Sodium in PDB 4r0c: Crystal Structure of the Alcanivorax Borkumensis Ydah Transporter Reveals An Unusual Topology

The structure of Crystal Structure of the Alcanivorax Borkumensis Ydah Transporter Reveals An Unusual Topology, PDB code: 4r0c was solved by C.-C.Su, J.R.Bolla, E.W.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.43 / 2.96
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	94.145, 200.984, 101.493, 90.00, 91.82, 90.00
R / Rfree (%)	20.6 / 25

The binding sites of Sodium atom in the Crystal Structure of the Alcanivorax Borkumensis Ydah Transporter Reveals An Unusual Topology (pdb code 4r0c). 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 the Alcanivorax Borkumensis Ydah Transporter Reveals An Unusual Topology, PDB code: 4r0c:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Alcanivorax Borkumensis Ydah Transporter Reveals An Unusual Topology


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 the Alcanivorax Borkumensis Ydah Transporter Reveals An Unusual Topology within 5.0Å range: probe atom residue distance (Å) B Occ A:Na801 b:61.2 occ:1.00 O A:GLY394 2.4 64.5 1.0 OD1 A:ASN390 2.4 69.6 1.0 OD1 A:ASN433 2.4 64.1 1.0 O A:ASP429 2.6 61.1 1.0 O A:HOH901 2.6 62.5 1.0 OD1 A:ASP429 2.7 65.7 1.0 CG A:ASN433 3.2 64.5 1.0 ND2 A:ASN433 3.2 60.5 1.0 CG A:ASN390 3.4 68.9 1.0 CG A:ASP429 3.4 67.4 1.0 C A:GLY394 3.4 62.8 1.0 C A:ASP429 3.6 65.0 1.0 ND2 A:ASN390 3.8 68.4 1.0 OD2 A:ASP429 3.8 65.6 1.0 NZ A:LYS399 3.9 69.0 1.0 CA A:GLY394 3.9 70.5 1.0 CA A:ASP429 4.3 67.4 1.0 CB A:ASP429 4.4 64.5 1.0 N A:ALA396 4.5 73.3 1.0 CB A:ASN433 4.6 69.7 1.0 N A:SER395 4.6 63.7 1.0 N A:SER430 4.6 60.7 1.0 CB A:ASN390 4.7 67.7 1.0 C A:SER395 4.8 70.6 1.0 CA A:SER430 5.0 63.2 1.0 CA A:ALA396 5.0 66.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Alcanivorax Borkumensis Ydah Transporter Reveals An Unusual Topology


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 the Alcanivorax Borkumensis Ydah Transporter Reveals An Unusual Topology within 5.0Å range: probe atom residue distance (Å) B Occ B:Na801 b:64.2 occ:1.00 O B:GLY394 2.3 65.3 1.0 O B:HOH901 2.5 63.2 1.0 OD1 B:ASN433 2.6 77.8 1.0 OD1 B:ASP429 2.6 70.3 1.0 O B:ASP429 2.7 75.7 1.0 OD1 B:ASN390 2.7 75.3 1.0 ND2 B:ASN390 3.3 74.1 1.0 CG B:ASN433 3.3 77.2 1.0 CG B:ASN390 3.3 76.7 1.0 CG B:ASP429 3.4 71.3 1.0 ND2 B:ASN433 3.4 73.3 1.0 C B:GLY394 3.4 66.1 1.0 C B:ASP429 3.7 77.1 1.0 NZ B:LYS399 3.8 67.3 1.0 OD2 B:ASP429 3.8 68.6 1.0 CA B:GLY394 4.1 62.3 1.0 CA B:ASP429 4.2 78.0 1.0 N B:ALA396 4.3 69.9 1.0 CB B:ASP429 4.3 71.1 1.0 N B:SER395 4.5 68.6 1.0 C B:SER395 4.6 70.2 1.0 N B:SER430 4.7 77.4 1.0 CB B:ASN433 4.7 82.8 1.0 CB B:ASN390 4.7 76.9 1.0 CA B:SER395 4.8 65.3 1.0 CA B:ALA396 4.9 66.2 1.0 CE B:LYS399 5.0 67.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Alcanivorax Borkumensis Ydah Transporter Reveals An Unusual Topology


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 the Alcanivorax Borkumensis Ydah Transporter Reveals An Unusual Topology within 5.0Å range: probe atom residue distance (Å) B Occ C:Na801 b:58.2 occ:1.00 O C:GLY394 2.3 62.4 1.0 OD1 C:ASP429 2.4 66.4 1.0 O C:ASP429 2.5 66.7 1.0 O C:HOH901 2.5 55.1 1.0 OD1 C:ASN433 2.6 59.9 1.0 OD1 C:ASN390 2.8 67.3 1.0 CG C:ASP429 3.0 66.2 1.0 ND2 C:ASN390 3.3 64.1 1.0 CG C:ASN390 3.4 64.7 1.0 C C:GLY394 3.4 63.5 1.0 OD2 C:ASP429 3.4 67.3 1.0 CG C:ASN433 3.5 56.7 1.0 C C:ASP429 3.5 66.5 1.0 ND2 C:ASN433 3.7 54.4 1.0 NZ C:LYS399 3.7 65.4 1.0 CA C:GLY394 4.0 62.8 1.0 CA C:ASP429 4.0 62.0 1.0 CB C:ASP429 4.1 62.6 1.0 N C:ALA396 4.4 61.6 1.0 N C:SER395 4.5 63.0 1.0 C C:SER395 4.6 63.4 1.0 N C:SER430 4.7 61.0 1.0 CE C:LYS399 4.8 65.5 1.0 CA C:ALA396 4.8 58.5 1.0 CB C:ASN390 4.8 66.4 1.0 CB C:ASN433 4.8 62.6 1.0 CA C:SER395 4.9 59.1 1.0 CB C:ALA396 5.0 48.2 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Alcanivorax Borkumensis Ydah Transporter Reveals An Unusual Topology


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 the Alcanivorax Borkumensis Ydah Transporter Reveals An Unusual Topology within 5.0Å range: probe atom residue distance (Å) B Occ D:Na801 b:50.5 occ:1.00 O D:GLY394 2.3 51.2 1.0 OD1 D:ASN390 2.4 58.8 1.0 O D:HOH901 2.5 54.6 1.0 OD1 D:ASN433 2.5 57.8 1.0 OD1 D:ASP429 2.5 51.2 1.0 O D:ASP429 2.6 59.7 1.0 CG D:ASN390 3.2 61.8 1.0 CG D:ASP429 3.2 55.1 1.0 CG D:ASN433 3.3 64.7 1.0 ND2 D:ASN390 3.4 54.9 1.0 C D:GLY394 3.5 54.6 1.0 ND2 D:ASN433 3.5 68.4 1.0 NZ D:LYS399 3.6 53.9 1.0 C D:ASP429 3.6 62.1 1.0 OD2 D:ASP429 3.7 55.9 1.0 CA D:GLY394 4.0 54.1 1.0 CA D:ASP429 4.1 56.6 1.0 CB D:ASP429 4.2 54.6 1.0 N D:ALA396 4.5 60.3 1.0 C D:SER395 4.5 59.7 1.0 CB D:ASN390 4.6 57.1 1.0 N D:SER395 4.6 56.1 1.0 N D:SER430 4.7 58.9 1.0 CB D:ASN433 4.7 59.5 1.0 O D:SER395 4.8 59.3 1.0 CA D:ALA396 4.9 51.0 1.0 CA D:SER395 4.9 58.4 1.0 O D:ILE393 5.0 64.1 1.0

J.R.Bolla, C.C.Su, J.A.Delmar, A.Radhakrishnan, N.Kumar, T.H.Chou, F.Long, K.R.Rajashankar, E.W.Yu. Crystal Structure of the Alcanivorax Borkumensis Ydah Transporter Reveals An Unusual Topology. Nat Commun V. 6 6874 2015.
ISSN: ESSN 2041-1723
PubMed: 25892120
DOI: 10.1038/NCOMMS7874