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

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

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

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

Zinc

(Zn)

7 atoms

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

Calcium binding site 1 out of 4 in the Crystal Structure of NSD1 Mutant-Y1869C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of NSD1 Mutant-Y1869C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3004 b:14.4 occ:1.00 SG A:CYS1793 2.1 23.9 1.0 CA A:CA3006 2.3 31.9 1.0 SG A:CYS1818 2.4 27.8 1.0 SG A:CYS1823 2.6 25.9 1.0 ZN A:ZN3003 3.2 28.4 1.0 CB A:CYS1818 3.2 24.2 1.0 CB A:CYS1823 3.4 22.2 1.0 CB A:CYS1793 3.4 20.9 1.0 ZN A:ZN3002 3.6 29.0 1.0 CA A:CYS1823 4.0 22.5 1.0 OD1 A:ASN1811 4.0 24.7 1.0 SG A:CYS1803 4.1 24.7 1.0 N A:CYS1793 4.1 23.6 1.0 CD A:PRO1824 4.2 25.6 1.0 CA A:CYS1818 4.3 24.2 1.0 CA A:CYS1793 4.3 21.8 1.0 CG A:ASN1811 4.3 27.7 1.0 SG A:CYS1809 4.5 23.1 1.0 C A:CYS1793 4.8 27.0 1.0 ND2 A:ASN1811 4.8 18.0 1.0 C A:CYS1823 4.8 27.9 1.0 CB A:ASN1811 4.9 17.8 1.0 N A:PRO1824 4.9 24.5 1.0 O A:CYS1793 4.9 27.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of NSD1 Mutant-Y1869C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of NSD1 Mutant-Y1869C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3006 b:31.9 occ:1.00 CA A:CA3004 2.3 14.4 1.0 OD1 A:ASN1811 3.7 24.7 1.0 CB A:CYS1818 3.7 24.2 1.0 CD A:ARG1792 3.8 31.1 1.0 N A:CYS1793 3.8 23.6 1.0 SG A:CYS1793 3.8 23.9 1.0 CA A:CYS1823 3.8 22.5 1.0 SG A:CYS1818 3.8 27.8 1.0 CB A:CYS1823 3.9 22.2 1.0 ND2 A:ASN1811 4.0 18.0 1.0 CG A:ASN1811 4.1 27.7 1.0 CA A:CYS1818 4.1 24.2 1.0 SG A:CYS1823 4.1 25.9 1.0 CA A:ARG1792 4.2 22.8 1.0 N A:HIS1819 4.2 29.7 1.0 O A:PRO1791 4.2 25.1 1.0 N A:CYS1823 4.3 22.9 1.0 CD A:PRO1824 4.5 25.6 1.0 C A:ARG1792 4.5 27.3 1.0 CB A:CYS1793 4.6 20.9 1.0 NE A:ARG1792 4.6 33.0 1.0 CG A:ARG1792 4.6 32.0 1.0 CG2 A:VAL1822 4.7 30.6 1.0 C A:CYS1818 4.7 30.4 1.0 CA A:CYS1793 4.7 21.8 1.0 C A:VAL1822 4.7 27.4 1.0 O A:VAL1822 4.7 26.0 1.0 O A:HIS1819 4.7 38.8 1.0 CB A:ARG1792 4.9 22.2 1.0 O A:CYS1793 5.0 27.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of NSD1 Mutant-Y1869C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of NSD1 Mutant-Y1869C within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3006 b:63.5 occ:1.00 CE B:SAM3005 4.0 18.9 1.0 O B:ALA1914 4.0 13.8 1.0 CD1 B:LEU1897 4.2 29.0 1.0 CA B:ARG1915 4.4 12.0 1.0 CZ B:PHE1954 4.4 14.9 1.0 CE1 B:PHE1954 4.6 15.9 1.0 C B:ALA1914 4.7 14.2 1.0 O B:TYR1895 4.7 17.0 1.0 N B:ARG1915 4.8 12.9 1.0 SG B:CYS1869 4.8 22.7 1.0 CA B:TYR1895 4.9 16.9 1.0 C B:TYR1895 4.9 19.5 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of NSD1 Mutant-Y1869C within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3007 b:34.3 occ:1.00 ZN B:ZN3004 2.4 35.2 1.0 N B:HIS1819 3.3 27.4 1.0 CB B:CYS1818 3.7 19.5 1.0 O B:PRO1791 3.8 34.8 1.0 CA B:CYS1823 3.8 29.1 1.0 CB B:CYS1823 3.9 28.6 1.0 CA B:CYS1818 3.9 19.6 1.0 N B:CYS1793 3.9 23.4 1.0 CB B:HIS1819 3.9 31.2 1.0 SG B:CYS1818 4.0 22.9 1.0 CA B:ARG1792 4.0 28.4 1.0 OD1 B:ASN1811 4.0 33.8 1.0 ND2 B:ASN1811 4.1 17.4 1.0 C B:CYS1818 4.1 25.7 1.0 CG B:ARG1792 4.1 39.7 1.0 SG B:CYS1793 4.1 24.6 1.0 SG B:CYS1823 4.2 32.0 1.0 CG B:ASN1811 4.2 29.8 1.0 CA B:HIS1819 4.2 29.5 1.0 N B:CYS1823 4.3 29.8 1.0 C B:ARG1792 4.5 28.8 1.0 CD B:PRO1824 4.5 36.2 1.0 CB B:ARG1792 4.6 29.0 1.0 CB B:CYS1793 4.7 21.9 1.0 C B:PRO1791 4.8 34.3 1.0 C B:VAL1822 4.8 34.4 1.0 O B:HIS1819 4.9 34.0 1.0 CA B:CYS1793 4.9 22.6 1.0 O B:VAL1822 4.9 33.7 1.0 N B:ARG1792 4.9 29.7 1.0

K.Providokhina, A.Dong, C.H.Arrowsmith, A.M.Edwards, J.Min, Structural Genomics Consortium (Sgc). Crystal Structure of NSD1 To Be Published.