Sodium in PDB 3t46: Crystal Structure of Staphylococcal Complement Inhibitor D (Scin-D) at 1.5 Angstrom

The structure of Crystal Structure of Staphylococcal Complement Inhibitor D (Scin-D) at 1.5 Angstrom, PDB code: 3t46 was solved by B.L.Garcia, B.V.Geisbrecht, B.J.Summers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.99 / 1.50
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	28.860, 28.860, 262.600, 90.00, 90.00, 120.00
R / Rfree (%)	22.2 / 24.5

The binding sites of Sodium atom in the Crystal Structure of Staphylococcal Complement Inhibitor D (Scin-D) at 1.5 Angstrom (pdb code 3t46). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Staphylococcal Complement Inhibitor D (Scin-D) at 1.5 Angstrom, PDB code: 3t46:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Staphylococcal Complement Inhibitor D (Scin-D) at 1.5 Angstrom


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 Staphylococcal Complement Inhibitor D (Scin-D) at 1.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:11.8 occ:0.50 O A:HOH93 3.1 15.1 1.0 HA A:SER32 3.2 19.5 1.0 NZ A:LYS41 3.2 16.2 1.0 H A:LEU36 3.4 25.0 1.0 O A:SER32 3.8 13.8 1.0 CE A:LYS41 3.9 20.6 1.0 CA A:ASN35 4.0 14.8 1.0 O A:LEU36 4.0 17.6 1.0 N A:LEU36 4.0 20.9 1.0 CA A:SER32 4.2 16.3 1.0 N A:ASN35 4.3 17.3 1.0 C A:SER32 4.4 15.8 1.0 C A:ASN35 4.4 15.9 1.0 HB3 A:SER32 4.5 24.1 1.0 HB2 A:LEU36 4.7 19.7 1.0 O A:LEU31 4.9 9.3 1.0 CB A:SER32 4.9 20.1 1.0 C A:LEU36 4.9 19.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Staphylococcal Complement Inhibitor D (Scin-D) at 1.5 Angstrom


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 Staphylococcal Complement Inhibitor D (Scin-D) at 1.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:22.6 occ:0.50 HE A:ARG42 2.2 24.1 1.0 HH21 A:ARG42 2.5 19.0 1.0 NE A:ARG42 3.2 20.1 1.0 NH2 A:ARG42 3.4 15.9 1.0 HD1 A:PHE39 3.6 29.3 1.0 CZ A:ARG42 3.7 14.8 1.0 HE1 A:PHE39 4.0 25.3 1.0 HD3 A:ARG42 4.1 23.6 1.0 HH22 A:ARG42 4.2 19.0 1.0 CD1 A:PHE39 4.3 24.5 1.0 CD A:ARG42 4.3 19.7 1.0 CE1 A:PHE39 4.5 21.1 1.0 HB2 A:ARG42 4.5 12.4 1.0 HB3 A:ARG42 4.5 12.4 1.0 HA A:PHE39 4.6 15.9 1.0 CB A:ARG42 4.9 10.4 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Staphylococcal Complement Inhibitor D (Scin-D) at 1.5 Angstrom


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 Staphylococcal Complement Inhibitor D (Scin-D) at 1.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:27.0 occ:1.00 OD2 A:ASP61 2.8 15.9 1.0 CG A:ASP61 3.6 14.4 1.0 OD1 A:ASP61 3.7 12.5 1.0 O A:HOH95 3.9 13.1 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Staphylococcal Complement Inhibitor D (Scin-D) at 1.5 Angstrom


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 Staphylococcal Complement Inhibitor D (Scin-D) at 1.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:17.7 occ:1.00 HH22 A:ARG56 2.3 29.7 1.0 HH12 A:ARG56 2.6 31.8 1.0 NH2 A:ARG56 3.2 24.8 1.0 NH1 A:ARG56 3.4 26.5 1.0 CZ A:ARG56 3.8 24.0 1.0 HH21 A:ARG56 4.0 29.7 1.0 HH11 A:ARG56 4.3 31.8 1.0

B.L.Garcia, B.J.Summers, Z.Lin, K.X.Ramyar, D.Ricklin, D.V.Kamath, Z.Q.Fu, J.D.Lambris, B.V.Geisbrecht. Diversity in the C3B Convertase Contact Residues and Tertiary Structures of the Staphylococcal Complement Inhibitor (Scin) Protein Family. J.Biol.Chem. V. 287 628 2012.
ISSN: ISSN 0021-9258
PubMed: 22086928
DOI: 10.1074/JBC.M111.298984