Zinc in PDB 8fbg: Crystal Structure of NSD1 Mutant-Y1869C

Enzymatic activity of Crystal Structure of NSD1 Mutant-Y1869C

All present enzymatic activity of Crystal Structure of NSD1 Mutant-Y1869C:
2.1.1.357;

Protein crystallography data

The structure of Crystal Structure of NSD1 Mutant-Y1869C, PDB code: 8fbg was solved by K.Providokhina, A.Dong, C.H.Arrowsmith, A.M.Edwards, J.Min, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.09 / 2.29
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.449, 64.947, 81.408, 90, 93.17, 90
R / Rfree (%) 21.4 / 27.1

Other elements in 8fbg:

The structure of Crystal Structure of NSD1 Mutant-Y1869C also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of NSD1 Mutant-Y1869C (pdb code 8fbg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of NSD1 Mutant-Y1869C, PDB code: 8fbg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 8fbg

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Zinc binding site 1 out of 7 in the Crystal Structure of NSD1 Mutant-Y1869C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of NSD1 Mutant-Y1869C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3001

b:33.4
occ:1.00
 SG A:CYS1968 2.3 29.5 1.0
SG A:CYS1970 2.3 24.4 1.0
SG A:CYS1975 2.3 31.9 1.0
SG A:CYS1921 2.5 23.6 1.0
CB A:CYS1975 3.3 27.9 1.0
CB A:CYS1921 3.5 20.0 1.0
CB A:CYS1970 3.5 21.5 1.0
CB A:CYS1968 3.5 26.5 1.0
CA A:CYS1975 3.8 27.1 1.0
N A:CYS1921 3.9 22.3 1.0
N A:CYS1970 4.1 23.6 1.0
O A:HOH3136 4.1 23.1 1.0
CA A:CYS1921 4.3 20.8 1.0
CA A:CYS1970 4.3 22.6 1.0
N A:SER1976 4.5 27.3 1.0
NE2 A:HIS1919 4.5 26.8 1.0
C A:CYS1975 4.6 29.2 1.0
CD2 A:HIS1919 4.7 27.1 1.0
C A:CYS1968 4.7 32.6 1.0
CA A:CYS1968 4.7 27.6 1.0
O A:CYS1968 4.8 34.4 1.0
N A:GLY1971 4.8 29.7 1.0
N A:GLY1977 4.8 31.5 1.0
C A:CYS1920 4.9 26.7 1.0
O A:PHE1978 4.9 39.8 1.0
C A:CYS1970 4.9 31.5 1.0

Zinc binding site 2 out of 7 in 8fbg

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Zinc binding site 2 out of 7 in the Crystal Structure of NSD1 Mutant-Y1869C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of NSD1 Mutant-Y1869C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3002

b:29.0
occ:1.00
 SG A:CYS1809 2.3 23.1 1.0
SG A:CYS1803 2.4 24.7 1.0
SG A:CYS1793 2.5 23.9 1.0
SG A:CYS1795 2.5 29.4 1.0
CB A:CYS1793 3.1 20.9 1.0
CB A:CYS1809 3.1 20.5 1.0
CB A:CYS1803 3.2 21.2 1.0
CB A:CYS1795 3.2 26.2 1.0
CA A:CA3004 3.6 14.4 1.0
CA A:CYS1803 3.6 21.5 1.0
CA A:CYS1809 3.8 21.6 1.0
ZN A:ZN3003 3.9 28.4 1.0
SG A:CYS1818 4.0 27.8 1.0
N A:CYS1803 4.1 21.7 1.0
N A:CYS1795 4.2 26.6 1.0
CA A:CYS1795 4.3 26.8 1.0
SG A:CYS1823 4.4 25.9 1.0
CA A:CYS1793 4.5 21.8 1.0
C A:CYS1809 4.8 24.6 1.0
N A:CYS1809 4.8 24.0 1.0
N A:ASN1794 4.9 25.2 1.0
C A:CYS1803 4.9 28.0 1.0
C A:CYS1793 5.0 27.0 1.0

Zinc binding site 3 out of 7 in 8fbg

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Zinc binding site 3 out of 7 in the Crystal Structure of NSD1 Mutant-Y1869C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of NSD1 Mutant-Y1869C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3003

b:28.4
occ:1.00
 SG A:CYS1829 2.3 28.4 1.0
SG A:CYS1823 2.3 25.9 1.0
SG A:CYS1803 2.4 24.7 1.0
SG A:CYS1818 2.7 27.8 1.0
CB A:CYS1818 3.2 24.2 1.0
CB A:CYS1829 3.2 24.6 1.0
CA A:CA3004 3.2 14.4 1.0
CB A:CYS1803 3.2 21.2 1.0
CB A:CYS1823 3.5 22.2 1.0
ZN A:ZN3002 3.9 29.0 1.0
CA A:CYS1829 3.9 24.5 1.0
CB A:ALA1825 4.3 24.8 1.0
SG A:CYS1793 4.3 23.9 1.0
CB A:ASN1831 4.3 16.9 1.0
N A:GLN1830 4.6 24.8 1.0
C A:CYS1829 4.6 27.9 1.0
N A:ASN1831 4.6 18.8 1.0
CA A:CYS1818 4.7 24.2 1.0
CA A:CYS1803 4.7 21.5 1.0
CA A:CYS1823 4.8 22.5 1.0
NE2 A:GLN1832 4.9 27.4 1.0
SG A:CYS1809 4.9 23.1 1.0
CA A:ASN1831 5.0 18.8 1.0

Zinc binding site 4 out of 7 in 8fbg

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Zinc binding site 4 out of 7 in the Crystal Structure of NSD1 Mutant-Y1869C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of NSD1 Mutant-Y1869C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3001

b:21.2
occ:1.00
 SG B:CYS1968 2.3 18.9 1.0
SG B:CYS1975 2.3 20.2 1.0
SG B:CYS1921 2.4 20.4 1.0
SG B:CYS1970 2.4 19.6 1.0
CB B:CYS1975 3.2 17.5 1.0
CB B:CYS1921 3.3 16.4 1.0
CB B:CYS1968 3.4 15.5 1.0
CB B:CYS1970 3.6 16.2 1.0
CA B:CYS1975 3.6 18.5 1.0
N B:CYS1921 3.9 17.1 1.0
N B:CYS1970 4.2 17.2 1.0
CA B:CYS1921 4.2 17.0 1.0
NE2 B:HIS1919 4.2 14.6 1.0
N B:SER1976 4.4 20.0 1.0
C B:CYS1975 4.4 22.4 1.0
CA B:CYS1970 4.4 16.4 1.0
CD2 B:HIS1919 4.5 14.8 1.0
N B:GLY1977 4.6 21.8 1.0
CA B:CYS1968 4.6 17.0 1.0
C B:CYS1968 4.6 17.8 1.0
O B:PHE1978 4.7 27.2 1.0
N B:CYS1975 4.8 20.0 1.0
O B:CYS1968 4.8 16.4 1.0
C B:CYS1920 4.9 20.8 1.0
N B:LYS1969 5.0 15.6 1.0

Zinc binding site 5 out of 7 in 8fbg

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Zinc binding site 5 out of 7 in the Crystal Structure of NSD1 Mutant-Y1869C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of NSD1 Mutant-Y1869C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3002

b:29.9
occ:1.00
 SG B:CYS1809 2.3 27.2 1.0
SG B:CYS1793 2.4 24.6 1.0
SG B:CYS1803 2.5 20.0 1.0
SG B:CYS1795 2.6 30.6 1.0
CB B:CYS1793 3.0 21.9 1.0
CB B:CYS1795 3.2 26.8 1.0
CB B:CYS1809 3.2 24.1 1.0
CB B:CYS1803 3.3 16.0 1.0
ZN B:ZN3004 3.6 35.2 1.0
CA B:CYS1803 3.8 15.2 1.0
ZN B:ZN3003 3.8 25.3 1.0
CA B:CYS1809 3.9 25.2 1.0
SG B:CYS1818 3.9 22.9 1.0
N B:CYS1803 4.3 14.6 1.0
N B:CYS1795 4.3 28.3 1.0
CA B:CYS1795 4.3 27.2 1.0
CA B:CYS1793 4.5 22.6 1.0
SG B:CYS1823 4.5 32.0 1.0
C B:CYS1809 4.8 26.9 1.0
C B:CYS1793 4.9 28.9 1.0
O B:HOH3154 4.9 48.6 1.0
N B:CYS1809 5.0 27.6 1.0

Zinc binding site 6 out of 7 in 8fbg

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Zinc binding site 6 out of 7 in the Crystal Structure of NSD1 Mutant-Y1869C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of NSD1 Mutant-Y1869C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3003

b:25.3
occ:1.00
 SG B:CYS1829 2.2 22.4 1.0
SG B:CYS1803 2.2 20.0 1.0
SG B:CYS1823 2.3 32.0 1.0
SG B:CYS1818 2.5 22.9 1.0
CB B:CYS1829 3.0 19.0 1.0
CB B:CYS1803 3.1 16.0 1.0
ZN B:ZN3004 3.1 35.2 1.0
CB B:CYS1818 3.2 19.5 1.0
CB B:CYS1823 3.6 28.6 1.0
ZN B:ZN3002 3.8 29.9 1.0
CA B:CYS1829 3.9 19.3 1.0
CB B:ALA1825 4.2 28.5 1.0
SG B:CYS1793 4.3 24.6 1.0
CB B:ASN1831 4.4 17.3 1.0
CA B:CYS1803 4.6 15.2 1.0
C B:CYS1829 4.6 23.9 1.0
CA B:CYS1818 4.7 19.6 1.0
N B:GLN1830 4.7 20.2 1.0
N B:ASN1831 4.7 20.1 1.0
NE2 B:GLN1832 4.7 51.4 1.0
SG B:CYS1809 4.9 27.2 1.0
CA B:CYS1823 4.9 29.1 1.0

Zinc binding site 7 out of 7 in 8fbg

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Zinc binding site 7 out of 7 in the Crystal Structure of NSD1 Mutant-Y1869C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of NSD1 Mutant-Y1869C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3004

b:35.2
occ:1.00
 SG B:CYS1793 2.3 24.6 1.0
SG B:CYS1818 2.4 22.9 1.0
CA B:CA3007 2.4 34.3 1.0
SG B:CYS1823 2.6 32.0 1.0
ZN B:ZN3003 3.1 25.3 1.0
CB B:CYS1818 3.2 19.5 1.0
CB B:CYS1823 3.4 28.6 1.0
CB B:CYS1793 3.5 21.9 1.0
ZN B:ZN3002 3.6 29.9 1.0
CA B:CYS1823 4.0 29.1 1.0
OD1 B:ASN1811 4.0 33.8 1.0
N B:CYS1793 4.1 23.4 1.0
CA B:CYS1818 4.1 19.6 1.0
SG B:CYS1803 4.1 20.0 1.0
CD B:PRO1824 4.1 36.2 1.0
CA B:CYS1793 4.3 22.6 1.0
CG B:ASN1811 4.4 29.8 1.0
SG B:CYS1809 4.6 27.2 1.0
N B:HIS1819 4.7 27.4 1.0
ND2 B:ASN1811 4.8 17.4 1.0
N B:PRO1824 4.8 34.2 1.0
C B:CYS1823 4.8 35.5 1.0
O B:CYS1793 4.9 28.4 1.0
CB B:ASN1811 4.9 20.4 1.0
C B:CYS1793 4.9 28.9 1.0
C B:CYS1818 4.9 25.7 1.0

Reference:

K.Providokhina, A.Dong, C.H.Arrowsmith, A.M.Edwards, J.Min, Structural Genomics Consortium (Sgc). Crystal Structure of NSD1 To Be Published.
Page generated: Wed Oct 30 20:16:35 2024

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