Sodium in PDB 7sez: Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP

The structure of Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP, PDB code: 7sez was solved by J.K.Peters, R.W.Tibble, M.Warminski, J.Jemielity, J.D.Gross, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.50 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	52.55, 140.1, 75.98, 90, 90, 90
R / Rfree (%)	19.3 / 22.4

The binding sites of Sodium atom in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP (pdb code 7sez). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP, PDB code: 7sez:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP


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 Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:36.6 occ:0.59 O A:HOH462 2.3 45.7 1.0 O A:HOH484 2.3 36.6 1.0 NH1 A:ARG92 3.1 30.1 1.0 NE A:ARG92 3.4 27.4 1.0 CZ A:ARG92 3.7 28.6 1.0 O A:LYS93 3.9 28.4 1.0 O A:HOH478 4.4 39.6 1.0 O A:HOH434 4.5 31.2 1.0 CD A:ARG92 4.7 30.4 1.0 O A:HOH480 4.7 47.0 1.0 O A:GLY94 4.8 40.0 1.0 CB A:ARG92 4.9 27.8 1.0 O A:HOH542 4.9 37.6 1.0

Sodium binding site 2 out of 9 in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP


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 Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:98.7 occ:0.50 O A:HOH589 2.4 43.4 1.0 CG2 A:ILE99 3.0 24.3 1.0 CB A:ILE99 4.2 21.0 1.0 CD1 A:LEU84 4.5 22.7 1.0 CB A:PRO101 4.6 20.9 1.0 CG1 A:ILE99 4.7 32.2 1.0 CA A:PRO101 4.8 19.2 1.0 CD1 A:TYR81 4.9 24.1 1.0

Sodium binding site 3 out of 9 in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:56.6 occ:0.50 O A:HOH474 2.6 48.2 0.5 NE2 A:GLN169 2.7 32.8 1.0 O A:HOH556 3.2 42.0 1.0 O A:HOH433 3.2 40.1 1.0 CG A:GLN169 3.5 31.6 1.0 CD A:GLN169 3.5 35.9 1.0 NA A:NA305 4.2 72.0 1.0 CB A:GLN169 4.6 32.8 1.0 O A:ARG134 4.7 38.4 1.0 CA A:GLN169 4.7 36.0 1.0 OE1 A:GLN169 4.7 31.3 1.0 OD2 A:ASP173 4.8 43.5 1.0 N A:GLN169 4.9 31.8 1.0

Sodium binding site 4 out of 9 in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:72.0 occ:1.00 O A:ARG134 2.4 38.4 1.0 NE2 A:GLN169 2.4 32.8 1.0 N A:THR136 2.6 30.0 1.0 C A:ARG134 2.6 46.2 1.0 C A:ILE135 2.7 25.6 1.0 CA A:ILE135 2.8 24.3 1.0 CD A:GLN169 2.8 35.9 1.0 N A:ILE135 2.8 26.8 1.0 CG2 A:THR136 3.1 33.3 1.0 OE1 A:GLN169 3.1 31.3 1.0 O A:ILE135 3.5 29.5 1.0 OG1 A:THR136 3.5 31.4 1.0 CB A:THR136 3.6 34.2 1.0 CA A:THR136 3.6 30.9 1.0 CA A:ARG134 3.7 27.3 1.0 CG A:GLN169 3.8 31.6 1.0 O A:HOH433 4.0 40.1 1.0 NA A:NA304 4.2 56.6 0.5 O A:GLU133 4.3 48.5 1.0 CB A:ILE135 4.3 24.1 1.0 O A:HOH556 4.4 42.0 1.0 N A:ARG134 4.5 33.7 1.0 C A:GLU133 4.7 32.5 1.0 C A:THR136 4.8 24.8 1.0 CB A:ARG134 4.9 38.8 1.0 O A:THR136 4.9 24.6 1.0 CG2 A:ILE135 5.0 29.1 1.0

Sodium binding site 5 out of 9 in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:55.8 occ:1.00 O A:HOH526 2.3 38.6 1.0 O A:HOH453 2.4 42.9 1.0 OH A:TYR201 2.8 25.9 1.0 O A:HOH436 2.8 54.0 1.0 O A:HOH512 2.9 36.7 1.0 O A:HOH475 3.1 27.0 1.0 CE1 A:TYR201 3.5 24.6 1.0 CZ A:TYR201 3.5 22.6 1.0 O A:HOH471 4.0 47.6 1.0 OE2 A:GLU16 4.4 27.6 1.0 CD1 A:ILE18 4.5 28.1 1.0 O A:HOH548 4.6 47.7 1.0 CD2 A:LEU202 4.7 21.7 1.0 CD1 A:TYR201 4.8 22.3 1.0 OG1 A:THR149 4.8 30.9 1.0 OE1 A:GLU16 4.8 26.6 1.0 CE2 A:TYR201 4.9 23.7 1.0 O2' A:8NK301 5.0 35.6 1.0

Sodium binding site 6 out of 9 in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:72.2 occ:1.00 O A:HOH517 2.4 30.1 1.0 O A:HOH418 2.5 31.8 1.0 CB A:ASP197 2.7 28.9 1.0 CG A:LYS198 2.8 19.0 1.0 O A:HOH431 2.9 22.9 1.0 N A:LYS198 3.3 20.9 1.0 O A:HOH468 3.5 20.9 1.0 CE A:LYS198 3.5 22.1 1.0 OD1 A:ASP196 3.5 22.7 1.0 CA A:ASP197 3.6 21.6 1.0 C A:ASP197 3.6 23.3 1.0 CG A:ASP197 3.7 48.7 1.0 CD A:LYS198 3.7 19.9 1.0 OD2 A:ASP197 3.7 44.1 1.0 CB A:LYS198 3.9 18.8 1.0 N A:ASP197 3.9 21.6 1.0 CA A:LYS198 4.1 18.9 1.0 NA A:NA309 4.2 43.1 1.0 O A:ASP197 4.5 23.4 1.0 NH2 A:ARG15 4.5 24.6 1.0 O A:HOH505 4.6 35.0 1.0 CG A:ASP196 4.6 24.8 1.0 NE A:ARG15 4.7 30.6 1.0 OE1 A:GLU16 4.7 26.6 1.0 OD1 A:ASP197 4.8 38.3 1.0 OG1 A:THR13 4.9 23.7 1.0 NZ A:LYS198 4.9 21.1 1.0 C A:ASP196 5.0 20.9 1.0

Sodium binding site 7 out of 9 in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:46.0 occ:1.00 O A:HOH591 2.6 46.7 1.0 N A:HIS33 2.8 28.9 1.0 O A:ILE159 2.9 29.1 1.0 O A:HOH515 3.0 56.2 1.0 CA A:THR32 3.5 49.4 1.0 C A:THR32 3.6 52.7 1.0 C A:ILE159 3.7 25.4 1.0 CA A:HIS33 3.7 27.1 1.0 CG2 A:THR32 3.8 37.4 1.0 CB A:HIS33 3.8 29.8 1.0 CE2 A:TYR161 3.8 30.3 1.0 CA A:GLY160 4.0 29.1 1.0 O A:HIS33 4.0 27.0 1.0 CD2 A:TYR161 4.1 29.6 1.0 N A:GLY160 4.2 28.4 1.0 CB A:THR32 4.2 50.8 1.0 O A:ASP31 4.3 73.5 1.0 C A:HIS33 4.3 25.6 1.0 CG2 A:ILE159 4.4 33.1 1.0 CB A:ILE159 4.4 31.8 1.0 ND1 A:HIS33 4.4 56.0 1.0 O A:HOH420 4.5 52.7 1.0 CG A:HIS33 4.6 43.7 1.0 N A:THR32 4.6 67.2 1.0 CA A:ILE159 4.6 25.4 1.0 OG1 A:THR32 4.8 64.9 1.0 O A:THR32 4.8 48.5 1.0 C A:GLY160 4.8 26.7 1.0 C A:ASP31 4.9 81.3 1.0 O A:HOH524 5.0 38.3 1.0 CZ A:TYR161 5.0 32.3 1.0

Sodium binding site 8 out of 9 in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP within 5.0Å range: probe atom residue distance (Å) B Occ A:Na309 b:43.1 occ:1.00 O A:HOH428 2.3 44.5 1.0 O A:HOH505 2.5 35.0 1.0 O A:HOH517 2.8 30.1 1.0 O A:HOH449 3.0 23.9 1.0 O A:HOH454 3.0 24.3 1.0 CD1 A:PHE103 3.6 21.9 1.0 OD2 A:ASP197 3.6 44.1 1.0 CE1 A:PHE103 3.9 20.4 1.0 CG A:ASP197 4.0 48.7 1.0 CD1 A:PHE78 4.0 24.2 1.0 O A:HOH418 4.1 31.8 1.0 CE1 A:PHE78 4.2 25.3 1.0 NA A:NA307 4.2 72.2 1.0 O A:HOH468 4.4 20.9 1.0 O A:HOH528 4.4 52.6 1.0 CB A:ASP197 4.5 28.9 1.0 OD2 A:ASP100 4.5 26.9 1.0 OD2 A:ASP196 4.5 24.8 1.0 OD1 A:ASP197 4.6 38.3 1.0 O A:GLU104 4.6 20.5 1.0 N A:ASP197 4.7 21.6 1.0 CG A:PHE103 4.8 17.2 1.0 O A:HOH423 4.8 37.3 1.0 OD1 A:ASP196 4.9 22.7 1.0 CG A:ASP196 4.9 24.8 1.0

Sodium binding site 9 out of 9 in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with M7GDP within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:48.6 occ:1.00 O A:HOH554 2.3 47.6 1.0 O A:HOH531 3.0 52.1 1.0 N A:ASN97 3.0 23.2 1.0 CA A:ILE96 3.6 20.6 1.0 NZ A:LYS93 3.8 36.5 1.0 C A:ILE96 3.8 20.4 1.0 CB A:ASN97 3.9 25.2 1.0 CB A:ILE96 3.9 22.2 1.0 CA A:ASN97 3.9 23.3 1.0 CE A:LYS93 4.3 34.7 1.0 O A:ASN97 4.3 24.3 1.0 CG A:ASN97 4.3 35.5 1.0 ND2 A:ASN97 4.3 49.5 1.0 CG2 A:ILE96 4.4 29.8 1.0 O A:HOH490 4.4 58.0 1.0 C A:ASN97 4.5 22.6 1.0 O A:SER95 4.7 26.2 1.0 CD1 A:LEU76 4.8 26.4 1.0 N A:ILE96 4.9 21.6 1.0 O A:HOH426 4.9 46.2 1.0 O A:ILE96 5.0 22.1 1.0

J.K.Peters, R.W.Tibble, M.Warminski, J.Jemielity, J.D.Gross. Structure of the Poxvirus Decapping Enzyme D9 Reveals Its Mechanism of Cap Recognition and Catalysis. Structure V. 30 721 2022.
ISSN: ISSN 0969-2126
PubMed: 35290794
DOI: 10.1016/J.STR.2022.02.012