Calcium in PDB 4jdz: Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands

The structure of Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands, PDB code: 4jdz was solved by X.Wang, J.Ge, M.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.410, 73.880, 90.030, 90.00, 102.42, 90.00
R / Rfree (%)	18.5 / 23.2

The binding sites of Calcium atom in the Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands (pdb code 4jdz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands, PDB code: 4jdz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:21.2 occ:1.00 OD1 B:ASN565 2.3 29.2 1.0 O B:HOH808 2.3 31.3 1.0 O B:LEU663 2.3 36.3 1.0 O B:HOH885 2.4 25.1 1.0 O B:HOH839 2.5 43.0 1.0 OD1 B:ASP666 2.6 35.4 1.0 OD2 B:ASP666 2.6 31.7 1.0 CG B:ASP666 3.0 42.7 1.0 CG B:ASN565 3.2 40.6 1.0 C B:LEU663 3.5 41.8 1.0 ND2 B:ASN565 4.0 38.4 1.0 CA B:SER664 4.2 42.7 1.0 CB B:TYR566 4.2 35.1 1.0 CB B:ASN565 4.2 48.6 1.0 O B:GLY564 4.2 35.4 1.0 O B:HOH910 4.2 31.6 1.0 N B:SER664 4.3 37.7 1.0 CB B:LEU663 4.4 39.0 1.0 CB B:ASP666 4.5 35.1 1.0 O B:GLU645 4.5 39.3 1.0 OE2 B:GLU315 4.5 41.3 1.0 CA B:LEU663 4.5 42.3 1.0 O B:HOH974 4.6 57.6 1.0 N B:TYR566 4.6 34.3 1.0 OE1 B:GLN577 4.6 34.5 1.0 C B:SER664 4.7 42.1 1.0 C B:ASN565 4.8 38.4 1.0 NE2 B:GLN577 4.8 30.5 1.0 CA B:ASN565 4.9 49.1 1.0

Calcium binding site 2 out of 8 in the Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:28.5 occ:1.00 OD1 B:ASN649 2.4 43.2 1.0 O B:HOH801 2.4 42.6 1.0 OD1 B:ASP647 2.4 39.9 1.0 O B:GLU644 2.4 46.3 1.0 O B:SER664 2.5 48.7 1.0 O B:HOH986 2.8 45.7 1.0 CG B:ASN649 3.5 42.3 1.0 C B:GLU644 3.5 43.2 1.0 CG B:ASP647 3.5 50.6 1.0 C B:SER664 3.7 42.1 1.0 OD2 B:ASP647 3.8 53.3 1.0 ND2 B:ASN649 4.0 44.6 1.0 CA B:GLU644 4.0 58.1 1.0 CB B:SER664 4.1 43.5 1.0 O B:ASP647 4.3 35.9 1.0 CB B:GLU644 4.3 64.8 1.0 OG B:SER664 4.3 38.5 1.0 CA B:SER664 4.4 42.7 1.0 N B:GLU645 4.6 42.4 1.0 N B:ASP666 4.6 35.0 1.0 C B:ASP647 4.6 38.8 1.0 N B:ALA665 4.7 36.2 1.0 CB B:ASN649 4.7 41.0 1.0 N B:ASN649 4.7 37.9 1.0 CA B:GLU645 4.8 45.9 1.0 N B:ASP647 4.8 36.1 1.0 CB B:ASP647 4.8 41.6 1.0 OD2 B:ASP666 4.8 31.7 1.0 CA B:ALA665 4.9 37.1 1.0 CA B:ASN649 4.9 43.0 1.0 C B:SER648 5.0 41.4 1.0 CA B:ASP647 5.0 42.7 1.0

Calcium binding site 3 out of 8 in the Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca703 b:25.7 occ:1.00 OD1 B:ASP570 2.3 36.1 1.0 O B:VAL576 2.4 41.1 1.0 OD2 B:ASP578 2.4 43.0 1.0 OD1 B:ASN574 2.5 36.2 1.0 OE2 B:GLU581 2.5 42.0 1.0 OE1 B:GLU581 2.8 43.6 1.0 CD B:GLU581 3.0 46.6 1.0 CB B:ASN572 3.0 52.6 1.0 CG B:ASN574 3.3 41.8 1.0 CG B:ASP578 3.3 52.5 1.0 CG B:ASP570 3.5 41.7 1.0 CG B:ASN572 3.5 66.5 1.0 C B:VAL576 3.6 45.0 1.0 ND2 B:ASN574 3.6 39.0 1.0 OD1 B:ASN572 3.9 72.7 1.0 CB B:ASP578 4.0 46.0 1.0 N B:VAL576 4.0 36.4 1.0 N B:ASP578 4.1 41.3 1.0 OD1 B:ASP578 4.2 54.5 1.0 ND2 B:ASN572 4.2 76.0 1.0 OD2 B:ASP570 4.2 37.9 1.0 NE1 B:TRP568 4.2 34.4 1.0 CA B:ASN572 4.2 62.1 1.0 N B:ASN572 4.3 65.2 1.0 CA B:VAL576 4.3 45.2 1.0 N B:ASN574 4.4 44.9 1.0 CA B:ASP570 4.5 38.2 1.0 CG B:GLU581 4.5 47.6 1.0 CB B:ASP570 4.5 40.8 1.0 N B:GLN577 4.6 43.6 1.0 CB B:ASN574 4.6 45.8 1.0 C B:ASP570 4.7 43.0 1.0 CB B:VAL576 4.7 47.1 1.0 N B:LYS573 4.7 47.9 1.0 CA B:ASP578 4.7 44.4 1.0 CA B:GLN577 4.7 25.6 1.0 C B:GLN577 4.8 41.7 1.0 N B:GLY575 4.8 40.1 1.0 C B:ASN572 4.8 51.6 1.0 CA B:ASN574 4.9 39.3 1.0 N B:THR571 4.9 43.7 1.0

Calcium binding site 4 out of 8 in the Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca704 b:25.7 occ:1.00 O B:LYS258 2.3 34.7 1.0 OD2 B:ASP252 2.4 43.0 1.0 OD1 B:ASN256 2.5 33.4 1.0 OD2 B:ASP264 2.6 32.9 1.0 OD1 B:ASP264 2.6 34.7 1.0 CG2 B:ILE254 2.9 38.9 1.0 CG B:ASP264 3.0 38.0 1.0 C B:LYS258 3.5 42.1 1.0 CG B:ASN256 3.5 41.2 1.0 CG B:ASP252 3.6 41.1 1.0 ND2 B:ASN256 4.0 36.2 1.0 OD1 B:ASP252 4.3 45.3 1.0 N B:LYS258 4.3 43.3 1.0 CB B:ILE254 4.4 62.6 1.0 N B:ILE259 4.4 35.0 1.0 CA B:LYS258 4.4 36.8 1.0 CA B:ILE259 4.4 36.2 1.0 N B:ASN256 4.4 49.4 1.0 CA B:ASP252 4.5 39.1 1.0 CB B:ASP264 4.5 25.2 1.0 N B:VAL260 4.6 24.4 1.0 N B:ILE254 4.6 38.9 1.0 CB B:ASP252 4.6 36.1 1.0 CB B:GLN263 4.6 42.5 1.0 CG2 B:VAL260 4.7 30.0 1.0 C B:ASP252 4.7 43.4 1.0 CB B:ASN256 4.8 40.4 1.0 CD1 B:ILE259 4.8 37.0 1.0 N B:ALA253 4.8 35.0 1.0 N B:LYS255 4.8 54.8 1.0 CB B:LYS258 4.8 40.1 1.0 OE1 B:GLN263 4.8 62.0 1.0 CA B:ILE254 4.9 37.3 1.0 C B:ILE259 5.0 34.7 1.0 CA B:ASN256 5.0 43.1 1.0

Calcium binding site 5 out of 8 in the Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:44.2 occ:1.00 O A:LYS258 2.4 58.1 1.0 OD1 A:ASN256 2.5 68.7 1.0 OD1 A:ASP264 2.6 48.4 1.0 OD2 A:ASP252 2.6 71.1 1.0 OD2 A:ASP264 2.7 43.5 1.0 CG2 A:ILE254 2.9 79.9 1.0 CG A:ASP264 3.0 48.8 1.0 CG A:ASN256 3.4 65.2 1.0 C A:LYS258 3.5 59.2 1.0 ND2 A:ASN256 3.6 67.2 1.0 CG A:ASP252 3.7 69.6 1.0 OD1 A:ASP252 4.2 73.0 1.0 N A:LYS258 4.2 66.6 1.0 CA A:LYS258 4.3 66.4 1.0 CB A:ILE254 4.3 91.0 1.0 CB A:LYS258 4.4 67.9 1.0 N A:ILE259 4.5 48.8 1.0 N A:ILE254 4.5 61.9 1.0 CB A:ASP264 4.5 45.4 1.0 CA A:ILE259 4.6 44.3 1.0 CB A:GLN263 4.6 51.8 1.0 N A:VAL260 4.6 37.6 1.0 N A:ASN256 4.7 68.2 1.0 CB A:ASN256 4.7 61.2 1.0 CA A:ASP252 4.8 60.8 1.0 CB A:ASP252 4.8 66.3 1.0 CA A:ILE254 4.9 59.2 1.0 N A:ALA253 4.9 59.0 1.0 C A:ASP252 4.9 61.4 1.0 CG2 A:VAL260 4.9 44.9 1.0

Calcium binding site 6 out of 8 in the Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:42.1 occ:1.00 O A:LEU662 2.4 61.0 1.0 OD1 A:ASN564 2.4 71.9 1.0 OD2 A:ASP665 2.5 69.2 1.0 O A:HOH938 2.5 48.6 1.0 OD1 A:ASP665 2.7 57.7 1.0 CG A:ASP665 2.9 64.7 1.0 CG A:ASN564 3.4 62.1 1.0 C A:LEU662 3.6 68.3 1.0 N A:ASN564 4.1 70.6 1.0 CB A:TYR565 4.1 71.4 1.0 ND2 A:ASN564 4.1 57.0 1.0 CA A:SER663 4.2 67.0 1.0 O A:GLU644 4.3 94.3 1.0 O A:HOH830 4.3 39.4 1.0 N A:SER663 4.4 65.5 1.0 OE2 A:GLU315 4.4 80.1 1.0 CB A:ASP665 4.4 60.1 1.0 CB A:ASN564 4.5 60.4 1.0 N A:TYR565 4.5 64.6 1.0 CB A:LEU662 4.5 59.0 1.0 OE1 A:GLN576 4.5 61.8 1.0 CA A:ASN564 4.6 67.2 1.0 C A:ASN564 4.7 66.8 1.0 CA A:LEU662 4.7 67.2 1.0 C A:SER663 4.7 66.1 1.0 C A:GLY563 4.8 75.0 1.0 NE2 A:GLN576 4.8 61.3 1.0 O A:GLY563 4.9 71.7 1.0 CA A:TYR565 5.0 66.8 1.0

Calcium binding site 7 out of 8 in the Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:46.8 occ:1.00 O A:SER663 2.5 64.9 1.0 O A:HOH936 2.5 51.1 1.0 OD1 A:ASN648 2.6 83.9 1.0 OD1 A:ASP646 2.6 82.7 1.0 O A:GLU643 2.7 90.5 1.0 C A:GLU643 3.4 93.3 1.0 CG A:ASN648 3.4 82.1 1.0 C A:SER663 3.5 66.1 1.0 ND2 A:ASN648 3.7 79.3 1.0 CB A:SER663 3.7 69.7 1.0 CG A:ASP646 3.7 84.3 1.0 CA A:GLU643 4.0 90.8 1.0 OG A:SER663 4.0 64.9 1.0 CA A:SER663 4.1 67.0 1.0 OD2 A:ASP646 4.1 84.7 1.0 O A:ASP646 4.2 71.0 1.0 CB A:GLU643 4.2 89.0 1.0 N A:GLU644 4.3 98.7 1.0 N A:ASP665 4.6 58.2 1.0 CA A:GLU644 4.6 0.9 1.0 N A:ALA664 4.6 65.4 1.0 C A:ASP646 4.7 77.6 1.0 OD2 A:ASP665 4.8 69.2 1.0 CB A:ASN648 4.8 84.6 1.0 N A:ASP646 4.9 87.6 1.0 NZ A:LYS637 4.9 0.7 1.0 CA A:ALA664 5.0 66.8 1.0 CB A:ASP646 5.0 83.9 1.0

Calcium binding site 8 out of 8 in the Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:53.8 occ:1.00 OD1 A:ASP569 2.5 88.9 1.0 O A:VAL575 2.5 74.2 1.0 OD1 A:ASN573 2.6 0.5 1.0 OE2 A:GLU580 2.8 94.6 1.0 OE1 A:GLU580 2.8 83.2 1.0 OD2 A:ASP577 2.8 89.4 1.0 OD1 A:ASN571 3.1 0.2 1.0 CD A:GLU580 3.1 91.5 1.0 ND2 A:ASN573 3.1 0.8 1.0 CG A:ASN573 3.2 0.4 1.0 CB A:ASN571 3.2 0.8 1.0 CG A:ASN571 3.6 0.1 1.0 CG A:ASP577 3.6 91.2 1.0 C A:VAL575 3.7 73.2 1.0 CG A:ASP569 3.7 86.3 1.0 CB A:ASP577 3.8 93.6 1.0 N A:VAL575 4.2 81.5 1.0 N A:ASP577 4.2 91.3 1.0 OD2 A:ASP569 4.3 83.3 1.0 CA A:VAL575 4.3 74.3 1.0 CA A:ASN571 4.4 0.9 1.0 N A:ASN571 4.5 0.9 1.0 CB A:ASN573 4.6 0.8 1.0 CB A:VAL575 4.6 73.4 1.0 CG A:GLU580 4.6 98.1 1.0 NE1 A:TRP567 4.6 69.1 1.0 CA A:ASP577 4.7 94.8 1.0 OD1 A:ASP577 4.7 89.6 1.0 N A:GLN576 4.7 73.3 1.0 CA A:ASP569 4.8 84.8 1.0 N A:ASN573 4.8 0.6 1.0 CB A:ASP569 4.9 83.7 1.0 ND2 A:ASN571 4.9 0.6 1.0 C A:GLN576 4.9 84.8 1.0 C A:ASP569 4.9 92.5 1.0 CA A:GLN576 4.9 74.8 1.0 N A:THR570 5.0 99.2 1.0

X.Wang, J.Ge, B.Liu, Y.Hu, M.Yang. Structures of Sdrd From Staphylococcus Aureus Reveal the Molecular Mechanism of How the Cell Surface Receptors Recognize Their Ligands Protein Cell V. 4 277 2013.
ISSN: ISSN 1674-800X
PubMed: 23549613
DOI: 10.1007/S13238-013-3009-X