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Zinc in PDB 6crn: Structure of the USP15 Deubiquitinase Domain in Complex with A High- Affinity First-Generation Ubv

Enzymatic activity of Structure of the USP15 Deubiquitinase Domain in Complex with A High- Affinity First-Generation Ubv

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

Protein crystallography data

The structure of Structure of the USP15 Deubiquitinase Domain in Complex with A High- Affinity First-Generation Ubv, PDB code: 6crn 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) 111.72 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 41.770, 98.942, 122.043, 66.49, 88.31, 78.10
R / Rfree (%) 18.8 / 23.6

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 6crn

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Zinc binding site 1 out of 4 in the Structure of the USP15 Deubiquitinase Domain in Complex with A High- Affinity First-Generation Ubv


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the USP15 Deubiquitinase Domain in Complex with A High- Affinity First-Generation Ubv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn700

b:0.6
occ:1.00
 SG A:CYS499 2.2 0.6 1.0
SG A:CYS448 2.3 0.6 1.0
SG A:CYS502 2.3 0.5 1.0
SG A:CYS451 2.3 0.7 1.0
CB A:CYS502 2.6 0.5 1.0
CB A:CYS499 2.8 0.4 1.0
CB A:CYS448 3.0 1.0 1.0
N A:CYS502 3.4 0.4 1.0
CA A:CYS502 3.6 0.3 1.0
CB A:CYS451 4.1 0.6 1.0
CA A:CYS499 4.2 0.1 1.0
N A:CYS451 4.3 0.4 1.0
CA A:CYS448 4.5 0.8 1.0
C A:CYS502 4.6 0.8 1.0
C A:ASN501 4.6 0.3 1.0
C A:CYS499 4.7 0.2 1.0
O A:CYS499 4.8 96.8 1.0
CA A:CYS451 4.8 0.6 1.0
CB A:ASN501 4.8 1.0 1.0
N A:LYS503 4.8 0.2 1.0
CZ3 A:TRP497 4.9 83.9 1.0
O A:GLU504 5.0 0.0 1.0
N A:ASN501 5.0 0.5 1.0

Zinc binding site 2 out of 4 in 6crn

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Zinc binding site 2 out of 4 in the Structure of the USP15 Deubiquitinase Domain in Complex with A High- Affinity First-Generation Ubv


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the USP15 Deubiquitinase Domain in Complex with A High- Affinity First-Generation Ubv within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:57.6
occ:1.00
 CB B:CYS451 1.9 78.5 1.0
SG B:CYS499 2.3 47.4 1.0
SG B:CYS502 2.4 65.3 1.0
SG B:CYS448 2.4 55.5 1.0
SG B:CYS451 2.6 82.3 1.0
CB B:CYS448 3.0 53.0 1.0
CA B:CYS451 3.2 67.0 1.0
CB B:CYS502 3.2 62.0 1.0
N B:CYS451 3.4 66.4 1.0
N B:CYS502 3.6 56.7 1.0
CB B:CYS499 3.6 50.0 1.0
CA B:CYS502 3.9 58.1 1.0
C B:CYS451 4.1 62.9 1.0
CB B:ASN501 4.2 55.5 1.0
ND2 B:ASN501 4.4 54.1 1.0
N B:ALA452 4.5 59.7 1.0
C B:ASN501 4.5 53.9 1.0
CA B:CYS448 4.5 53.2 1.0
C B:GLU450 4.7 63.1 1.0
CA B:ASN501 4.8 55.3 1.0
CG B:ASN501 4.9 56.3 1.0
N B:LYS453 4.9 49.6 1.0
O B:CYS451 4.9 56.6 1.0
CB B:LYS453 4.9 57.6 1.0
N B:ASN501 5.0 55.8 1.0
CA B:CYS499 5.0 54.6 1.0
CG B:GLN506 5.0 51.6 1.0

Zinc binding site 3 out of 4 in 6crn

Go back to Zinc Binding Sites List in 6crn
Zinc binding site 3 out of 4 in the Structure of the USP15 Deubiquitinase Domain in Complex with A High- Affinity First-Generation Ubv


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the USP15 Deubiquitinase Domain in Complex with A High- Affinity First-Generation Ubv within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn701

b:69.5
occ:1.00
 CB C:CYS451 1.9 95.4 1.0
SG C:CYS502 2.3 50.3 1.0
SG C:CYS499 2.4 54.0 1.0
SG C:CYS448 2.4 56.4 1.0
SG C:CYS451 2.5 88.8 1.0
CB C:CYS448 3.1 52.5 1.0
CA C:CYS451 3.2 82.8 1.0
N C:CYS451 3.4 77.6 1.0
CB C:CYS502 3.5 48.8 1.0
CB C:CYS499 3.6 53.6 1.0
N C:CYS502 3.8 53.6 1.0
C C:CYS451 4.0 79.0 1.0
CA C:CYS502 4.2 54.0 1.0
CB C:ASN501 4.3 65.4 1.0
N C:ALA452 4.4 74.4 1.0
ND2 C:ASN501 4.5 55.6 1.0
O C:HOH874 4.5 46.1 1.0
CA C:CYS448 4.6 56.0 1.0
C C:GLU450 4.7 76.2 1.0
C C:ASN501 4.7 57.6 1.0
O C:CYS451 4.8 78.4 1.0
N C:LYS453 4.9 66.6 1.0
CA C:ASN501 4.9 63.5 1.0
CG C:ASN501 5.0 63.2 1.0
CA C:CYS499 5.0 55.6 1.0

Zinc binding site 4 out of 4 in 6crn

Go back to Zinc Binding Sites List in 6crn
Zinc binding site 4 out of 4 in the Structure of the USP15 Deubiquitinase Domain in Complex with A High- Affinity First-Generation Ubv


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the USP15 Deubiquitinase Domain in Complex with A High- Affinity First-Generation Ubv within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn701

b:0.7
occ:1.00
 SG D:CYS448 2.1 1.0 1.0
CB D:CYS502 2.2 0.0 1.0
SG D:CYS502 2.2 0.4 1.0
SG D:CYS451 2.3 0.5 1.0
SG D:CYS499 2.8 0.9 1.0
CB D:CYS448 3.1 0.4 1.0
CB D:CYS451 3.2 0.7 1.0
N D:CYS451 3.2 0.7 1.0
CA D:CYS502 3.5 0.1 1.0
CB D:CYS499 3.7 0.8 1.0
N D:CYS502 3.8 0.2 1.0
CB D:GLU450 3.8 0.6 1.0
CA D:CYS451 3.8 0.1 1.0
C D:GLU450 4.2 0.8 1.0
N D:GLU450 4.3 1.0 1.0
CG D:GLU450 4.3 0.3 1.0
CA D:GLU450 4.3 1.0 1.0
CA D:CYS448 4.5 0.8 1.0
C D:CYS502 4.6 0.2 1.0
C D:CYS448 4.8 0.0 1.0
CG D:GLN506 4.8 0.7 1.0
C D:CYS451 4.9 0.8 1.0
NE2 D:GLN506 4.9 0.1 1.0
N D:ALA452 5.0 0.6 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: Mon Oct 28 19:05:10 2024

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