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Calcium in PDB 6cpm: Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv

Enzymatic activity of Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv

All present enzymatic activity of Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv:
3.4.19.12;

Protein crystallography data

The structure of Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv, PDB code: 6cpm was solved by A.U.Singer, J.Teyra, G.Boehmelt, M.Lenter, F.Sicheri, S.S.Sidhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.21 / 2.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.552, 115.080, 95.701, 90.00, 92.59, 90.00
R / Rfree (%) 16.7 / 21.2

Other elements in 6cpm:

The structure of Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv (pdb code 6cpm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv, PDB code: 6cpm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 6cpm

Go back to Calcium Binding Sites List in 6cpm
Calcium binding site 1 out of 5 in the Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv


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 USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca701

b:19.8
occ:1.00
 O D:HOH832 2.3 18.4 1.0
OD1 D:ASP548 2.3 25.1 1.0
O C:HOH826 2.4 21.3 1.0
OD1 C:ASP548 2.4 23.9 1.0
OE1 C:GLN614 2.5 20.8 1.0
OE1 D:GLN614 2.5 20.5 1.0
OD2 C:ASP548 2.7 26.6 1.0
OD2 D:ASP548 2.8 27.8 1.0
CG C:ASP548 2.9 23.7 1.0
CG D:ASP548 2.9 28.3 1.0
CD C:GLN614 3.4 23.8 1.0
CD D:GLN614 3.4 24.7 1.0
NE2 D:GLN614 3.7 15.8 1.0
NE2 C:GLN614 3.8 19.0 1.0
OD1 D:ASN557 4.2 22.1 1.0
OD1 C:ASN557 4.3 19.8 1.0
CB C:ASP548 4.3 24.3 1.0
CB D:ASP548 4.4 21.5 1.0
ND2 D:ASN557 4.4 18.1 1.0
ND2 C:ASN557 4.5 20.0 1.0
CD D:ARG555 4.6 27.2 1.0
CD C:ARG555 4.6 27.6 1.0
O C:HOH992 4.6 39.6 1.0
CG C:GLN614 4.8 24.7 1.0
CG D:ASN557 4.8 20.1 1.0
CG D:GLN614 4.8 24.5 1.0
CG C:ASN557 4.9 22.2 1.0
N D:ASP548 4.9 18.7 1.0
N C:ASP548 4.9 20.6 1.0
O D:HOH883 4.9 45.8 1.0
CA C:ASP548 5.0 19.8 1.0
CA D:ASP548 5.0 23.8 1.0

Calcium binding site 2 out of 5 in 6cpm

Go back to Calcium Binding Sites List in 6cpm
Calcium binding site 2 out of 5 in the Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv


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 USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca702

b:65.0
occ:1.00
 OE1 C:GLU598 2.5 41.6 1.0
OG D:SER616 2.5 43.4 1.0
O C:HOH879 2.5 44.7 1.0
CD C:GLU598 3.3 48.5 1.0
CB D:SER616 3.4 52.5 1.0
CG C:GLU598 3.5 37.4 1.0
CG1 C:ILE546 3.8 20.2 1.0
CB C:ILE546 3.9 20.4 1.0
O C:HOH851 4.1 45.9 1.0
CG2 C:ILE546 4.1 18.2 1.0
CB C:GLU598 4.2 33.7 1.0
OD1 C:ASP599 4.2 46.5 1.0
OE2 C:GLU598 4.5 55.2 1.0
N D:SER616 4.5 48.8 1.0
CA D:SER616 4.5 53.0 1.0
ND2 C:ASN547 4.5 29.3 1.0
O D:HOH963 4.7 27.2 1.0
O C:HOH891 4.7 38.6 1.0

Calcium binding site 3 out of 5 in 6cpm

Go back to Calcium Binding Sites List in 6cpm
Calcium binding site 3 out of 5 in the Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv


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 USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:63.3
occ:1.00
 OE1 C:GLN612 2.4 33.3 1.0
O C:HOH1008 2.6 25.6 1.0
O C:HOH996 3.1 33.1 1.0
CD C:GLN612 3.4 25.9 1.0
CG C:PRO311 3.7 21.8 1.0
CG2 C:ILE559 3.9 19.9 1.0
NE2 C:GLN612 4.0 27.8 1.0
O C:HOH1005 4.2 30.6 1.0
CD C:PRO311 4.3 20.0 1.0
O D:HOH958 4.6 46.0 1.0
O C:HOH969 4.6 34.1 1.0
O C:HOH942 4.6 43.5 1.0
CB C:PRO311 4.6 21.9 1.0
CG C:GLN612 4.6 23.8 1.0
O C:HOH841 4.6 22.8 1.0
CB C:GLN612 4.8 21.1 1.0

Calcium binding site 4 out of 5 in 6cpm

Go back to Calcium Binding Sites List in 6cpm
Calcium binding site 4 out of 5 in the Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv


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 USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca701

b:79.7
occ:1.00
 O D:HOH1005 2.5 47.9 1.0
O D:HOH835 2.7 53.2 1.0
O D:HOH1007 2.9 49.4 1.0
O D:HOH951 3.1 30.2 1.0
OD2 D:ASP459 3.3 30.2 1.0
CG D:ASP459 3.5 25.6 1.0
OD1 D:ASP459 3.5 29.2 1.0
OG1 D:THR457 3.9 25.6 1.0
CG2 E:THR48 4.1 21.4 1.0
OG D:SER444 4.4 35.1 1.0
CB D:ASP459 4.5 19.9 1.0
CB D:SER444 4.5 27.4 1.0
O E:HOH242 4.8 28.1 1.0
O D:HOH953 4.9 31.4 1.0

Calcium binding site 5 out of 5 in 6cpm

Go back to Calcium Binding Sites List in 6cpm
Calcium binding site 5 out of 5 in the Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca101

b:34.2
occ:1.00
 OE1 E:GLN31 2.3 35.1 1.0
OD1 E:ASP32 2.4 34.6 1.0
O E:HOH226 2.5 32.4 1.0
CD E:GLN31 3.5 41.4 1.0
CG E:ASP32 3.6 34.2 1.0
NE2 E:GLN31 4.1 30.1 1.0
CA E:ASP32 4.1 32.8 1.0
O E:HOH245 4.2 38.4 1.0
N E:ASP32 4.3 30.3 1.0
OD2 E:ASP32 4.4 30.3 1.0
CB E:ASP32 4.5 31.5 1.0
O E:ALA28 4.6 33.8 1.0
CG E:GLN31 4.6 35.3 1.0
C E:GLN31 4.7 36.6 1.0
CB E:GLN31 4.8 33.3 1.0
O E:HOH216 4.8 33.2 1.0

Reference:

J.Teyra, A.U.Singer, F.W.Schmitges, P.Jaynes, S.Kit Leng Lui, M.J.Polyak, N.Fodil, J.R.Krieger, J.Tong, C.Schwerdtfeger, B.B.Brasher, D.F.J.Ceccarelli, J.Moffat, F.Sicheri, M.F.Moran, P.Gros, P.J.A.Eichhorn, M.Lenter, G.Boehmelt, S.S.Sidhu. Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15. Structure V. 27 590 2019.
ISSN: ISSN 1878-4186
PubMed: 30713027
DOI: 10.1016/J.STR.2019.01.002
Page generated: Wed Jul 9 13:08:26 2025

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