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Sodium in PDB 5w6h: Crystal Structure of Bacteriophage CBA120 Tailspike Protein 4 Enzymatically Active Domain (TSP4DN, ORF213)

Protein crystallography data

The structure of Crystal Structure of Bacteriophage CBA120 Tailspike Protein 4 Enzymatically Active Domain (TSP4DN, ORF213), PDB code: 5w6h was solved by M.Plattner, M.M.Shneider, P.G.Leiman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.29 / 2.29
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 170.079, 170.079, 246.384, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 17

Other elements in 5w6h:

The structure of Crystal Structure of Bacteriophage CBA120 Tailspike Protein 4 Enzymatically Active Domain (TSP4DN, ORF213) also contains other interesting chemical elements:

Potassium (K) 1 atom
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Bacteriophage CBA120 Tailspike Protein 4 Enzymatically Active Domain (TSP4DN, ORF213) (pdb code 5w6h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Bacteriophage CBA120 Tailspike Protein 4 Enzymatically Active Domain (TSP4DN, ORF213), PDB code: 5w6h:

Sodium binding site 1 out of 1 in 5w6h

Go back to Sodium Binding Sites List in 5w6h
Sodium binding site 1 out of 1 in the Crystal Structure of Bacteriophage CBA120 Tailspike Protein 4 Enzymatically Active Domain (TSP4DN, ORF213)


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 Bacteriophage CBA120 Tailspike Protein 4 Enzymatically Active Domain (TSP4DN, ORF213) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1112

b:39.5
occ:1.00
OH B:TYR1011 2.7 30.6 1.0
OH A:TYR1011 2.8 26.5 1.0
O B:HOH1868 2.8 31.2 1.0
OH C:TYR1011 2.8 30.1 1.0
O A:HOH1203 3.7 72.7 1.0
CZ B:TYR1011 3.7 30.0 1.0
CG2 A:ILE949 3.8 24.9 1.0
CZ A:TYR1011 3.8 33.2 1.0
CZ C:TYR1011 3.8 32.9 1.0
CG2 B:ILE949 3.8 25.8 1.0
CG2 C:ILE949 3.9 29.1 1.0
CE1 B:TYR1011 3.9 30.9 1.0
CE1 C:TYR1011 4.0 30.9 1.0
CE1 A:TYR1011 4.1 26.1 1.0
CD1 A:ILE949 4.2 25.5 1.0
CD1 C:ILE949 4.3 27.9 1.0
CD1 B:ILE949 4.4 29.8 1.0
O B:HOH1669 4.4 56.3 1.0
O A:HOH1568 4.6 46.5 1.0
O C:HOH1652 4.6 49.6 1.0
O B:HOH1492 4.7 35.4 1.0
CB A:ILE949 4.7 25.8 1.0
CB B:ILE949 4.8 31.6 1.0
CB C:ILE949 4.8 28.7 1.0
O C:HOH1427 4.9 39.2 1.0
CE2 B:TYR1011 4.9 26.9 1.0

Reference:

M.Plattner, M.M.Shneider, N.P.Arbatsky, A.S.Shashkov, A.O.Chizhov, S.Nazarov, N.S.Prokhorov, N.M.I.Taylor, S.A.Buth, M.Gambino, Y.E.Gencay, L.Brondsted, E.M.Kutter, Y.A.Knirel, P.G.Leiman. Structure and Function of the Branched Receptor-Binding Complex of Bacteriophage CBA120. J.Mol.Biol. V. 431 3718 2019.
ISSN: ESSN 1089-8638
PubMed: 31325442
DOI: 10.1016/J.JMB.2019.07.022
Page generated: Tue Dec 15 11:47:18 2020

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