Calcium in PDB 4s37: Crystal Structure of R2 Pyocin Membrane-Piercing Spike

The structure of Crystal Structure of R2 Pyocin Membrane-Piercing Spike, PDB code: 4s37 was solved by C.B.Browning, P.G.Leiman, M.M.Shneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.19 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	94.945, 137.471, 164.759, 90.00, 106.56, 90.00
R / Rfree (%)	16.3 / 20.8

The structure of Crystal Structure of R2 Pyocin Membrane-Piercing Spike also contains other interesting chemical elements:

Chlorine

(Cl)

19 atoms

The binding sites of Calcium atom in the Crystal Structure of R2 Pyocin Membrane-Piercing Spike (pdb code 4s37). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of R2 Pyocin Membrane-Piercing Spike, PDB code: 4s37:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of R2 Pyocin Membrane-Piercing Spike


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of R2 Pyocin Membrane-Piercing Spike within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca205 b:0.5 occ:1.00 ND1 B:HIS8 3.6 0.8 1.0 CG B:HIS8 3.7 0.4 1.0 CB B:HIS8 4.0 0.2 1.0 CD2 C:HIS8 4.0 1.0 1.0 OG B:SER5 4.1 0.8 1.0 CE1 B:HIS8 4.1 0.3 1.0 CD2 B:HIS8 4.3 0.3 1.0 NE2 B:HIS8 4.5 0.7 1.0 NE2 C:HIS8 4.7 0.4 1.0 CG C:HIS8 4.8 0.1 1.0 O C:HOH422 4.8 70.8 1.0 O B:SER5 4.9 0.6 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of R2 Pyocin Membrane-Piercing Spike


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of R2 Pyocin Membrane-Piercing Spike within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca204 b:99.4 occ:1.00 ND1 D:HIS8 3.5 0.0 1.0 CB D:SER5 3.9 0.5 1.0 OG F:SER5 4.0 0.7 1.0 CE1 D:HIS8 4.1 0.5 1.0 ND1 E:HIS8 4.2 0.6 1.0 CB F:SER5 4.3 0.5 1.0 CA D:SER5 4.3 0.6 1.0 CA F:SER5 4.3 0.2 1.0 CG D:HIS8 4.6 0.1 1.0 CD2 F:HIS8 4.6 0.3 1.0 CG F:HIS8 4.6 1.0 1.0 CB F:HIS8 4.8 0.4 1.0 N D:SER5 4.8 0.9 1.0 CB D:HIS8 4.9 0.7 1.0 O E:HOH443 4.9 62.2 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of R2 Pyocin Membrane-Piercing Spike


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of R2 Pyocin Membrane-Piercing Spike within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca204 b:72.3 occ:1.00 O C:HOH414 2.4 0.6 1.0 O C:HOH415 2.4 58.1 1.0 O C:HOH413 3.6 43.0 1.0 NE1 F:TRP42 3.6 42.0 1.0 O C:HOH412 3.8 51.2 1.0 NH1 F:ARG32 3.9 74.0 1.0 NH1 C:ARG32 4.0 45.2 1.0 NH2 C:ARG32 4.0 40.5 1.0 O C:HOH379 4.2 74.9 1.0 CZ C:ARG32 4.5 39.1 1.0 CD1 F:TRP42 4.5 45.4 1.0 CA C:GLY41 4.5 42.2 1.0 CE2 F:TRP42 4.6 38.5 1.0 CZ2 F:TRP42 4.8 36.8 1.0 O F:HOH396 5.0 83.6 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of R2 Pyocin Membrane-Piercing Spike


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of R2 Pyocin Membrane-Piercing Spike within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca205 b:69.6 occ:1.00 ND1 H:HIS8 3.5 61.2 1.0 OG G:SER5 3.7 71.1 1.0 ND1 I:HIS8 3.7 94.0 1.0 OG H:SER5 3.7 66.7 1.0 CD2 G:HIS8 3.8 63.0 1.0 OG I:SER5 3.8 0.6 1.0 CA H:SER5 4.2 61.3 1.0 CA G:SER5 4.4 79.6 1.0 CB G:SER5 4.4 71.6 1.0 CE1 H:HIS8 4.4 59.2 1.0 CG H:HIS8 4.4 56.2 1.0 CB H:HIS8 4.5 49.9 1.0 CA I:SER5 4.5 0.4 1.0 CB H:SER5 4.5 62.7 1.0 CG G:HIS8 4.5 61.4 1.0 CE1 I:HIS8 4.5 91.1 1.0 CB G:HIS8 4.6 60.3 1.0 CB I:SER5 4.6 0.7 1.0 CG I:HIS8 4.6 88.7 1.0 CB I:HIS8 4.7 80.8 1.0 NE2 G:HIS8 4.9 77.1 1.0 N H:SER5 4.9 50.0 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of R2 Pyocin Membrane-Piercing Spike


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of R2 Pyocin Membrane-Piercing Spike within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca204 b:94.9 occ:1.00 OG L:SER5 2.4 0.6 1.0 ND1 J:HIS8 3.3 83.7 1.0 OG J:SER5 3.4 0.3 1.0 CB L:SER5 3.5 97.0 1.0 ND1 L:HIS8 3.8 99.4 1.0 CE1 J:HIS8 3.8 85.7 1.0 CA L:SER5 4.0 92.0 1.0 ND1 K:HIS8 4.2 92.5 1.0 CB J:SER5 4.4 99.7 1.0 OG K:SER5 4.4 0.1 1.0 CG J:HIS8 4.4 78.3 1.0 CE1 L:HIS8 4.5 0.5 1.0 CA J:SER5 4.6 91.8 1.0 N L:SER5 4.7 94.7 1.0 CG L:HIS8 4.8 91.4 1.0 CB K:SER5 4.8 96.4 1.0 CB J:HIS8 4.9 75.5 1.0 CE1 K:HIS8 4.9 96.0 1.0 CB L:HIS8 4.9 79.8 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of R2 Pyocin Membrane-Piercing Spike


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of R2 Pyocin Membrane-Piercing Spike within 5.0Å range: probe atom residue distance (Å) B Occ O:Ca204 b:0.5 occ:1.00 OG O:SER5 2.4 0.2 1.0 CB O:SER5 3.4 0.8 1.0 CA O:SER5 3.9 0.8 1.0 CD2 M:HIS8 4.0 0.9 1.0 CB M:SER5 4.0 0.3 1.0 ND1 O:HIS8 4.2 1.0 1.0 CG M:HIS8 4.2 1.0 1.0 NE2 M:HIS8 4.3 0.4 1.0 CA M:SER5 4.4 0.3 1.0 ND1 M:HIS8 4.6 0.2 1.0 CE1 M:HIS8 4.6 0.9 1.0 N O:SER5 4.7 0.2 1.0 CB M:HIS8 4.7 0.3 1.0 CE1 O:HIS8 4.8 0.4 1.0 CG N:HIS8 4.9 0.5 1.0 N M:SER5 5.0 0.4 1.0

C.B.Browning, P.G.Leiman, M.M.Shneider. Crystal Structure of R2 Pyocin Membrane-Piercing Spike To Be Published.