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Sodium in PDB 6ml1: Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv

Enzymatic activity of Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv

All present enzymatic activity of Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv:
3.4.19.12;

Protein crystallography data

The structure of Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv, PDB code: 6ml1 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) 49.32 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.770, 115.290, 95.320, 90.00, 91.92, 90.00
R / Rfree (%) 18.9 / 22

Other elements in 6ml1:

The structure of Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Calcium (Ca) 4 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv (pdb code 6ml1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv, PDB code: 6ml1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6ml1

Go back to Sodium Binding Sites List in 6ml1
Sodium binding site 1 out of 4 in the Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1004

b:50.8
occ:1.00
 O A:GLY333 3.0 29.9 1.0
O A:LEU332 3.6 25.2 1.0
C A:LEU332 3.8 25.3 1.0
C A:GLY333 4.1 32.4 1.0
O A:PRO331 4.1 27.5 1.0
N A:GLY333 4.2 24.9 1.0
CA A:LEU332 4.3 26.8 1.0
CE A:MET334 4.5 35.1 1.0
O A:HOH1246 4.6 40.7 1.0
CA A:GLY333 4.7 26.1 1.0
CD C:LYS55 4.7 45.6 1.0
CE C:LYS55 4.9 34.8 1.0
C A:PRO331 4.9 31.3 1.0

Sodium binding site 2 out of 4 in 6ml1

Go back to Sodium Binding Sites List in 6ml1
Sodium binding site 2 out of 4 in the Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1005

b:27.7
occ:1.00
 O A:HOH1212 2.7 32.7 0.4
N A:LYS789 3.1 29.6 1.0
N A:LEU788 3.5 24.8 1.0
CB A:LYS789 3.6 38.2 1.0
O B:HOH1208 3.7 44.5 1.0
CB A:LEU788 3.8 21.2 1.0
CD A:PRO855 3.9 19.8 1.0
CB A:LYS787 3.9 26.5 0.5
CA A:LYS789 3.9 32.1 1.0
CB A:LYS787 3.9 26.6 0.5
CA A:LEU788 3.9 22.7 1.0
O A:ASP853 3.9 24.1 1.0
C A:LEU788 4.0 28.3 1.0
CG A:PRO855 4.0 20.2 1.0
C A:LYS787 4.2 26.8 0.5
C A:LYS787 4.2 26.8 0.5
CA A:LYS787 4.4 25.2 0.5
CA A:LYS787 4.4 25.2 0.5
O B:GLY937 4.5 55.7 1.0
CG A:LYS787 4.7 28.8 0.5
CD A:LYS787 4.8 28.3 0.5
CE A:LYS787 4.8 30.4 0.5
CD1 A:LEU859 4.9 21.1 1.0
CG A:LYS787 4.9 29.7 0.5
N A:PRO855 4.9 21.7 1.0
CG A:LEU788 5.0 24.9 1.0
O A:HOH1212 5.0 22.4 0.6

Sodium binding site 3 out of 4 in 6ml1

Go back to Sodium Binding Sites List in 6ml1
Sodium binding site 3 out of 4 in the Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1005

b:28.6
occ:1.00
 O B:HOH1205 2.9 39.2 1.0
N B:LYS789 3.3 28.2 1.0
N B:LEU788 3.5 27.2 1.0
CB B:LYS789 3.8 32.7 1.0
CB B:LEU788 3.9 21.0 1.0
CD B:PRO855 3.9 19.7 1.0
O B:ASP853 4.0 28.1 1.0
CA B:LEU788 4.0 24.3 1.0
CB B:LYS787 4.0 34.3 1.0
C B:LEU788 4.1 27.8 1.0
CG B:PRO855 4.1 22.2 1.0
CA B:LYS789 4.1 32.7 1.0
C B:LYS787 4.2 28.0 1.0
CD B:LYS787 4.3 43.4 1.0
CA B:LYS787 4.4 28.7 1.0
CG B:LYS787 4.7 34.8 1.0
CD1 B:LEU859 4.8 20.8 1.0

Sodium binding site 4 out of 4 in 6ml1

Go back to Sodium Binding Sites List in 6ml1
Sodium binding site 4 out of 4 in the Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1006

b:45.4
occ:1.00
 N B:LEU468 2.9 27.4 1.0
O B:LYS836 3.0 32.1 1.0
OG B:SER839 3.1 52.2 1.0
CB B:SER839 3.4 55.2 1.0
CA B:PRO467 3.6 28.7 1.0
O B:LEU468 3.6 29.9 1.0
C B:PRO467 3.7 30.5 1.0
CA B:LEU468 3.9 23.9 1.0
CB B:PRO467 4.0 25.8 1.0
CD1 B:LEU848 4.0 45.9 1.0
CG B:LYS836 4.0 43.3 1.0
C B:LYS836 4.1 33.2 1.0
CB B:LEU468 4.1 28.8 1.0
CB B:LYS836 4.1 31.9 1.0
C B:LEU468 4.2 35.9 1.0
CG B:LEU468 4.5 40.8 1.0
CE B:MET470 4.6 54.2 1.0
CA B:LYS836 4.7 31.0 1.0
O B:HOH1217 4.7 43.5 1.0
CA B:SER839 4.8 54.4 1.0
O B:LEU466 4.8 29.7 1.0
N B:PRO467 4.9 31.2 1.0
O B:PRO467 5.0 27.1 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: Tue Dec 15 12:36:14 2020

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