylglucosamine 4,6-Dehydratase From Vibrio Fischeri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Udp-N-Acetylglucosamine 4,6-Dehydratase From Vibrio Fischeri within 5.0Å range: probe atom residue distance (Å) B Occ A:Na608 b:43.4 occ:1.00 O A:HOH413 2.4 20.4 1.0 O D:GLN32 2.4 28.4 1.0 O D:HOH428 2.4 21.0 1.0 O D:HOH465 2.4 33.2 1.0 O D:HOH507 2.5 38.6 1.0 O A:ALA106 2.5 24.9 1.0 C A:ALA106 3.5 23.9 1.0 C D:GLN32 3.6 28.9 1.0 O D:HOH508 4.0 26.4 1.0 CB D:GLN32 4.2 31.6 1.0 OE1 D:GLN58 4.3 30.6 1.0 N A:ASP107 4.3 24.5 1.0 O A:LYS105 4.3 25.7 1.0 CA A:ALA106 4.4 24.7 1.0 CG D:GLN32 4.4 31.8 1.0 CA A:ASP107 4.4 24.5 1.0 NE2 D:GLN58 4.4 31.2 1.0 CA D:GLN32 4.5 28.9 1.0 OD2 D:ASP111 4.5 18.9 1.0 N D:SER33 4.6 27.2 1.0 CA D:SER33 4.6 26.1 1.0 O A:ASP107 4.7 28.1 1.0 OE1 D:GLN32 4.8 40.8 1.0 CD D:GLN58 4.8 31.5 1.0

J.Osipiuk, N.Marshall, C.Tesar, L.Pearson, K.Buck, A.Joachimiak. Udp-N-Acetylglucosamine 4,6-Dehydratase From Vibrio Fischeri. To Be Published.