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

Go back to Zinc Binding Sites List in 8fbg
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

Go back to Zinc Binding Sites List in 8fbg
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

Go back to Zinc Binding Sites List in 8fbg
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

Go back to Zinc Binding Sites List in 8fbg
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

Go back to Zinc Binding Sites List in 8fbg
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

Go back to Zinc Binding Sites List in 8fbg
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

Go back to Zinc Binding Sites List in 8fbg
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy