Calcium in PDB 6sjw: Structure of the Self-Processing Module of Iron-Regulated Frpc of N. Meningitidis with Calcium Ions

The binding sites of Calcium atom in the Structure of the Self-Processing Module of Iron-Regulated Frpc of N. Meningitidis with Calcium Ions (pdb code 6sjw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of the Self-Processing Module of Iron-Regulated Frpc of N. Meningitidis with Calcium Ions, PDB code: 6sjw:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of the Self-Processing Module of Iron-Regulated Frpc of N. Meningitidis with Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Self-Processing Module of Iron-Regulated Frpc of N. Meningitidis with Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:0.0 occ:1.00 OD1 A:ASP7 2.5 0.0 1.0 OD1 A:ASP9 2.5 0.0 1.0 OD2 A:ASP5 2.6 0.0 1.0 OE1 A:GLU12 2.6 0.0 1.0 OD1 A:ASP42 2.6 0.0 1.0 O A:GLY10 2.7 0.0 1.0 OD2 A:ASP42 2.7 0.0 1.0 CG A:ASP42 3.1 0.0 1.0 H A:ASP9 3.6 0.0 1.0 CD A:GLU12 3.7 0.0 1.0 CG A:ASP7 3.7 0.0 1.0 CG A:ASP9 3.7 0.0 1.0 CG A:ASP5 3.7 0.0 1.0 H A:ASP7 3.8 0.0 1.0 HB2 A:ASP41 3.8 0.0 1.0 C A:GLY10 3.8 0.0 1.0 HA A:ASP5 3.8 0.0 1.0 HG2 A:GLU12 4.0 0.0 1.0 HA A:ILE11 4.1 0.0 1.0 H A:LEU6 4.1 0.0 1.0 OD2 A:ASP7 4.1 0.0 1.0 HG A:SER39 4.1 0.0 1.0 H A:GLY8 4.2 0.0 1.0 OD2 A:ASP9 4.4 0.0 1.0 N A:GLY10 4.4 0.0 1.0 H A:GLY10 4.4 0.0 1.0 N A:ASP9 4.4 0.0 1.0 CG A:GLU12 4.4 0.0 1.0 HB3 A:ASP41 4.4 0.0 1.0 OE2 A:GLU12 4.5 0.0 1.0 C A:ASP9 4.5 0.0 1.0 CB A:ASP5 4.5 0.0 1.0 H A:GLU12 4.5 0.0 1.0 HB2 A:ASP5 4.6 0.0 1.0 CB A:ASP42 4.6 0.0 1.0 CA A:ASP5 4.6 0.0 1.0 OD1 A:ASP5 4.6 0.0 1.0 CB A:ASP41 4.6 0.0 1.0 N A:ASP7 4.7 0.0 1.0 N A:LEU6 4.7 0.0 1.0 CA A:GLY10 4.7 0.0 1.0 N A:ILE11 4.7 0.0 1.0 CA A:ASP9 4.8 0.0 1.0 CA A:ILE11 4.8 0.0 1.0 CB A:ASP9 4.8 0.0 1.0 N A:GLY8 4.8 0.0 1.0 OG A:SER39 4.9 0.0 1.0 HB3 A:GLU12 4.9 0.0 1.0 O A:ASP9 4.9 0.0 1.0 N A:GLU12 5.0 0.0 1.0 CB A:ASP7 5.0 0.0 1.0 C A:ASP5 5.0 0.0 1.0

Calcium binding site 2 out of 4 in the Structure of the Self-Processing Module of Iron-Regulated Frpc of N. Meningitidis with Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Self-Processing Module of Iron-Regulated Frpc of N. Meningitidis with Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:0.0 occ:1.00 OD2 A:ASP56 2.6 0.0 1.0 OD1 A:ASP48 2.6 0.0 1.0 OE1 A:GLU60 2.6 0.0 1.0 OD1 A:ASN52 2.6 0.0 1.0 OE2 A:GLU60 2.6 0.0 1.0 OD1 A:ASN50 2.6 0.0 1.0 O A:ILE54 2.6 0.0 1.0 CD A:GLU60 3.0 0.0 1.0 HD21 A:ASN52 3.2 0.0 1.0 CG A:ASN52 3.4 0.0 1.0 H A:ASP56 3.5 0.0 1.0 ND2 A:ASN52 3.6 0.0 1.0 CG A:ASP56 3.6 0.0 1.0 CG A:ASP48 3.6 0.0 1.0 H A:ASN50 3.6 0.0 1.0 CG A:ASN50 3.7 0.0 1.0 H A:LEU49 3.8 0.0 1.0 C A:ILE54 3.8 0.0 1.0 HG13 A:ILE54 3.8 0.0 1.0 HA A:ILE55 3.8 0.0 1.0 HA A:ASP48 3.8 0.0 1.0 H A:ASN52 3.9 0.0 1.0 H A:ILE54 4.0 0.0 1.0 HD22 A:ASN50 4.0 0.0 1.0 OD1 A:ASP56 4.0 0.0 1.0 N A:ASP56 4.2 0.0 1.0 ND2 A:ASN50 4.3 0.0 1.0 OD2 A:ASP48 4.3 0.0 1.0 HD22 A:ASN52 4.5 0.0 1.0 N A:ASN50 4.5 0.0 1.0 N A:LEU49 4.5 0.0 1.0 CG A:GLU60 4.5 0.0 1.0 CB A:ASP48 4.5 0.0 1.0 CA A:ILE55 4.6 0.0 1.0 HD11 A:ILE55 4.6 0.0 1.0 N A:ILE55 4.6 0.0 1.0 CA A:ASP48 4.6 0.0 1.0 H A:ASN57 4.6 0.0 1.0 CB A:ASN52 4.7 0.0 1.0 H A:GLY51 4.7 0.0 1.0 HB2 A:ASP48 4.7 0.0 1.0 N A:ILE54 4.7 0.0 1.0 CB A:ASP56 4.7 0.0 1.0 CG1 A:ILE54 4.8 0.0 1.0 CB A:ASN50 4.8 0.0 1.0 HB3 A:ASN57 4.8 0.0 1.0 CA A:ILE54 4.8 0.0 1.0 N A:ASN52 4.8 0.0 1.0 HG12 A:ILE54 4.8 0.0 1.0 C A:ILE55 4.8 0.0 1.0 HB3 A:ASN52 4.9 0.0 1.0 HG2 A:GLU60 4.9 0.0 1.0 HB3 A:ASP56 5.0 0.0 1.0 CA A:ASP56 5.0 0.0 1.0 HB3 A:ASN50 5.0 0.0 1.0 H A:GLY53 5.0 0.0 1.0 C A:ASP48 5.0 0.0 1.0

Calcium binding site 3 out of 4 in the Structure of the Self-Processing Module of Iron-Regulated Frpc of N. Meningitidis with Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Self-Processing Module of Iron-Regulated Frpc of N. Meningitidis with Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:0.0 occ:1.00 OD1 A:ASP89 2.6 0.0 1.0 OD2 A:ASP96 2.6 0.0 1.0 OD1 A:ASP85 2.6 0.0 1.0 OD1 A:ASN87 2.6 0.0 1.0 OD1 A:ASN93 2.6 0.0 1.0 O A:ILE91 2.6 0.0 1.0 OD1 A:ASP96 2.7 0.0 1.0 OD2 A:ASP89 2.7 0.0 1.0 CG A:ASP89 3.0 0.0 1.0 CG A:ASP96 3.0 0.0 1.0 HG13 A:ILE91 3.4 0.0 1.0 H A:SER86 3.7 0.0 1.0 HD22 A:ASN87 3.7 0.0 1.0 CG A:ASP85 3.7 0.0 1.0 H A:ASN87 3.7 0.0 1.0 CG A:ASN87 3.7 0.0 1.0 H A:ASN93 3.8 0.0 1.0 CG A:ASN93 3.8 0.0 1.0 H A:ILE91 3.8 0.0 1.0 C A:ILE91 3.8 0.0 1.0 HA A:ASP85 3.8 0.0 1.0 HA A:ILE92 3.9 0.0 1.0 HG A:SER86 3.9 0.0 1.0 HD22 A:ASN93 4.0 0.0 1.0 H A:ASP89 4.0 0.0 1.0 ND2 A:ASN87 4.2 0.0 1.0 ND2 A:ASN93 4.4 0.0 1.0 CG1 A:ILE91 4.4 0.0 1.0 HG12 A:ILE91 4.4 0.0 1.0 OD2 A:ASP85 4.4 0.0 1.0 N A:SER86 4.5 0.0 1.0 CB A:ASP89 4.5 0.0 1.0 N A:ASN93 4.5 0.0 1.0 H A:GLY88 4.6 0.0 1.0 CB A:ASP96 4.6 0.0 1.0 N A:ILE91 4.6 0.0 1.0 CA A:ASP85 4.6 0.0 1.0 CB A:ASP85 4.6 0.0 1.0 HD11 A:ILE92 4.7 0.0 1.0 N A:ILE92 4.7 0.0 1.0 CA A:ILE91 4.7 0.0 1.0 CA A:ILE92 4.7 0.0 1.0 N A:ASN87 4.7 0.0 1.0 OG A:SER86 4.7 0.0 1.0 HB2 A:ASP85 4.8 0.0 1.0 HB3 A:ASP89 4.8 0.0 1.0 N A:ASP89 4.9 0.0 1.0 HB3 A:ALA95 4.9 0.0 1.0 H A:ASP96 4.9 0.0 1.0 H A:ASN90 5.0 0.0 1.0 CB A:ASN87 5.0 0.0 1.0 CB A:ASN93 5.0 0.0 1.0 C A:ASP85 5.0 0.0 1.0

Calcium binding site 4 out of 4 in the Structure of the Self-Processing Module of Iron-Regulated Frpc of N. Meningitidis with Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Self-Processing Module of Iron-Regulated Frpc of N. Meningitidis with Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:0.0 occ:1.00 O A:ILE113 2.6 0.0 1.0 OD1 A:ASP111 2.6 0.0 1.0 OE1 A:GLU118 2.6 0.0 1.0 OD1 A:ASP107 2.6 0.0 1.0 OD2 A:ASP107 2.6 0.0 1.0 OD1 A:ASN109 2.7 0.0 1.0 OE1 A:GLN115 2.7 0.0 1.0 OE2 A:GLU118 2.8 0.0 1.0 CG A:ASP107 3.0 0.0 1.0 CD A:GLU118 3.1 0.0 1.0 H A:ILE113 3.4 0.0 1.0 HE21 A:GLN115 3.4 0.0 1.0 CG A:ASP111 3.6 0.0 1.0 H A:ASN109 3.7 0.0 1.0 CD A:GLN115 3.7 0.0 1.0 C A:ILE113 3.8 0.0 1.0 H A:ASP111 3.8 0.0 1.0 CG A:ASN109 3.9 0.0 1.0 H A:LEU108 3.9 0.0 1.0 NE2 A:GLN115 4.0 0.0 1.0 OD2 A:ASP111 4.0 0.0 1.0 H A:GLY112 4.1 0.0 1.0 HA A:ASP107 4.1 0.0 1.0 HB A:ILE113 4.2 0.0 1.0 HA A:SER114 4.2 0.0 1.0 N A:ILE113 4.2 0.0 1.0 HE1 A:TRP105 4.3 0.0 1.0 HD21 A:ASN109 4.3 0.0 1.0 HZ2 A:TRP105 4.3 0.0 1.0 CB A:ASP107 4.3 0.0 1.0 H A:GLN115 4.4 0.0 1.0 H A:GLN110 4.5 0.0 1.0 CA A:ILE113 4.5 0.0 1.0 CG A:GLU118 4.6 0.0 1.0 ND2 A:ASN109 4.6 0.0 1.0 N A:LEU108 4.6 0.0 1.0 N A:ASN109 4.6 0.0 1.0 CA A:ASP107 4.7 0.0 1.0 HB2 A:ASP107 4.7 0.0 1.0 N A:SER114 4.7 0.0 1.0 N A:ASP111 4.7 0.0 1.0 N A:GLY112 4.8 0.0 1.0 CA A:SER114 4.9 0.0 1.0 HG3 A:GLU118 4.9 0.0 1.0 HB2 A:GLN115 4.9 0.0 1.0 N A:GLN115 4.9 0.0 1.0 CB A:ASP111 4.9 0.0 1.0 CB A:ILE113 4.9 0.0 1.0 C A:ASP107 4.9 0.0 1.0 HE22 A:GLN115 5.0 0.0 1.0

V.Kuban, P.Macek, J.Hritz, K.Nechvatalova, K.Nedbalcova, M.Faldyna, L.Zidek, L.Bumba. Structural Basis of Ca 2+ -Dependent Self-Processing Activity of Repeat-in-Toxin Proteins Mbio 2020.
ISSN: ESSN 2150-7511
DOI: 10.1128/MBIO.00226-20