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Zinc in PDB 3ooi: Crystal Structure of Human Histone-Lysine N-Methyltransferase NSD1 Set Domain in Complex with S-Adenosyl-L-Methionine

Enzymatic activity of Crystal Structure of Human Histone-Lysine N-Methyltransferase NSD1 Set Domain in Complex with S-Adenosyl-L-Methionine

All present enzymatic activity of Crystal Structure of Human Histone-Lysine N-Methyltransferase NSD1 Set Domain in Complex with S-Adenosyl-L-Methionine:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of Human Histone-Lysine N-Methyltransferase NSD1 Set Domain in Complex with S-Adenosyl-L-Methionine, PDB code: 3ooi was solved by Q.Qiao, M.Wang, R.M.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.61 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.875, 67.751, 69.086, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 18.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Histone-Lysine N-Methyltransferase NSD1 Set Domain in Complex with S-Adenosyl-L-Methionine (pdb code 3ooi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Human Histone-Lysine N-Methyltransferase NSD1 Set Domain in Complex with S-Adenosyl-L-Methionine, PDB code: 3ooi:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3ooi

Go back to Zinc Binding Sites List in 3ooi
Zinc binding site 1 out of 3 in the Crystal Structure of Human Histone-Lysine N-Methyltransferase NSD1 Set Domain in Complex with S-Adenosyl-L-Methionine


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 Human Histone-Lysine N-Methyltransferase NSD1 Set Domain in Complex with S-Adenosyl-L-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn232

b:20.8
occ:1.00
 SG A:CYS219 2.3 19.2 1.0
SG A:CYS221 2.3 21.4 1.0
SG A:CYS226 2.4 22.7 1.0
SG A:CYS172 2.4 21.9 1.0
CB A:CYS226 3.3 25.9 1.0
CB A:CYS219 3.3 19.8 1.0
CB A:CYS221 3.4 22.5 1.0
CB A:CYS172 3.4 20.9 1.0
CA A:CYS226 3.8 25.7 1.0
N A:CYS172 4.0 19.8 1.0
N A:CYS221 4.1 22.6 1.0
CA A:CYS221 4.2 22.9 1.0
NE2 A:HIS170 4.2 14.4 1.0
N A:SER227 4.3 24.3 1.0
O A:HOH286 4.3 21.5 1.0
CA A:CYS172 4.3 21.2 1.0
CD2 A:HIS170 4.4 14.9 1.0
C A:CYS226 4.5 25.6 1.0
O A:PHE229 4.6 18.3 1.0
CA A:CYS219 4.6 20.3 1.0
N A:GLY228 4.7 22.7 1.0
C A:CYS219 4.7 21.6 1.0
N A:GLY222 4.8 25.8 1.0
C A:CYS221 4.8 24.9 1.0
OG A:SER227 4.9 23.1 1.0
O A:CYS219 4.9 22.6 1.0
C A:CYS171 5.0 18.5 1.0
N A:CYS226 5.0 27.9 1.0

Zinc binding site 2 out of 3 in 3ooi

Go back to Zinc Binding Sites List in 3ooi
Zinc binding site 2 out of 3 in the Crystal Structure of Human Histone-Lysine N-Methyltransferase NSD1 Set Domain in Complex with S-Adenosyl-L-Methionine


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 Human Histone-Lysine N-Methyltransferase NSD1 Set Domain in Complex with S-Adenosyl-L-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn233

b:17.6
occ:1.00
 SG A:CYS44 2.3 17.2 1.0
SG A:CYS60 2.3 17.7 1.0
SG A:CYS54 2.4 17.5 1.0
SG A:CYS46 2.4 18.5 1.0
CB A:CYS46 3.1 18.3 1.0
CB A:CYS44 3.2 16.2 1.0
CB A:CYS60 3.2 17.3 1.0
CB A:CYS54 3.2 16.6 1.0
CA A:CYS54 3.5 17.6 1.0
ZN A:ZN234 3.9 17.2 1.0
N A:CYS54 3.9 17.9 1.0
CA A:CYS60 3.9 17.6 1.0
N A:CYS46 4.0 18.0 1.0
CA A:CYS46 4.2 18.6 1.0
SG A:CYS69 4.4 17.5 1.0
CA A:CYS44 4.6 16.0 1.0
N A:ASN45 4.7 16.4 1.0
SG A:CYS74 4.8 17.7 1.0
C A:CYS60 4.8 17.0 1.0
C A:CYS44 4.9 16.7 1.0
C A:PRO53 4.9 19.7 1.0
OD1 A:ASN45 4.9 20.3 1.0
O A:HOH244 4.9 12.5 1.0
C A:CYS54 5.0 17.7 1.0
N A:CYS60 5.0 18.5 1.0

Zinc binding site 3 out of 3 in 3ooi

Go back to Zinc Binding Sites List in 3ooi
Zinc binding site 3 out of 3 in the Crystal Structure of Human Histone-Lysine N-Methyltransferase NSD1 Set Domain in Complex with S-Adenosyl-L-Methionine


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 Human Histone-Lysine N-Methyltransferase NSD1 Set Domain in Complex with S-Adenosyl-L-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn234

b:17.2
occ:1.00
 SG A:CYS74 2.3 17.7 1.0
SG A:CYS69 2.4 17.5 1.0
SG A:CYS80 2.4 16.5 1.0
SG A:CYS54 2.4 17.5 1.0
CB A:CYS69 3.1 17.4 1.0
CB A:CYS80 3.3 18.0 1.0
CB A:CYS54 3.3 16.6 1.0
CB A:CYS74 3.4 17.8 1.0
ZN A:ZN233 3.9 17.6 1.0
O A:HOH244 3.9 12.5 1.0
CA A:CYS80 4.1 18.2 1.0
SG A:CYS44 4.2 17.2 1.0
CB A:ASN82 4.3 15.5 1.0
CA A:CYS69 4.6 17.2 1.0
CA A:CYS74 4.6 17.8 1.0
CA A:CYS54 4.8 17.6 1.0
CB A:ALA76 4.8 19.6 1.0
N A:ASN82 4.8 16.5 1.0
C A:CYS80 4.9 18.6 1.0
N A:GLN81 4.9 17.9 1.0

Reference:

Q.Qiao, Y.Li, Z.Chen, M.Wang, D.Reinberg, R.M.Xu. The Structure of NSD1 Reveals An Autoregulatory Mechanism Underlying Histone H3K36 Methylation J.Biol.Chem. V. 286 8361 2010.
ISSN: ISSN 0021-9258
PubMed: 21196496
DOI: 10.1074/JBC.M110.204115
Page generated: Sat Oct 26 11:03:06 2024

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