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Sodium in PDB 2okq: Crystal Structure of Unknown Conserved Ybaa Protein From Shigella Flexneri

Protein crystallography data

The structure of Crystal Structure of Unknown Conserved Ybaa Protein From Shigella Flexneri, PDB code: 2okq was solved by G.Minasov, I.I.Vorontsov, L.Shuvalova, J.S.Brunzelle, O.Kiryukhina, F.R.Collart, A.Joachimiak, W.F.Anderson, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.39 / 1.80
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.843, 61.843, 137.320, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Unknown Conserved Ybaa Protein From Shigella Flexneri (pdb code 2okq). 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 Unknown Conserved Ybaa Protein From Shigella Flexneri, PDB code: 2okq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2okq

Go back to Sodium Binding Sites List in 2okq
Sodium binding site 1 out of 2 in the Crystal Structure of Unknown Conserved Ybaa Protein From Shigella Flexneri


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 Unknown Conserved Ybaa Protein From Shigella Flexneri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na118

b:18.4
occ:1.00
OE1 A:GLN84 2.2 21.6 1.0
O A:HOH122 2.5 20.7 1.0
CD A:GLN84 3.3 21.5 1.0
NE2 A:GLN84 3.9 23.0 1.0
CG A:GLN84 4.4 21.5 1.0
CB A:GLN84 4.6 21.0 1.0
O A:ASP80 4.9 17.3 1.0

Sodium binding site 2 out of 2 in 2okq

Go back to Sodium Binding Sites List in 2okq
Sodium binding site 2 out of 2 in the Crystal Structure of Unknown Conserved Ybaa Protein From Shigella Flexneri


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 Unknown Conserved Ybaa Protein From Shigella Flexneri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na119

b:30.4
occ:1.00
O A:HOH143 2.2 45.9 1.0
O A:GLY49 2.3 22.4 1.0
OD1 A:ASP48 2.3 27.8 1.0
O A:HOH155 2.4 36.6 1.0
OD2 A:ASP53 2.4 23.3 1.0
CG A:ASP48 3.2 26.2 1.0
SD A:MET56 3.3 33.2 0.7
C A:GLY49 3.4 22.4 1.0
N A:GLY49 3.6 22.0 1.0
CG A:ASP53 3.6 22.0 1.0
O A:HOH140 3.7 28.1 1.0
OD2 A:ASP48 3.7 30.3 1.0
CG A:MET56 3.8 25.5 0.7
O A:HOH148 3.9 35.7 1.0
OD1 A:ASP53 4.1 23.7 1.0
CA A:GLY49 4.1 22.3 1.0
CE A:MET56 4.2 26.4 0.3
C A:ASP48 4.3 21.5 1.0
CB A:ASP48 4.4 22.4 1.0
O A:HOH204 4.4 34.8 0.5
CA A:ASP48 4.5 21.5 1.0
N A:LYS50 4.5 23.4 1.0
CE A:MET56 4.6 34.4 0.7
CA A:LYS50 4.7 24.7 1.0
CB A:ASP53 4.7 18.7 1.0

Reference:

G.Minasov, I.I.Vorontsov, L.Shuvalova, J.S.Brunzelle, O.Kiryukhina, F.R.Collart, A.Joachimiak, W.F.Anderson. Crystal Structure of Unknown Conserved Ybaa Protein From Shigella Flexneri To Be Published.
Page generated: Tue Dec 15 05:52:30 2020

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