Sodium in PDB 7ads: Orf Virus Apoptosis Inhibitor ORFV125

The structure of Orf Virus Apoptosis Inhibitor ORFV125, PDB code: 7ads was solved by C.D.Suraweera, M.G.Hinds, M.Kvansakul, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.66 / 2.22
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	106.613, 106.613, 60.589, 90, 90, 120
R / Rfree (%)	24.4 / 26

The structure of Orf Virus Apoptosis Inhibitor ORFV125 also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Magnesium	(Mg)	4 atoms

The binding sites of Sodium atom in the Orf Virus Apoptosis Inhibitor ORFV125 (pdb code 7ads). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Orf Virus Apoptosis Inhibitor ORFV125, PDB code: 7ads:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Orf Virus Apoptosis Inhibitor ORFV125


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Orf Virus Apoptosis Inhibitor ORFV125 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:104.1 occ:1.00 HO1 A:EDO301 2.7 161.8 1.0 HB2 A:PRO31 3.1 94.3 1.0 OD1 A:ASP35 3.2 81.4 1.0 O1 A:EDO301 3.5 134.8 1.0 HA A:ARG32 3.7 85.5 1.0 H11 A:EDO301 3.7 164.6 1.0 HB2 A:ARG32 3.8 97.2 1.0 CB A:PRO31 3.9 78.6 1.0 HB3 A:PRO31 3.9 94.3 1.0 N A:ARG32 4.0 71.0 1.0 C1 A:EDO301 4.1 137.2 1.0 C A:PRO31 4.1 71.8 1.0 H A:ARG32 4.2 85.2 1.0 O A:HOH410 4.2 81.4 1.0 CA A:ARG32 4.2 71.3 1.0 H12 A:EDO301 4.3 164.6 1.0 O A:PRO31 4.4 72.1 1.0 CG A:ASP35 4.4 77.1 1.0 CB A:ARG32 4.5 81.0 1.0 CA A:PRO31 4.7 73.0 1.0 HG3 A:ARG32 4.9 102.1 1.0 HG2 A:PRO31 4.9 98.5 1.0

Sodium binding site 2 out of 5 in the Orf Virus Apoptosis Inhibitor ORFV125


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Orf Virus Apoptosis Inhibitor ORFV125 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na309 b:105.5 occ:1.00 O A:HOH404 2.7 78.9 1.0 HG A:SER10 2.7 91.0 1.0 HA3 A:GLY105 3.3 104.7 1.0 OG A:SER10 3.3 75.9 1.0 HB2 A:SER10 3.3 83.4 1.0 HG3 A:ARG106 3.5 130.0 1.0 C A:GLY105 3.8 81.4 1.0 CB A:SER10 3.8 69.6 1.0 HA A:ARG106 3.9 107.5 1.0 CA A:GLY105 4.0 87.3 1.0 N A:ARG106 4.0 84.2 1.0 O A:GLY105 4.1 76.2 1.0 O A:HOH413 4.1 74.1 1.0 OD1 A:ASP8 4.1 78.8 1.0 HB3 A:SER10 4.2 83.4 1.0 H A:ARG106 4.3 101.0 1.0 HA2 A:GLY105 4.4 104.7 1.0 CA A:ARG106 4.4 89.7 1.0 CG A:ARG106 4.4 108.4 1.0 H A:SER10 4.5 79.3 1.0 HE A:ARG106 4.7 143.3 1.0 HD2 A:ARG106 4.8 138.2 1.0 NE A:ARG106 4.9 119.5 1.0 CB A:ARG106 4.9 98.5 1.0 CD A:ARG106 5.0 115.2 1.0

Sodium binding site 3 out of 5 in the Orf Virus Apoptosis Inhibitor ORFV125


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Orf Virus Apoptosis Inhibitor ORFV125 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:59.7 occ:0.50 OG A:SER49 2.9 55.7 1.0 HG A:SER49 3.0 66.8 1.0 HD12 A:LEU51 3.2 65.8 1.0 HB2 A:SER49 3.4 71.8 1.0 HB2 A:LEU51 3.5 69.4 1.0 CB A:SER49 3.6 59.9 1.0 HA A:SER49 3.7 68.9 1.0 HD11 A:LEU74 3.8 62.4 1.0 HD13 A:LEU74 4.0 62.4 1.0 CD1 A:LEU51 4.2 54.9 1.0 CA A:SER49 4.2 57.5 1.0 HD21 A:LEU74 4.3 73.2 1.0 CD1 A:LEU74 4.4 52.0 1.0 H A:LEU51 4.4 69.5 1.0 CB A:LEU51 4.4 57.9 1.0 HB3 A:SER49 4.5 71.8 1.0 HG A:LEU51 4.5 69.2 1.0 HD22 A:LEU74 4.6 73.2 1.0 HG A:LEU52 4.6 73.6 1.0 HD13 A:LEU51 4.6 65.8 1.0 CG A:LEU51 4.7 57.7 1.0 H A:LEU52 4.7 64.0 1.0 HD11 A:LEU51 4.7 65.8 1.0 HD12 A:LEU52 4.8 73.0 1.0 CD2 A:LEU74 4.8 61.0 1.0 HD2 A:PRO50 4.9 67.2 1.0 HB3 A:LEU51 4.9 69.4 1.0 C A:SER49 5.0 55.6 1.0

Sodium binding site 4 out of 5 in the Orf Virus Apoptosis Inhibitor ORFV125


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Orf Virus Apoptosis Inhibitor ORFV125 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na311 b:106.4 occ:1.00 O A:LEU79 2.7 67.3 1.0 O A:ARG121 2.8 79.2 1.0 HB3 A:LEU79 2.9 78.3 1.0 HD3 A:PRO123 3.0 85.8 1.0 HB3 A:PRO123 3.1 95.3 1.0 N A:PRO123 3.4 73.3 1.0 HG21 A:THR83 3.5 91.2 1.0 C A:LEU122 3.6 75.2 1.0 CD A:PRO123 3.6 71.5 1.0 HA A:PRO123 3.7 95.3 1.0 CB A:PRO123 3.8 79.5 1.0 C A:LEU79 3.8 68.1 1.0 CB A:LEU79 3.8 65.3 1.0 HA A:LEU122 3.8 84.7 1.0 O A:LEU122 3.8 81.4 1.0 CA A:PRO123 3.9 79.5 1.0 HD22 A:LEU79 3.9 75.5 1.0 C A:ARG121 3.9 79.1 1.0 HG22 A:THR83 3.9 91.2 1.0 HG3 A:PRO123 4.0 88.5 1.0 HA A:LEU79 4.0 76.8 1.0 CG A:PRO123 4.0 73.8 1.0 CA A:LEU79 4.1 64.1 1.0 CG2 A:THR83 4.1 76.0 1.0 CA A:LEU122 4.1 70.6 1.0 HB A:THR83 4.2 92.8 1.0 HB2 A:LEU79 4.3 78.3 1.0 HD2 A:PRO123 4.5 85.8 1.0 HD23 A:LEU79 4.5 75.5 1.0 N A:LEU122 4.5 73.9 1.0 CD2 A:LEU79 4.5 63.0 1.0 HB3 A:ARG121 4.6 108.0 1.0 HB2 A:PRO123 4.6 95.3 1.0 CG A:LEU79 4.7 63.8 1.0 CB A:THR83 4.8 77.4 1.0 O A:GLU80 4.8 92.4 1.0 HD13 A:LEU79 4.9 76.0 1.0 HG23 A:THR83 4.9 91.2 1.0 N A:GLU80 5.0 75.3 1.0 HG2 A:PRO123 5.0 88.5 1.0

Sodium binding site 5 out of 5 in the Orf Virus Apoptosis Inhibitor ORFV125


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Orf Virus Apoptosis Inhibitor ORFV125 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na312 b:95.2 occ:1.00 HE1 A:HIS141 3.1 135.7 1.0 HG21 A:VAL140 3.3 76.6 1.0 HG12 A:VAL137 3.3 79.0 1.0 HA A:VAL137 3.3 72.8 1.0 HG11 A:VAL140 3.5 71.8 1.0 HB A:VAL140 3.5 76.0 1.0 CE1 A:HIS141 4.0 113.1 1.0 CG2 A:VAL140 4.0 63.9 1.0 CB A:VAL140 4.1 63.4 1.0 CG1 A:VAL140 4.2 59.8 1.0 CA A:VAL137 4.2 60.7 1.0 CG1 A:VAL137 4.2 65.9 1.0 HG23 A:VAL140 4.3 76.6 1.0 O A:ALA136 4.4 66.0 1.0 HG13 A:VAL137 4.5 79.0 1.0 ND1 A:HIS141 4.5 113.1 1.0 N A:VAL137 4.5 58.7 1.0 HG12 A:VAL140 4.5 71.8 1.0 HB1 A:ALA136 4.6 76.8 1.0 CB A:VAL137 4.6 67.9 1.0 C A:ALA136 4.6 65.2 1.0 HB A:VAL137 4.6 81.4 1.0 HO1 A:EDO305 4.7 115.3 1.0 HG22 A:VAL140 4.8 76.6 1.0 HG11 A:VAL137 4.8 79.0 1.0 HG13 A:VAL140 4.9 71.8 1.0 H A:VAL137 5.0 70.4 1.0

C.D.Suraweera, M.G.Hinds, M.Kvansakul. Orf Virus Apoptosis Inhibitor ORFV125 To Be Published.