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Calcium in PDB 9d9z: Structure of Human UBR4-KCMF1-Cam E3 Ligase Complex (Silencing Factor of the Integrated Stress Response, Sifi)

Enzymatic activity of Structure of Human UBR4-KCMF1-Cam E3 Ligase Complex (Silencing Factor of the Integrated Stress Response, Sifi)

All present enzymatic activity of Structure of Human UBR4-KCMF1-Cam E3 Ligase Complex (Silencing Factor of the Integrated Stress Response, Sifi):
2.3.2.27;

Other elements in 9d9z:

The structure of Structure of Human UBR4-KCMF1-Cam E3 Ligase Complex (Silencing Factor of the Integrated Stress Response, Sifi) also contains other interesting chemical elements:

Zinc (Zn) 20 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Human UBR4-KCMF1-Cam E3 Ligase Complex (Silencing Factor of the Integrated Stress Response, Sifi) (pdb code 9d9z). 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 Human UBR4-KCMF1-Cam E3 Ligase Complex (Silencing Factor of the Integrated Stress Response, Sifi), PDB code: 9d9z:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 9d9z

Go back to Calcium Binding Sites List in 9d9z
Calcium binding site 1 out of 4 in the Structure of Human UBR4-KCMF1-Cam E3 Ligase Complex (Silencing Factor of the Integrated Stress Response, Sifi)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Human UBR4-KCMF1-Cam E3 Ligase Complex (Silencing Factor of the Integrated Stress Response, Sifi) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:66.7
occ:1.00
 OE2 C:GLU141 1.9 68.1 1.0
OD1 C:ASP132 2.4 85.5 1.0
CD C:GLU141 2.7 68.4 1.0
CG C:ASP132 3.0 85.5 1.0
OE1 C:GLU141 3.0 69.8 1.0
OD2 C:ASP132 3.1 85.4 1.0
OE2 C:GLU140 3.1 84.2 1.0
OD1 C:ASP134 3.2 86.0 1.0
O C:GLN136 3.2 76.4 1.0
OD2 C:ASP134 3.4 87.3 1.0
OD1 C:ASP130 3.4 82.7 1.0
CG C:ASP134 3.6 86.3 1.0
CG C:GLU141 3.9 69.4 1.0
CD C:GLU140 4.1 82.2 1.0
C C:GLN136 4.1 77.6 1.0
CB C:ASP132 4.4 84.7 1.0
CE1 C:TYR100 4.5 78.0 1.0
CG C:ASP130 4.5 83.2 1.0
N C:ASP132 4.5 82.3 1.0
N C:ASN138 4.7 74.1 1.0
CA C:VAL137 4.7 75.8 1.0
N C:VAL137 4.8 76.5 1.0
CG C:GLU140 4.9 79.7 1.0
CB C:ASP134 4.9 85.5 1.0
N C:ILE131 4.9 81.6 1.0
CB C:GLN136 5.0 79.5 1.0
OE1 C:GLU140 5.0 83.0 1.0
CA C:ASP132 5.0 83.0 1.0
CD1 C:TYR100 5.0 77.7 1.0

Calcium binding site 2 out of 4 in 9d9z

Go back to Calcium Binding Sites List in 9d9z
Calcium binding site 2 out of 4 in the Structure of Human UBR4-KCMF1-Cam E3 Ligase Complex (Silencing Factor of the Integrated Stress Response, Sifi)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Human UBR4-KCMF1-Cam E3 Ligase Complex (Silencing Factor of the Integrated Stress Response, Sifi) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:79.1
occ:1.00
 O C:TYR100 2.8 75.3 1.0
OE2 C:GLU105 3.3 87.2 1.0
OD1 C:ASP94 3.3 69.5 1.0
OD1 C:ASP96 3.4 84.7 1.0
OD2 C:ASP96 3.7 80.8 1.0
OG C:SER102 3.7 79.7 1.0
CG C:ASP96 3.8 81.5 1.0
C C:TYR100 4.0 76.2 1.0
CG C:ASP94 4.1 70.7 1.0
OD2 C:ASP94 4.1 69.3 1.0
CD C:GLU105 4.3 88.1 1.0
OE1 C:GLU105 4.6 88.7 1.0
O C:ASP96 4.7 79.7 1.0
N C:TYR100 4.7 76.2 1.0
CB C:SER102 4.8 80.6 1.0
CA C:TYR100 4.8 76.3 1.0
N C:SER102 4.9 79.7 1.0
CB C:TYR100 5.0 76.6 1.0

Calcium binding site 3 out of 4 in 9d9z

Go back to Calcium Binding Sites List in 9d9z
Calcium binding site 3 out of 4 in the Structure of Human UBR4-KCMF1-Cam E3 Ligase Complex (Silencing Factor of the Integrated Stress Response, Sifi)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Human UBR4-KCMF1-Cam E3 Ligase Complex (Silencing Factor of the Integrated Stress Response, Sifi) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:66.7
occ:1.00
 OE2 D:GLU141 3.0 68.1 1.0
NE2 D:GLN136 3.5 81.3 1.0
O D:GLN136 3.5 76.4 1.0
OE2 D:GLU140 3.7 84.2 1.0
CE1 D:TYR100 3.7 78.0 1.0
OD2 D:ASP132 3.8 85.4 1.0
OD2 D:ASP134 3.9 87.3 1.0
CD D:GLU141 4.1 68.4 1.0
OD1 D:ASP132 4.2 85.5 1.0
CG D:GLN136 4.2 80.6 1.0
CD1 D:TYR100 4.2 77.7 1.0
C D:GLN136 4.3 77.6 1.0
CD D:GLN136 4.3 81.8 1.0
OD1 D:ASP134 4.4 86.0 1.0
CG D:ASP132 4.4 85.5 1.0
N D:ASN138 4.4 74.1 1.0
CG D:ASP134 4.6 86.3 1.0
CB D:ASN138 4.6 72.4 1.0
CZ D:TYR100 4.8 78.1 1.0
CB D:GLN136 4.8 79.5 1.0
CG D:GLU141 4.9 69.4 1.0
CD D:GLU140 4.9 82.2 1.0
CA D:VAL137 4.9 75.8 1.0
N D:VAL137 4.9 76.5 1.0
OH D:TYR100 5.0 78.0 1.0

Calcium binding site 4 out of 4 in 9d9z

Go back to Calcium Binding Sites List in 9d9z
Calcium binding site 4 out of 4 in the Structure of Human UBR4-KCMF1-Cam E3 Ligase Complex (Silencing Factor of the Integrated Stress Response, Sifi)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Human UBR4-KCMF1-Cam E3 Ligase Complex (Silencing Factor of the Integrated Stress Response, Sifi) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:79.1
occ:1.00
 CB D:ASN98 1.8 77.7 1.0
OE2 D:GLU105 2.0 87.2 1.0
OD1 D:ASP96 2.3 84.7 1.0
CG D:ASN98 2.9 78.3 1.0
CA D:ASN98 2.9 76.5 1.0
N D:ASN98 3.1 76.6 1.0
CD D:GLU105 3.2 88.1 1.0
CG D:ASP96 3.3 81.5 1.0
OD1 D:ASP94 3.4 69.5 1.0
OD1 D:ASN98 3.5 77.3 1.0
ND2 D:ASN98 3.6 78.8 1.0
OD2 D:ASP96 3.6 80.8 1.0
CG D:GLU105 3.9 88.5 1.0
OG D:SER102 4.0 79.7 1.0
CG D:ASP94 4.0 70.7 1.0
O D:TYR100 4.0 75.3 1.0
C D:ASN98 4.1 75.7 1.0
OE1 D:GLU105 4.2 88.7 1.0
C D:GLY97 4.4 76.9 1.0
CB D:SER102 4.5 80.6 1.0
OD2 D:ASP94 4.6 69.3 1.0
CB D:ASP96 4.6 78.9 1.0
N D:GLY99 4.6 75.2 1.0
CB D:ASP94 4.6 71.8 1.0
N D:GLY97 4.7 78.0 1.0
C D:ASP96 4.7 78.7 1.0
CA D:ASP94 4.7 73.4 1.0
CB D:GLU105 4.9 88.4 1.0
N D:ASP96 4.9 77.7 1.0
CA D:ASP96 5.0 78.0 1.0
O D:ASN98 5.0 75.6 1.0

Reference:

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
Page generated: Thu Jul 10 09:16:37 2025

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