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Zinc in PDB 6kqq: NSD1 Set Domain in Complex with BT3 and Sam

Enzymatic activity of NSD1 Set Domain in Complex with BT3 and Sam

All present enzymatic activity of NSD1 Set Domain in Complex with BT3 and Sam:
2.1.1.43;

Protein crystallography data

The structure of NSD1 Set Domain in Complex with BT3 and Sam, PDB code: 6kqq was solved by H.J.Cho, T.Cierpicki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.35 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 40.469, 60.811, 64.255, 101.18, 107.76, 93.59
R / Rfree (%) 16.3 / 20.1

Other elements in 6kqq:

The structure of NSD1 Set Domain in Complex with BT3 and Sam also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the NSD1 Set Domain in Complex with BT3 and Sam (pdb code 6kqq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the NSD1 Set Domain in Complex with BT3 and Sam, PDB code: 6kqq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6kqq

Go back to Zinc Binding Sites List in 6kqq
Zinc binding site 1 out of 6 in the NSD1 Set Domain in Complex with BT3 and Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of NSD1 Set Domain in Complex with BT3 and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2104

b:20.5
occ:1.00
 SG A:CYS2072 2.3 24.0 1.0
SG A:CYS2070 2.3 18.8 1.0
SG A:CYS2077 2.4 21.5 1.0
SG A:CYS2023 2.4 20.2 1.0
CB A:CYS2077 3.3 23.4 1.0
CB A:CYS2072 3.4 21.2 1.0
CB A:CYS2070 3.4 18.1 1.0
CB A:CYS2023 3.4 19.6 1.0
CA A:CYS2077 3.7 28.7 1.0
N A:CYS2023 4.0 16.1 1.0
O A:HOH2317 4.1 27.6 1.0
N A:CYS2072 4.1 20.6 1.0
N A:SER2078 4.3 22.7 1.0
CE1 A:HIS2021 4.3 11.4 1.0
CA A:CYS2072 4.3 24.0 1.0
CA A:CYS2023 4.3 18.1 1.0
C A:CYS2077 4.4 29.5 1.0
ND1 A:HIS2021 4.5 15.8 1.0
N A:GLY2073 4.6 29.9 1.0
CA A:CYS2070 4.6 18.6 1.0
N A:GLY2079 4.7 18.6 1.0
C A:CYS2070 4.7 22.6 1.0
O A:CYS2070 4.8 19.2 1.0
C A:CYS2072 4.8 32.8 1.0
N A:CYS2077 5.0 26.5 1.0
C A:CYS2022 5.0 17.5 1.0

Zinc binding site 2 out of 6 in 6kqq

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Zinc binding site 2 out of 6 in the NSD1 Set Domain in Complex with BT3 and Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of NSD1 Set Domain in Complex with BT3 and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2105

b:19.6
occ:1.00
 SG A:CYS1931 2.3 19.5 1.0
SG A:CYS1920 2.3 18.9 1.0
SG A:CYS1905 2.4 19.9 1.0
SG A:CYS1925 2.4 21.4 1.0
CB A:CYS1920 3.1 20.4 1.0
CB A:CYS1905 3.2 22.1 1.0
CB A:CYS1931 3.3 21.3 1.0
CB A:CYS1925 3.4 21.5 1.0
ZN A:ZN2106 3.8 22.0 1.0
CA A:CYS1931 4.2 23.3 1.0
CB A:ASN1933 4.2 19.9 1.0
SG A:CYS1895 4.2 22.3 1.0
CA A:CYS1920 4.5 20.6 1.0
CB A:ALA1927 4.6 22.8 1.0
CA A:CYS1905 4.7 23.1 1.0
N A:ASN1933 4.7 17.9 1.0
CA A:CYS1925 4.8 25.4 1.0
SG A:CYS1911 4.9 22.6 1.0
C A:CYS1931 4.9 21.2 1.0
NE2 A:GLN1934 4.9 27.1 1.0
CA A:ASN1933 5.0 21.2 1.0
N A:GLN1932 5.0 19.3 1.0

Zinc binding site 3 out of 6 in 6kqq

Go back to Zinc Binding Sites List in 6kqq
Zinc binding site 3 out of 6 in the NSD1 Set Domain in Complex with BT3 and Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of NSD1 Set Domain in Complex with BT3 and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2106

b:22.0
occ:1.00
 SG A:CYS1895 2.2 22.3 1.0
SG A:CYS1911 2.4 22.6 1.0
SG A:CYS1905 2.4 19.9 1.0
SG A:CYS1897 2.4 23.0 1.0
CB A:CYS1911 3.1 23.8 1.0
CB A:CYS1895 3.2 27.2 1.0
CB A:CYS1905 3.2 22.1 1.0
CB A:CYS1897 3.3 22.0 1.0
CA A:CYS1905 3.6 23.1 1.0
ZN A:ZN2105 3.8 19.6 1.0
CA A:CYS1911 3.9 25.6 1.0
N A:CYS1905 4.1 23.0 1.0
N A:CYS1897 4.2 23.3 1.0
SG A:CYS1920 4.2 18.9 1.0
CA A:CYS1897 4.3 21.7 1.0
CA A:CYS1895 4.6 26.5 1.0
SG A:CYS1925 4.7 21.4 1.0
C A:CYS1911 4.8 23.6 1.0
O A:HOH2408 4.8 32.3 1.0
N A:ASN1896 4.9 26.2 1.0
C A:CYS1895 4.9 26.0 1.0
C A:CYS1905 4.9 24.4 1.0
N A:CYS1911 5.0 27.4 1.0
N A:ILE1912 5.0 22.8 1.0
O A:HOH2355 5.0 27.6 1.0

Zinc binding site 4 out of 6 in 6kqq

Go back to Zinc Binding Sites List in 6kqq
Zinc binding site 4 out of 6 in the NSD1 Set Domain in Complex with BT3 and Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of NSD1 Set Domain in Complex with BT3 and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2104

b:11.5
occ:1.00
 SG B:CYS1925 2.3 11.4 1.0
SG B:CYS1920 2.3 12.6 1.0
SG B:CYS1931 2.3 10.8 1.0
SG B:CYS1905 2.3 11.2 1.0
CB B:CYS1920 3.1 13.7 1.0
CB B:CYS1905 3.2 12.5 1.0
CB B:CYS1931 3.3 12.3 1.0
CB B:CYS1925 3.3 12.1 1.0
ZN B:ZN2105 3.9 11.7 1.0
CA B:CYS1931 4.2 12.6 1.0
SG B:CYS1895 4.3 12.7 1.0
CB B:ASN1933 4.3 10.1 1.0
CA B:CYS1920 4.6 11.8 1.0
CA B:CYS1925 4.7 10.6 1.0
CA B:CYS1905 4.7 13.3 1.0
CB B:ALA1927 4.8 13.0 1.0
N B:ASN1933 4.8 12.5 1.0
C B:CYS1931 4.9 13.0 1.0
OE1 B:GLN1934 5.0 20.5 1.0
N B:GLN1932 5.0 10.1 1.0

Zinc binding site 5 out of 6 in 6kqq

Go back to Zinc Binding Sites List in 6kqq
Zinc binding site 5 out of 6 in the NSD1 Set Domain in Complex with BT3 and Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of NSD1 Set Domain in Complex with BT3 and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2105

b:11.7
occ:1.00
 SG B:CYS1895 2.3 12.7 1.0
SG B:CYS1911 2.3 11.5 1.0
SG B:CYS1905 2.4 11.2 1.0
SG B:CYS1897 2.4 16.4 1.0
CB B:CYS1895 3.1 11.3 1.0
CB B:CYS1897 3.2 12.2 1.0
CB B:CYS1905 3.3 12.5 1.0
CB B:CYS1911 3.3 11.6 1.0
CA B:CYS1905 3.6 13.3 1.0
N B:CYS1905 3.8 12.7 1.0
ZN B:ZN2104 3.9 11.5 1.0
N B:CYS1897 4.2 12.8 1.0
CA B:CYS1911 4.3 10.6 1.0
CA B:CYS1897 4.3 12.6 1.0
O B:HOH2372 4.4 20.3 1.0
SG B:CYS1920 4.5 12.6 1.0
CA B:CYS1895 4.6 10.0 1.0
SG B:CYS1925 4.6 11.4 1.0
OD1 B:ASN1913 4.8 12.7 1.0
C B:PRO1904 4.9 14.3 1.0
C B:CYS1911 5.0 10.0 1.0

Zinc binding site 6 out of 6 in 6kqq

Go back to Zinc Binding Sites List in 6kqq
Zinc binding site 6 out of 6 in the NSD1 Set Domain in Complex with BT3 and Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of NSD1 Set Domain in Complex with BT3 and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2106

b:33.1
occ:1.00
 SG B:CYS2070 2.2 30.6 1.0
SG B:CYS2072 2.3 32.7 1.0
SG B:CYS2023 2.4 32.1 1.0
SG B:CYS2077 2.4 35.3 1.0
CB B:CYS2077 3.3 35.6 1.0
CB B:CYS2072 3.3 29.8 1.0
CB B:CYS2070 3.4 33.2 1.0
CB B:CYS2023 3.5 28.6 1.0
CA B:CYS2077 3.7 43.9 1.0
N B:CYS2023 4.0 27.3 1.0
N B:CYS2072 4.1 32.1 1.0
O B:HOH2227 4.1 39.0 1.0
CE1 B:HIS2021 4.2 22.0 1.0
N B:SER2078 4.2 45.3 1.0
CA B:CYS2072 4.2 31.6 1.0
C B:CYS2077 4.3 41.4 1.0
CA B:CYS2023 4.4 25.2 1.0
ND1 B:HIS2021 4.5 24.1 1.0
N B:GLY2073 4.5 40.5 1.0
O B:CYS2070 4.7 36.0 1.0
N B:GLY2079 4.7 38.6 1.0
CA B:CYS2070 4.7 29.4 1.0
C B:CYS2070 4.7 33.9 1.0
C B:CYS2072 4.7 40.7 1.0
N B:ALA2074 5.0 45.9 1.0
C B:CYS2022 5.0 24.9 1.0
N B:CYS2077 5.0 44.0 1.0

Reference:

H.Huang, C.A.Howard, S.Zari, H.J.Cho, S.Shukla, H.Li, J.Ndoj, P.Gonzalez-Alonso, C.Nikolaidis, J.Abbott, D.S.Rogawski, M.A.Potopnyk, K.Kempinska, H.Miao, T.Purohit, A.Henderson, A.Mapp, M.L.Sulis, A.Ferrando, J.Grembecka, T.Cierpicki. Covalent Inhibition of NSD1 Histone Methyltransferase. Nat.Chem.Biol. V. 16 1403 2020.
ISSN: ESSN 1552-4469
PubMed: 32868895
DOI: 10.1038/S41589-020-0626-6
Page generated: Tue Oct 29 02:01:54 2024

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