Calcium in PDB 7kld: Crystal Structure of An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide

The structure of Crystal Structure of An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide, PDB code: 7kld was solved by H.T.Wright, D.Peterson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.31 / 2.25
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	53.482, 66.556, 93.446, 90, 103.44, 90
R / Rfree (%)	24.6 / 27.9

The binding sites of Calcium atom in the Crystal Structure of An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide (pdb code 7kld). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide, PDB code: 7kld:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide


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 An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:35.7 occ:1.00 O A:TYR105 2.5 29.6 1.0 OD1 A:ASN104 2.7 31.8 1.0 O A:HOH327 3.4 45.3 1.0 C A:TYR105 3.7 29.4 1.0 H A:TYR105 3.7 27.3 1.0 CG A:ASN104 3.9 31.6 1.0 N A:TYR105 4.0 22.6 1.0 HB2 A:TYR105 4.3 35.0 1.0 CA A:TYR105 4.3 26.8 1.0 HA A:ASN104 4.4 28.8 1.0 HA A:LYS106 4.4 34.7 1.0 HD21 A:ASN104 4.4 39.6 1.0 ND2 A:ASN104 4.6 32.8 1.0 HG2 A:LYS106 4.6 38.8 1.0 C A:ASN104 4.7 21.7 1.0 N A:LYS106 4.8 31.3 1.0 CB A:TYR105 4.8 29.0 1.0 CA A:ASN104 4.9 23.8 1.0 CB A:ASN104 4.9 28.3 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide


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 An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:56.1 occ:0.95 O A:HOH320 2.1 35.4 1.0 O A:LEU51 2.8 24.4 1.0 OE2 A:GLU78 3.8 41.5 1.0 OE1 A:GLU78 3.9 40.2 1.0 C A:LEU51 3.9 22.8 1.0 HB3 A:LEU51 4.2 30.1 1.0 HA A:LEU51 4.2 28.8 1.0 CD A:GLU78 4.2 35.1 1.0 HA A:THR52 4.3 32.3 1.0 CA A:LEU51 4.6 23.8 1.0 N A:THR52 4.9 25.3 1.0 CB A:LEU51 4.9 24.9 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide


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 An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:27.4 occ:0.76 OD1 A:ASN59 2.1 24.2 1.0 OD2 A:ASP57 2.3 26.5 1.0 OD2 B:ASP20 2.4 36.8 1.0 OD1 A:ASP57 2.5 23.8 1.0 CG A:ASP57 2.7 21.6 1.0 OD1 B:ASP20 2.8 33.4 1.0 CG B:ASP20 3.0 38.3 1.0 O B:HOH311 3.2 38.3 1.0 CG A:ASN59 3.3 20.6 1.0 HE1 A:HIS68 3.8 34.0 1.0 HD21 A:ASN59 4.0 28.8 1.0 O A:HOH303 4.1 33.3 1.0 HB2 A:ASN59 4.1 30.4 1.0 ND2 A:ASN59 4.1 23.8 1.0 CB A:ASP57 4.1 26.6 1.0 HD1 B:HIS66 4.2 34.2 1.0 HB2 B:HIS66 4.2 33.9 1.0 H B:GLY21 4.3 53.0 1.0 CB A:ASN59 4.3 25.1 1.0 HB3 A:ASP57 4.4 32.1 1.0 O B:GLY65 4.4 40.3 1.0 CE1 A:HIS68 4.4 28.1 1.0 CB B:ASP20 4.4 36.5 1.0 ND1 A:HIS68 4.5 22.9 1.0 C A:ASP57 4.6 22.5 1.0 O A:ASP57 4.6 28.2 1.0 N B:GLY21 4.7 44.0 1.0 HB2 A:ASP57 4.7 32.1 1.0 HA2 B:GLY21 4.7 51.7 1.0 N A:ILE58 4.8 21.0 1.0 HB3 B:ASP20 4.8 44.1 1.0 O A:ILE58 4.8 31.5 1.0 ND1 B:HIS66 4.8 28.3 1.0 C A:ILE58 4.9 28.6 1.0 H A:ILE58 4.9 25.5 1.0 CA A:ASP57 4.9 23.8 1.0 HB2 B:ASP20 4.9 44.1 1.0 HD22 A:ASN59 5.0 28.8 1.0 N A:ASN59 5.0 23.1 1.0 HB3 A:ASN59 5.0 30.4 1.0 HA B:ASP20 5.0 43.5 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide


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 An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:21.3 occ:0.80 O A:ASN98 2.2 26.8 1.0 OE2 A:GLU94 2.4 28.0 1.0 O A:ILE101 2.4 27.3 1.0 HA A:ASN98 3.1 36.9 1.0 C A:ASN98 3.2 25.7 1.0 HA A:ARG102 3.2 33.1 1.0 CD A:GLU94 3.4 24.5 1.0 HG2 A:GLU94 3.4 32.1 1.0 HB3 A:ASN98 3.6 34.0 1.0 CA A:ASN98 3.6 30.6 1.0 C A:ILE101 3.6 30.9 1.0 HE2 A:MET1 3.7 38.7 1.0 CG A:GLU94 3.8 26.6 1.0 HG3 A:GLU94 3.9 32.1 1.0 CA A:ARG102 4.1 27.4 1.0 CB A:ASN98 4.1 28.1 1.0 N A:ARG102 4.3 28.3 1.0 H A:ILE101 4.3 33.0 1.0 HE1 A:MET1 4.4 38.7 1.0 N A:GLU99 4.4 29.6 1.0 HB2 A:ARG102 4.4 40.6 1.0 CE A:MET1 4.4 38.7 1.0 OE1 A:GLU94 4.5 28.8 1.0 HA A:GLU99 4.6 35.5 1.0 HB2 A:ASN98 4.6 34.0 1.0 H A:LEU103 4.6 36.7 1.0 HE3 A:MET1 4.7 38.7 1.0 HD21 A:ASN98 4.7 46.9 1.0 HG3 A:ARG102 4.8 41.2 1.0 CB A:ARG102 4.8 33.7 1.0 CA A:ILE101 4.8 29.1 1.0 HB A:ILE101 4.8 27.3 1.0 N A:ILE101 4.8 27.3 1.0 N A:ASN98 4.9 26.4 1.0 CA A:GLU99 4.9 29.4 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide


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 An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:55.8 occ:0.70 O B:HOH308 2.3 46.4 1.0 O D:HOH315 2.4 38.2 1.0 O B:HOH317 2.6 36.5 1.0 O B:LEU51 2.8 27.9 1.0 OE2 B:GLU78 2.9 45.3 1.0 HB3 B:LEU51 3.8 28.2 1.0 CD B:GLU78 3.8 39.8 1.0 C B:LEU51 3.9 29.9 1.0 HD13 D:LEU81 4.0 32.9 1.0 OE1 B:GLU78 4.1 48.4 1.0 HA B:LEU51 4.3 29.1 1.0 HA B:THR52 4.3 35.5 1.0 CA B:LEU51 4.6 24.1 1.0 CB B:LEU51 4.6 23.3 1.0 HD11 D:LEU81 4.7 32.9 1.0 CD1 D:LEU81 4.8 27.2 1.0 OE1 D:GLN84 4.8 25.7 1.0 HG22 B:THR52 4.8 26.7 1.0 HB3 B:GLU78 4.9 34.3 1.0 HB2 B:LEU51 4.9 28.2 1.0 N B:THR52 5.0 26.7 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide


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 An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:33.3 occ:0.89 OD1 B:ASN59 2.0 36.9 1.0 O A:HOH317 2.1 37.2 1.0 OD1 B:ASP57 2.3 31.4 1.0 OD1 A:ASP20 2.4 41.5 1.0 OD2 B:ASP57 2.7 38.1 1.0 CG B:ASP57 2.8 33.5 1.0 OD2 A:ASP20 3.0 36.9 1.0 CG A:ASP20 3.1 37.4 1.0 CG B:ASN59 3.1 32.4 1.0 HD21 B:ASN59 3.4 42.0 1.0 ND2 B:ASN59 3.7 34.8 1.0 O B:HOH314 3.7 40.7 1.0 O B:HOH315 3.7 37.6 1.0 H A:GLY21 4.0 49.4 1.0 O A:GLY65 4.2 35.5 1.0 CB B:ASP57 4.3 31.4 1.0 HB2 B:ASN59 4.4 36.0 1.0 CB B:ASN59 4.4 29.8 1.0 HB2 A:HIS66 4.4 33.5 1.0 HD22 B:ASN59 4.5 42.0 1.0 CB A:ASP20 4.5 34.3 1.0 N A:GLY21 4.6 41.0 1.0 HA2 A:GLY21 4.6 47.9 1.0 HB3 B:ASP57 4.7 37.9 1.0 O B:ILE58 4.7 32.8 1.0 C B:ASP57 4.7 27.5 1.0 HB2 B:ASP57 4.7 37.9 1.0 HE1 B:HIS68 4.7 36.6 1.0 N B:ILE58 4.8 20.4 1.0 H B:ILE58 4.8 24.7 1.0 HD1 A:HIS66 4.8 33.3 1.0 HB3 A:ASP20 4.8 41.4 1.0 C B:ILE58 4.9 26.4 1.0 O B:ASP57 5.0 30.4 1.0 CA B:ASP57 5.0 27.3 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:32.5 occ:0.73 OD1 D:ASN59 2.0 29.4 1.0 O D:HOH307 2.2 42.6 1.0 OD2 D:ASP57 2.4 35.9 1.0 OD1 D:ASP57 2.7 30.4 1.0 CG D:ASP57 2.9 31.4 1.0 CG D:ASN59 3.2 29.9 1.0 HD2 D:HIS68 3.6 33.5 1.0 HD21 D:ASN59 3.8 49.5 1.0 HE2 D:HIS68 3.9 40.4 1.0 ND2 D:ASN59 4.0 41.0 1.0 HB2 D:ASN59 4.2 33.3 1.0 CB D:ASP57 4.3 25.9 1.0 CD2 D:HIS68 4.3 27.8 1.0 CB D:ASN59 4.4 27.6 1.0 NE2 D:HIS68 4.4 33.5 1.0 HB3 D:ASP57 4.5 31.3 1.0 C D:ASP57 4.8 25.3 1.0 HB2 D:ASP57 4.8 31.3 1.0 HD22 D:ASN59 4.8 49.5 1.0 O D:ASP57 4.9 32.4 1.0 O D:ILE58 4.9 34.8 1.0 N D:ILE58 4.9 28.4 1.0 C D:ILE58 5.0 30.4 1.0 HD2 D:ARG70 5.0 40.0 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Covalently Linked Product Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca202 b:34.0 occ:0.43 OD2 D:ASP10 2.6 29.1 1.0 OD1 D:ASP10 2.7 28.3 1.0 CG D:ASP10 3.1 26.6 1.0 CB D:ASP10 4.6 23.6 1.0 HB2 D:ASP10 5.0 28.5 1.0 HB3 D:ASP10 5.0 28.5 1.0

H.T.Wright, D.Peterson, G.Christie. Crystal Structures of An Essential Ribosomal Processing Protease Prp From S. Aureus in Complex with A Substrate Peptide and with A Covalently Bound Product Peptide To Be Published.