Calcium in PDB 9nwe: E3 Ligase UBR4-KCMF1-Calmodulin Complex

All present enzymatic activity of E3 Ligase UBR4-KCMF1-Calmodulin Complex:
2.3.2.27;

The structure of E3 Ligase UBR4-KCMF1-Calmodulin Complex also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Calcium atom in the E3 Ligase UBR4-KCMF1-Calmodulin Complex (pdb code 9nwe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the E3 Ligase UBR4-KCMF1-Calmodulin Complex, PDB code: 9nwe:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the E3 Ligase UBR4-KCMF1-Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of E3 Ligase UBR4-KCMF1-Calmodulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:66.7 occ:1.00 OD1 C:ASP134 2.0 86.0 1.0 OD1 C:ASP132 2.3 85.5 1.0 OD1 C:ASP130 2.3 82.7 1.0 O C:GLN136 2.5 76.4 1.0 OE2 C:GLU141 2.5 68.1 1.0 CG C:ASP134 2.7 86.3 1.0 OD2 C:ASP134 2.9 87.3 1.0 OE1 C:GLU141 3.0 69.8 1.0 CG C:ASP132 3.1 85.5 1.0 CD C:GLU141 3.1 68.4 1.0 CG C:ASP130 3.2 83.2 1.0 OD2 C:ASP132 3.3 85.4 1.0 C C:GLN136 3.6 77.6 1.0 OD2 C:ASP130 3.7 82.8 1.0 N C:ASP134 3.9 84.6 1.0 CB C:ASP134 4.0 85.5 1.0 N C:GLN136 4.1 80.4 1.0 N C:GLY133 4.3 82.7 1.0 N C:ASP132 4.4 82.3 1.0 CB C:ASP130 4.4 83.4 1.0 CA C:GLN136 4.4 78.8 1.0 CB C:ASP132 4.4 84.7 1.0 N C:ILE131 4.4 81.6 1.0 CA C:ASP134 4.4 84.5 1.0 N C:VAL137 4.5 76.5 1.0 CA C:VAL137 4.5 75.8 1.0 CG C:GLU141 4.6 69.4 1.0 CA C:ASP130 4.6 83.8 1.0 N C:GLY135 4.7 82.2 1.0 OE2 C:GLU140 4.7 84.2 1.0 CA C:ASP132 4.8 83.0 1.0 C C:ASP134 4.9 83.3 1.0 C C:GLY133 5.0 83.7 1.0 CB C:GLN136 5.0 79.5 1.0

Calcium binding site 2 out of 4 in the E3 Ligase UBR4-KCMF1-Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of E3 Ligase UBR4-KCMF1-Calmodulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:79.1 occ:1.00 OD1 C:ASN98 2.0 30.0 1.0 OD1 C:ASP94 2.0 69.5 1.0 OE2 C:GLU105 2.0 87.2 1.0 O C:LYS95 2.4 78.3 1.0 CB C:ASN98 2.6 30.0 1.0 CG C:ASN98 2.6 30.0 1.0 CD C:GLU105 3.1 88.1 1.0 CG C:ASP94 3.2 70.7 1.0 O C:TYR100 3.4 75.3 1.0 C C:LYS95 3.5 78.3 1.0 CA C:ASN98 3.6 30.0 1.0 N C:LYS95 3.7 77.9 1.0 N C:ASN98 3.7 30.0 1.0 OE1 C:GLU105 3.8 88.7 1.0 OD2 C:ASP94 3.8 69.3 1.0 ND2 C:ASN98 3.9 30.0 1.0 C C:ASP94 4.1 75.7 1.0 CA C:LYS95 4.3 78.7 1.0 CA C:ASP94 4.3 73.4 1.0 CG C:GLU105 4.3 88.5 1.0 CB C:ASP94 4.3 71.8 1.0 CB C:ASP96 4.3 78.9 1.0 C C:TYR100 4.3 76.2 1.0 C C:ASN98 4.4 30.0 1.0 OG C:SER102 4.4 79.7 1.0 N C:ASP96 4.5 77.7 1.0 C C:ASP96 4.6 78.7 1.0 N C:SER102 4.6 79.7 1.0 CA C:ILE101 4.6 77.2 1.0 CA C:ASP96 4.7 78.0 1.0 O C:ASP96 4.7 79.7 1.0 O C:ASN98 4.7 30.0 1.0 O C:ASP94 4.9 77.2 1.0 N C:ILE101 4.9 76.4 1.0 C C:GLY97 4.9 30.0 1.0 C C:ILE101 4.9 78.5 1.0 N C:GLY97 4.9 30.0 1.0 N C:TYR100 5.0 76.2 1.0 CB C:SER102 5.0 80.6 1.0

Calcium binding site 3 out of 4 in the E3 Ligase UBR4-KCMF1-Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of E3 Ligase UBR4-KCMF1-Calmodulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:66.7 occ:1.00 O D:GLN136 1.8 76.4 1.0 OD1 D:ASP130 2.2 82.7 1.0 OD1 D:ASP132 2.3 85.5 1.0 OD1 D:ASP134 2.4 86.0 1.0 OE2 D:GLU141 2.7 68.1 1.0 C D:GLN136 3.1 77.6 1.0 OE1 D:GLU141 3.1 69.8 1.0 CG D:ASP134 3.2 86.3 1.0 CD D:GLU141 3.2 68.4 1.0 CG D:ASP132 3.3 85.5 1.0 CG D:ASP130 3.3 83.2 1.0 OD2 D:ASP134 3.5 87.3 1.0 OD2 D:ASP132 3.5 85.4 1.0 OD2 D:ASP130 3.8 82.8 1.0 CG D:GLN136 4.0 80.6 1.0 N D:VAL137 4.0 76.5 1.0 CA D:GLN136 4.0 78.8 1.0 CA D:VAL137 4.1 75.8 1.0 N D:GLN136 4.1 80.4 1.0 CB D:GLN136 4.5 79.5 1.0 N D:ASP134 4.5 84.6 1.0 N D:ASP132 4.5 82.3 1.0 CB D:ASP130 4.6 83.4 1.0 CB D:ASP134 4.6 85.5 1.0 CB D:ASP132 4.6 84.7 1.0 CG2 D:VAL137 4.7 76.4 1.0 CG D:GLU141 4.7 69.4 1.0 CA D:ASP130 4.7 83.8 1.0 N D:ILE131 4.8 81.6 1.0 N D:GLY133 4.8 82.7 1.0 NE2 D:GLN136 4.8 81.3 1.0 CB D:VAL137 4.9 76.3 1.0 CA D:ASP132 5.0 83.0 1.0

Calcium binding site 4 out of 4 in the E3 Ligase UBR4-KCMF1-Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of E3 Ligase UBR4-KCMF1-Calmodulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca202 b:79.1 occ:1.00 OD1 D:ASP96 2.0 84.7 1.0 OE2 D:GLU105 2.3 87.2 1.0 CG D:ASP96 2.7 81.5 1.0 CB D:ASN98 2.8 77.7 1.0 OD2 D:ASP96 2.9 80.8 1.0 OG D:SER102 3.2 79.7 1.0 CD D:GLU105 3.5 88.1 1.0 CG D:ASN98 3.5 78.3 1.0 OD1 D:ASN98 3.6 77.3 1.0 CB D:SER102 3.7 80.6 1.0 O D:ASP94 3.8 77.2 1.0 OD1 D:ASP94 3.9 69.5 1.0 O D:TYR100 4.0 75.3 1.0 CA D:ASN98 4.0 76.5 1.0 OE1 D:GLU105 4.1 88.7 1.0 CB D:ASP94 4.1 71.8 1.0 CB D:ASP96 4.2 78.9 1.0 N D:ASN98 4.2 76.6 1.0 CA D:ASP94 4.2 73.4 1.0 C D:ASP94 4.4 75.7 1.0 CG D:ASP94 4.5 70.7 1.0 CG D:GLU105 4.5 88.5 1.0 ND2 D:ASN98 4.7 78.8 1.0 N D:SER102 4.7 79.7 1.0 N D:GLY99 4.8 75.2 1.0 C D:ASN98 4.8 75.7 1.0 CA D:SER102 4.8 81.5 1.0 CA D:ASP96 4.9 78.0 1.0 N D:ASP96 5.0 77.7 1.0

Z.Yang, D.L.Haakonsen, M.Heider, S.R.Witus, A.Zelter, T.Beschauner, M.J.Maccoss, M.Rape. Molecular Basis of Sifi Activity in the Integrated Stress Response. Nature 2025.
ISSN: ESSN 1476-4687
PubMed: 40328314
DOI: 10.1038/S41586-025-09074-Z