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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

Protein crystallography data

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

Other elements in 2q3l:

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

Sodium Binding Sites:

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 2q3l

Go back to Sodium Binding Sites List in 2q3l
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 2q3l

Go back to Sodium Binding Sites List in 2q3l
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

Reference:

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
Page generated: Tue Dec 15 05:54:19 2020

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