Sodium in PDB 3f72: Crystal Structure of the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant

The structure of Crystal Structure of the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant, PDB code: 3f72 was solved by A.Kandegedara, S.Thiyagarajan, K.C.Kondapalli, T.L.Stemmler, B.P.Rosen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.30 / 2.31
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	89.471, 89.471, 148.536, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 28.8

The binding sites of Sodium atom in the Crystal Structure of the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant (pdb code 3f72). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant, PDB code: 3f72:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant


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 the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na123 b:41.2 occ:1.00 OD1 A:ASN64 2.5 33.1 1.0 CG A:ASN64 3.5 40.1 1.0 CA A:ASN64 3.7 40.1 1.0 O A:ASN64 4.0 40.0 1.0 CA A:GLY67 4.1 37.1 1.0 CB A:ASN64 4.2 39.5 1.0 O A:ALA63 4.3 41.3 1.0 C A:ASN64 4.4 39.7 1.0 N A:ASN64 4.6 40.2 1.0 ND2 A:ASN64 4.7 29.8 1.0 C A:GLY67 4.7 37.8 1.0 N A:GLY67 4.8 39.6 1.0 C A:ALA63 4.8 40.0 1.0 N A:VAL68 5.0 37.6 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant


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 the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na124 b:58.2 occ:1.00 CE1 A:HIS75 3.6 67.2 1.0 NH1 A:ARG44 3.6 42.9 1.0 NH2 A:ARG44 3.9 35.0 1.0 NE2 A:HIS75 4.0 70.4 1.0 CZ A:ARG44 4.2 42.9 1.0 O A:HOH145 4.5 64.2 1.0 ND1 A:HIS75 4.9 65.6 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant


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 the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na123 b:55.5 occ:1.00 O B:HOH138 2.3 53.6 1.0 N B:GLU102 3.3 38.8 1.0 N B:ALA103 3.5 35.8 1.0 CA B:GLY101 3.7 38.5 1.0 C B:GLY101 3.8 38.8 1.0 CB B:ALA103 3.9 34.0 1.0 CA B:GLU102 4.1 39.9 1.0 CB B:GLU102 4.2 42.6 1.0 C B:GLU102 4.3 36.8 1.0 CA B:ALA103 4.3 35.3 1.0 ND1 A:HIS114 4.5 61.0 1.0 O B:GLY101 4.9 37.8 1.0 O A:HOH141 5.0 51.2 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant


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 the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na124 b:55.1 occ:1.00 ND1 B:HIS76 3.3 43.8 1.0 CD2 B:HIS75 3.4 34.4 0.5 OG1 B:THR79 3.6 38.5 1.0 NH2 B:ARG44 3.6 44.6 1.0 NE B:ARG44 3.8 51.7 1.0 NE2 B:HIS75 3.8 36.7 0.5 CE1 B:HIS76 3.9 44.5 1.0 CA B:HIS76 4.1 35.4 1.0 CZ B:ARG44 4.2 47.4 1.0 CG B:HIS76 4.3 37.9 1.0 O B:HIS75 4.3 33.1 1.0 CB B:THR79 4.4 37.1 1.0 CG B:HIS75 4.5 34.1 0.5 N B:HIS76 4.5 35.9 1.0 C B:HIS75 4.5 35.5 1.0 CB B:HIS76 4.6 35.5 1.0 CG2 B:THR79 4.7 33.6 1.0 CD B:ARG44 4.9 39.3 1.0 NE2 B:HIS76 4.9 42.1 1.0 CE1 B:HIS75 5.0 32.0 0.5

Sodium binding site 5 out of 5 in the Crystal Structure of the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant


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 the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ F:Na123 b:70.0 occ:1.00 CD2 F:HIS76 3.4 71.5 1.0 NH2 F:ARG44 3.5 79.0 1.0 ND1 F:HIS75 3.6 77.7 1.0 NE2 F:HIS76 3.8 72.7 1.0 CE1 F:HIS75 4.0 75.8 1.0 NE F:ARG44 4.1 71.7 1.0 OG1 F:THR79 4.3 65.0 1.0 CZ F:ARG44 4.3 76.3 1.0 CG F:HIS76 4.4 68.6 1.0 CB F:THR79 4.6 66.6 1.0 CA F:HIS76 4.7 67.3 1.0 CG2 F:THR79 4.7 63.1 1.0 N F:HIS76 4.8 67.0 1.0 CG F:HIS75 4.8 74.5 1.0 CE1 F:HIS76 4.8 71.0 1.0 O F:HIS75 5.0 67.8 1.0 C F:HIS75 5.0 68.2 1.0

A.Kandegedara, S.Thiyagarajan, K.C.Kondapalli, T.L.Stemmler, B.P.Rosen. Role of Bound Zn(II) in the Cadc Cd(II)/Pb(II)/Zn(II)-Responsive Repressor. J.Biol.Chem. V. 284 14958 2009.
ISSN: ISSN 0021-9258
PubMed: 19286656
DOI: 10.1074/JBC.M809179200