Sodium in PDB 2q3l: Crystal Structure of An Uncharacterized Protein From DUF3478 Family with A Spoiiaa-Like Fold (SHEW_3102) From Shewanella Loihica Pv-4 at 2.25 A Resolution

The structure of Crystal Structure of An Uncharacterized Protein From DUF3478 Family with A Spoiiaa-Like Fold (SHEW_3102) From Shewanella Loihica Pv-4 at 2.25 A Resolution, PDB code: 2q3l was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.65 / 2.25
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	40.387, 113.963, 130.692, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 23.9

The structure of Crystal Structure of An Uncharacterized Protein From DUF3478 Family with A Spoiiaa-Like Fold (SHEW_3102) From Shewanella Loihica Pv-4 at 2.25 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of An Uncharacterized Protein From DUF3478 Family with A Spoiiaa-Like Fold (SHEW_3102) From Shewanella Loihica Pv-4 at 2.25 A Resolution (pdb code 2q3l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of An Uncharacterized Protein From DUF3478 Family with A Spoiiaa-Like Fold (SHEW_3102) From Shewanella Loihica Pv-4 at 2.25 A Resolution, PDB code: 2q3l:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of An Uncharacterized Protein From DUF3478 Family with A Spoiiaa-Like Fold (SHEW_3102) From Shewanella Loihica Pv-4 at 2.25 A Resolution


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 An Uncharacterized Protein From DUF3478 Family with A Spoiiaa-Like Fold (SHEW_3102) From Shewanella Loihica Pv-4 at 2.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na126 b:43.7 occ:1.00 O A:GLY109 2.2 51.8 1.0 O A:THR107 2.4 47.4 1.0 O A:HOH147 2.4 41.2 1.0 O A:ASN104 2.5 47.9 1.0 OG1 A:THR107 2.5 45.4 1.0 OD1 A:ASN104 2.5 43.0 1.0 C A:THR107 3.1 48.3 1.0 C A:ASN104 3.3 46.9 1.0 CG A:ASN104 3.4 46.7 1.0 C A:GLY109 3.4 50.3 1.0 CA A:ASN104 3.4 45.4 1.0 CB A:THR107 3.5 49.4 1.0 CA A:THR107 3.7 47.7 1.0 N A:THR107 3.8 51.0 1.0 CB A:ASN104 4.0 44.9 1.0 O A:HOH152 4.1 46.6 1.0 N A:GLY109 4.1 48.7 1.0 C A:PRO108 4.1 47.6 1.0 N A:PRO108 4.2 46.5 1.0 CA A:GLU110 4.2 50.4 1.0 N A:GLU110 4.3 50.3 1.0 N A:PHE111 4.3 47.7 1.0 CD1 A:PHE111 4.3 44.2 1.0 ND2 A:ASN104 4.3 37.1 1.0 O A:PRO108 4.4 52.8 1.0 CA A:GLY109 4.4 49.6 1.0 O A:ALA103 4.4 46.8 1.0 CA A:PRO108 4.5 45.7 1.0 N A:TRP105 4.6 45.4 1.0 C A:GLU110 4.7 47.5 1.0 N A:ASN104 4.7 45.9 1.0 CG2 A:THR107 4.8 40.1 1.0 OE2 A:GLU110 4.9 64.8 1.0 OE1 A:GLU110 4.9 71.7 1.0 CD A:GLU110 4.9 60.2 1.0 CE1 A:PHE111 5.0 46.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of An Uncharacterized Protein From DUF3478 Family with A Spoiiaa-Like Fold (SHEW_3102) From Shewanella Loihica Pv-4 at 2.25 A Resolution


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 An Uncharacterized Protein From DUF3478 Family with A Spoiiaa-Like Fold (SHEW_3102) From Shewanella Loihica Pv-4 at 2.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na126 b:37.4 occ:1.00 O B:GLY109 2.2 49.4 1.0 O B:THR107 2.3 43.9 1.0 O B:ASN104 2.4 50.4 1.0 O B:HOH154 2.4 50.9 1.0 OD1 B:ASN104 2.5 46.5 1.0 OG1 B:THR107 2.5 42.4 1.0 C B:THR107 3.2 44.5 1.0 C B:ASN104 3.3 47.0 1.0 C B:GLY109 3.3 49.6 1.0 CG B:ASN104 3.5 48.1 1.0 CA B:ASN104 3.6 45.3 1.0 CB B:THR107 3.6 44.2 1.0 O B:HOH153 3.7 50.8 1.0 CA B:THR107 3.8 42.5 1.0 N B:THR107 3.9 47.8 1.0 C B:PRO108 4.1 46.1 1.0 CA B:GLU110 4.1 50.1 1.0 N B:GLY109 4.1 48.2 1.0 CB B:ASN104 4.1 46.6 1.0 N B:GLU110 4.1 47.7 1.0 N B:PRO108 4.2 41.1 1.0 O B:PRO108 4.2 48.7 1.0 N B:PHE111 4.3 45.5 1.0 CD1 B:PHE111 4.3 47.4 1.0 CA B:GLY109 4.4 48.1 1.0 OE2 B:GLU110 4.4 69.5 1.0 ND2 B:ASN104 4.4 42.5 1.0 O B:ALA103 4.5 51.6 1.0 CA B:PRO108 4.5 45.3 1.0 N B:TRP105 4.6 45.1 1.0 C B:GLU110 4.6 46.1 1.0 N B:ASN104 4.8 46.9 1.0 CG2 B:THR107 4.9 41.6 1.0 CE1 B:PHE111 4.9 46.7 1.0 CD B:GLU110 5.0 68.3 1.0

A.Kumar, A.Lomize, K.K.Jin, D.Carlton, M.D.Miller, L.Jaroszewski, P.Abdubek, T.Astakhova, H.L.Axelrod, H.J.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, J.Feuerhelm, J.C.Grant, A.Grzechnik, G.W.Han, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, D.Marciano, D.Mcmullan, A.T.Morse, E.Nigoghossian, L.Okach, R.Reyes, C.L.Rife, N.Sefcovic, H.J.Tien, C.B.Trame, H.Van Den Bedem, D.Weekes, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson. Open and Closed Conformations of Two Spoiiaa-Like Proteins (YP_749275.1 and YP_001095227.1) Provide Insights Into Membrane Association and Ligand Binding. Acta Crystallogr.,Sect.F V. 66 1245 2010.
ISSN: ESSN 1744-3091
PubMed: 20944218
DOI: 10.1107/S1744309109042481