Sodium in PDB 7cn7: T4 Phage Spackle Protein GP61.3 Complex with Lysozyme Domain of GP5 Tail Lysozyme

All present enzymatic activity of T4 Phage Spackle Protein GP61.3 Complex with Lysozyme Domain of GP5 Tail Lysozyme:
3.2.1.17;

The structure of T4 Phage Spackle Protein GP61.3 Complex with Lysozyme Domain of GP5 Tail Lysozyme, PDB code: 7cn7 was solved by S.Kanamaru, P.G.Leiman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.92 / 1.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.720, 69.180, 83.820, 90.00, 90.00, 90.00
R / Rfree (%)	10.7 / 12.2

The structure of T4 Phage Spackle Protein GP61.3 Complex with Lysozyme Domain of GP5 Tail Lysozyme also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the T4 Phage Spackle Protein GP61.3 Complex with Lysozyme Domain of GP5 Tail Lysozyme (pdb code 7cn7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the T4 Phage Spackle Protein GP61.3 Complex with Lysozyme Domain of GP5 Tail Lysozyme, PDB code: 7cn7:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the T4 Phage Spackle Protein GP61.3 Complex with Lysozyme Domain of GP5 Tail Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of T4 Phage Spackle Protein GP61.3 Complex with Lysozyme Domain of GP5 Tail Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na803 b:37.8 occ:1.00 O A:HOH971 2.2 18.4 1.0 O A:HOH1101 2.2 38.6 1.0 O A:HOH948 2.8 37.5 1.0 HZ2 A:TRP266 2.8 11.5 1.0 OE2 A:GLU278 2.9 9.0 1.0 O A:HOH1085 3.0 33.1 1.0 HH12 A:ARG271 3.1 12.8 1.0 NE2 A:GLN253 3.2 10.8 1.0 HB3 A:GLN253 3.2 11.3 1.0 HE22 A:GLN253 3.2 13.0 1.0 HG2 A:GLN253 3.2 11.7 1.0 O A:HOH980 3.3 43.0 1.0 CD A:GLN253 3.3 10.1 1.0 HE21 A:GLN253 3.5 13.0 1.0 HH22 A:ARG271 3.5 13.6 1.0 NH1 A:ARG271 3.6 10.7 1.0 CG A:GLN253 3.6 9.8 1.0 CD A:GLU278 3.6 8.6 1.0 CZ2 A:TRP266 3.7 9.6 1.0 OE1 A:GLU278 3.8 9.0 1.0 OE1 A:GLN253 3.9 12.6 1.0 CB A:GLN253 3.9 9.4 1.0 NH2 A:ARG271 3.9 11.3 1.0 H12 A:EDO802 4.0 13.2 0.4 CZ A:ARG271 4.0 10.3 1.0 HE1 A:TRP266 4.1 10.1 1.0 HH11 A:ARG271 4.1 12.8 1.0 HD2 A:LYS257 4.1 14.2 1.0 HO1 A:EDO802 4.2 32.2 0.6 HO1 A:EDO802 4.2 21.8 0.4 H11 A:EDO802 4.4 13.2 0.4 HH2 A:TRP266 4.4 11.9 1.0 CE2 A:TRP266 4.4 8.6 1.0 O1 A:EDO802 4.5 18.2 0.4 C1 A:EDO802 4.5 11.0 0.4 O1 A:EDO802 4.5 26.9 0.6 CH2 A:TRP266 4.5 9.9 1.0 NE1 A:TRP266 4.5 8.4 1.0 HH21 A:ARG271 4.5 13.6 1.0 HB2 A:GLN253 4.6 11.3 1.0 HG3 A:GLN253 4.6 11.7 1.0 O A:HOH968 4.6 22.1 1.0 HA A:GLN253 4.6 10.3 1.0 CA A:GLN253 4.9 8.6 1.0 CG A:GLU278 5.0 7.7 1.0 HG2 A:GLU278 5.0 9.2 1.0

Sodium binding site 2 out of 3 in the T4 Phage Spackle Protein GP61.3 Complex with Lysozyme Domain of GP5 Tail Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of T4 Phage Spackle Protein GP61.3 Complex with Lysozyme Domain of GP5 Tail Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na804 b:51.0 occ:1.00 OE2 A:GLU246 2.2 25.7 1.0 O A:HOH1088 2.4 28.8 1.0 HG23 A:THR242 3.1 14.8 1.0 CD A:GLU246 3.3 21.5 1.0 HG22 A:THR242 3.4 14.8 1.0 HG21 A:THR242 3.4 14.8 1.0 HG2 A:GLU246 3.4 16.3 1.0 CG2 A:THR242 3.5 12.4 1.0 HG3 A:GLU246 3.6 16.3 1.0 CG A:GLU246 3.7 13.6 1.0 O A:HOH1052 3.8 32.6 1.0 O A:HOH1114 4.2 21.0 1.0 OE1 A:GLU246 4.4 27.5 1.0 O A:HOH1121 4.9 21.6 1.0 H13 A:1PG801 5.0 22.9 1.0

Sodium binding site 3 out of 3 in the T4 Phage Spackle Protein GP61.3 Complex with Lysozyme Domain of GP5 Tail Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of T4 Phage Spackle Protein GP61.3 Complex with Lysozyme Domain of GP5 Tail Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ C:Na104 b:43.5 occ:1.00 OE2 C:GLU30 2.1 16.7 0.5 O C:HOH228 2.1 46.9 1.0 HH C:TYR24 2.3 16.5 1.0 HE1 C:TYR24 2.9 16.2 1.0 OH C:TYR24 2.9 13.8 1.0 HG2 C:GLU30 3.1 17.9 0.5 HB3 C:CYS29 3.2 11.7 1.0 CD C:GLU30 3.2 16.0 0.5 CE1 C:TYR24 3.6 13.5 1.0 SG C:CYS29 3.6 11.6 1.0 CG C:GLU30 3.7 14.9 0.5 CZ C:TYR24 3.7 11.7 1.0 HA C:LYS26 3.7 18.0 0.5 HA C:LYS26 3.7 19.2 0.5 CB C:CYS29 3.8 9.7 1.0 HG3 C:LYS26 3.9 28.1 0.5 O C:LYS26 4.1 14.8 1.0 HG3 C:GLU30 4.1 17.9 0.5 H C:GLU30 4.2 12.0 1.0 HB2 C:GLU30 4.2 17.3 0.5 HE2 C:MET33 4.2 11.6 1.0 OE1 C:GLU30 4.3 17.9 0.5 HB2 C:CYS29 4.3 11.7 1.0 HE1 C:MET33 4.5 11.6 1.0 N C:GLU30 4.5 10.0 1.0 CA C:LYS26 4.5 15.0 0.5 CA C:LYS26 4.6 16.0 0.5 HB2 C:LYS26 4.6 19.6 0.5 OE1 C:GLU30 4.6 20.6 0.5 CG C:LYS26 4.7 23.4 0.5 HA C:GLU30 4.8 12.9 0.5 HA C:GLU30 4.8 12.9 0.5 C C:LYS26 4.8 14.5 1.0 CE C:MET33 4.8 9.7 1.0 CD1 C:TYR24 4.9 13.3 1.0 CB C:GLU30 4.9 13.2 0.5 C C:CYS29 4.9 9.1 1.0 CA C:CYS29 5.0 9.2 1.0 CA C:GLU30 5.0 10.7 0.5

S.Kanamaru, K.Uchida, M.Nemoto, A.Fraser, F.Arisaka, P.G.Leiman. Structure and Function of the T4 Spackle Protein GP61.3. Viruses V. 12 2020.
ISSN: ISSN 1999-4915
PubMed: 32987925
DOI: 10.3390/V12101070