Zinc in PDB 2pv0: Dna Methyltransferase 3 Like Protein (DNMT3L)

The structure of Dna Methyltransferase 3 Like Protein (DNMT3L), PDB code: 2pv0 was solved by X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.74 / 3.30
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	267.200, 267.200, 149.500, 90.00, 90.00, 120.00
R / Rfree (%)	24.8 / 27.2

The binding sites of Zinc atom in the Dna Methyltransferase 3 Like Protein (DNMT3L) (pdb code 2pv0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Dna Methyltransferase 3 Like Protein (DNMT3L), PDB code: 2pv0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Dna Methyltransferase 3 Like Protein (DNMT3L)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dna Methyltransferase 3 Like Protein (DNMT3L) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:48.3 occ:0.41 SG A:CYS121 2.2 79.5 1.0 SG A:CYS118 2.2 86.4 1.0 SG A:CYS99 2.3 78.4 1.0 SG A:CYS96 2.3 95.7 1.0 CB A:CYS118 2.7 71.6 1.0 CB A:CYS121 3.1 89.7 1.0 CB A:CYS99 3.3 83.0 1.0 CB A:CYS96 3.3 85.7 1.0 N A:CYS99 3.6 97.1 1.0 CA A:CYS118 3.9 0.3 1.0 N A:CYS118 4.0 0.1 1.0 CA A:CYS99 4.0 96.9 1.0 OG A:SER101 4.2 0.4 1.0 CA A:CYS121 4.3 94.8 1.0 N A:CYS100 4.4 0.3 1.0 CB A:SER101 4.4 0.5 1.0 N A:CYS121 4.5 92.3 1.0 CB A:ILE98 4.5 85.1 1.0 N A:SER101 4.5 0.3 1.0 C A:CYS99 4.6 98.7 1.0 C A:ILE98 4.6 96.1 1.0 CA A:CYS96 4.7 84.1 1.0 NH2 A:ARG35 4.8 0.9 1.0 N A:ILE98 4.8 84.7 1.0 CA A:ILE98 4.9 90.1 1.0

Zinc binding site 2 out of 9 in the Dna Methyltransferase 3 Like Protein (DNMT3L)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dna Methyltransferase 3 Like Protein (DNMT3L) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:75.5 occ:0.92 SG A:CYS142 2.3 83.7 1.0 SG A:CYS113 2.3 72.8 1.0 SG A:CYS145 2.3 84.7 1.0 SG A:CYS108 2.3 73.5 1.0 CB A:CYS113 3.1 75.9 1.0 CB A:CYS142 3.1 79.6 1.0 CB A:CYS108 3.3 84.4 1.0 CB A:CYS145 3.3 82.9 1.0 N A:CYS142 3.8 81.5 1.0 CA A:CYS142 4.0 78.3 1.0 N A:CYS145 4.2 85.2 1.0 CA A:CYS145 4.3 88.5 1.0 CA A:CYS113 4.5 87.1 1.0 CB A:ASN110 4.6 0.1 1.0 C A:CYS142 4.6 80.0 1.0 CA A:CYS108 4.7 86.4 1.0 O A:CYS142 4.7 81.3 1.0 C A:VAL141 4.8 92.5 1.0 CB A:ARG115 5.0 94.8 1.0

Zinc binding site 3 out of 9 in the Dna Methyltransferase 3 Like Protein (DNMT3L)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Dna Methyltransferase 3 Like Protein (DNMT3L) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:92.0 occ:0.85 SG A:CYS53 2.2 84.5 1.0 SG A:CYS56 2.3 0.0 1.0 SG A:CYS76 2.3 1.0 1.0 SG A:CYS73 2.3 86.6 1.0 CB A:CYS76 3.2 0.1 1.0 CB A:CYS56 3.2 0.6 1.0 CB A:CYS53 3.3 78.0 1.0 CB A:CYS73 3.3 79.8 1.0 N A:CYS56 3.5 0.7 1.0 CA A:CYS56 3.9 0.4 1.0 N A:CYS73 3.9 80.9 1.0 CB A:CYS55 4.1 0.8 1.0 CA A:CYS73 4.2 81.4 1.0 CA A:CYS76 4.3 0.8 1.0 N A:CYS76 4.3 0.8 1.0 N A:GLY57 4.5 0.2 1.0 C A:CYS55 4.6 1.0 1.0 O A:CYS53 4.6 78.7 1.0 CB A:SER58 4.6 99.0 1.0 O A:CYS73 4.6 90.4 1.0 C A:CYS56 4.7 0.6 1.0 CA A:CYS53 4.7 81.2 1.0 C A:CYS73 4.8 86.9 1.0 CA A:CYS55 4.8 0.4 1.0 N A:SER58 4.9 0.0 1.0 C A:CYS53 5.0 73.9 1.0

Zinc binding site 4 out of 9 in the Dna Methyltransferase 3 Like Protein (DNMT3L)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Dna Methyltransferase 3 Like Protein (DNMT3L) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn505 b:13.8 occ:0.41 SG B:CYS121 2.2 46.9 1.0 SG B:CYS118 2.2 55.3 1.0 SG B:CYS99 2.2 56.0 1.0 SG B:CYS96 2.2 49.0 1.0 CB B:CYS99 2.9 51.9 1.0 CB B:CYS121 2.9 40.0 1.0 CB B:CYS96 3.2 50.4 1.0 CB B:CYS118 3.3 59.6 1.0 OG B:SER101 3.5 96.0 1.0 N B:CYS99 3.8 58.0 1.0 NH1 B:ARG35 3.8 82.7 1.0 CA B:CYS99 3.9 64.5 1.0 CA B:CYS121 4.0 51.2 1.0 N B:CYS121 4.2 56.3 1.0 CA B:CYS118 4.3 68.7 1.0 N B:CYS118 4.3 77.5 1.0 NH2 B:ARG35 4.4 90.0 1.0 O B:CYS118 4.5 74.1 1.0 CB B:SER101 4.6 93.8 1.0 CZ B:ARG35 4.6 87.5 1.0 C B:CYS99 4.6 64.7 1.0 N B:CYS100 4.6 70.2 1.0 CA B:CYS96 4.7 57.0 1.0 C B:CYS118 4.7 76.8 1.0 N B:SER101 4.8 80.7 1.0 C B:ILE98 4.8 57.5 1.0 CB B:ILE98 4.9 45.1 1.0

Zinc binding site 5 out of 9 in the Dna Methyltransferase 3 Like Protein (DNMT3L)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Dna Methyltransferase 3 Like Protein (DNMT3L) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn506 b:67.3 occ:0.92 SG B:CYS113 2.3 65.4 1.0 SG B:CYS145 2.3 68.0 1.0 SG B:CYS108 2.3 71.2 1.0 SG B:CYS142 2.3 63.9 1.0 CB B:CYS142 3.1 48.3 1.0 CB B:CYS113 3.2 88.0 1.0 CB B:CYS145 3.2 57.9 1.0 CB B:CYS108 3.2 70.1 1.0 N B:CYS142 3.8 52.1 1.0 CA B:CYS142 4.0 51.8 1.0 CB B:ASN110 4.3 0.2 1.0 CA B:CYS145 4.3 66.5 1.0 CB B:ARG115 4.4 94.5 1.0 N B:CYS145 4.4 78.4 1.0 CG B:ARG115 4.6 0.0 1.0 CA B:CYS113 4.6 99.8 1.0 CA B:CYS108 4.6 77.6 1.0 C B:CYS142 4.7 47.1 1.0 C B:VAL141 4.9 69.7 1.0 CG B:ASN110 5.0 0.1 1.0

Zinc binding site 6 out of 9 in the Dna Methyltransferase 3 Like Protein (DNMT3L)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Dna Methyltransferase 3 Like Protein (DNMT3L) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:59.7 occ:0.85 SG B:CYS53 2.2 49.6 1.0 SG B:CYS76 2.3 68.5 1.0 SG B:CYS73 2.3 87.8 1.0 SG B:CYS56 2.3 98.2 1.0 CB B:CYS76 3.1 94.8 1.0 CB B:CYS73 3.2 82.8 1.0 CB B:CYS56 3.2 79.4 1.0 CB B:CYS53 3.3 34.4 1.0 N B:CYS56 3.5 83.7 1.0 N B:CYS73 3.8 75.7 1.0 CA B:CYS56 3.9 79.1 1.0 CB B:CYS55 4.0 79.4 1.0 CA B:CYS73 4.0 81.8 1.0 CA B:CYS76 4.3 90.8 1.0 N B:CYS76 4.4 90.8 1.0 O B:CYS53 4.5 54.9 1.0 O B:CYS73 4.6 72.9 1.0 C B:CYS55 4.6 74.0 1.0 C B:CYS73 4.7 80.0 1.0 CA B:CYS53 4.7 47.0 1.0 C B:CYS56 4.8 74.9 1.0 N B:GLY57 4.8 73.5 1.0 CA B:CYS55 4.8 69.7 1.0 CB B:SER58 4.9 64.7 1.0 C B:ILE72 4.9 60.1 1.0 C B:CYS53 5.0 44.6 1.0

Zinc binding site 7 out of 9 in the Dna Methyltransferase 3 Like Protein (DNMT3L)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Dna Methyltransferase 3 Like Protein (DNMT3L) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn508 b:0.2 occ:0.41 SG C:CYS96 2.3 0.2 1.0 SG C:CYS118 2.3 0.7 1.0 SG C:CYS121 2.3 0.2 1.0 SG C:CYS99 2.3 0.8 1.0 CB C:CYS96 3.0 0.6 1.0 CB C:CYS118 3.1 0.4 1.0 CB C:CYS121 3.3 0.9 1.0 CB C:CYS99 3.4 0.6 1.0 N C:CYS99 3.8 0.8 1.0 N C:CYS118 3.9 0.3 1.0 CA C:CYS118 4.1 0.1 1.0 CA C:CYS99 4.2 0.2 1.0 CB C:ILE98 4.2 94.5 1.0 C C:ILE98 4.4 0.6 1.0 CA C:CYS96 4.5 0.2 1.0 CA C:CYS121 4.5 0.4 1.0 N C:CYS100 4.6 0.5 1.0 CA C:ILE98 4.7 91.6 1.0 CG2 C:ILE98 4.8 87.7 1.0 N C:ILE98 4.8 89.0 1.0 C C:CYS99 4.8 0.5 1.0 N C:CYS121 4.9 0.2 1.0 C C:CYS96 4.9 0.6 1.0

Zinc binding site 8 out of 9 in the Dna Methyltransferase 3 Like Protein (DNMT3L)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Dna Methyltransferase 3 Like Protein (DNMT3L) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn509 b:0.2 occ:0.92 SG C:CYS142 2.3 0.5 1.0 SG C:CYS113 2.3 0.9 1.0 SG C:CYS145 2.3 0.5 1.0 SG C:CYS108 2.4 0.5 1.0 CB C:CYS113 3.0 0.5 1.0 CB C:CYS142 3.3 0.7 1.0 CB C:CYS108 3.3 0.7 1.0 CB C:CYS145 3.3 0.1 1.0 N C:CYS142 4.0 0.3 1.0 CB C:ASN110 4.1 0.2 1.0 OD1 C:ASN110 4.1 0.5 1.0 CA C:CYS142 4.1 0.9 1.0 O C:LEU144 4.2 0.6 1.0 CA C:CYS145 4.4 0.6 1.0 CA C:CYS113 4.5 0.7 1.0 C C:LEU144 4.5 0.3 1.0 CG C:ASN110 4.6 0.2 1.0 N C:CYS145 4.6 0.4 1.0 C C:CYS142 4.8 0.3 1.0 CA C:CYS108 4.8 0.4 1.0 OH C:TYR117 4.9 0.5 1.0

Zinc binding site 9 out of 9 in the Dna Methyltransferase 3 Like Protein (DNMT3L)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Dna Methyltransferase 3 Like Protein (DNMT3L) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn507 b:0.8 occ:0.85 SG C:CYS56 2.3 0.6 1.0 SG C:CYS76 2.3 0.7 1.0 SG C:CYS73 2.3 0.1 1.0 SG C:CYS53 2.3 1.0 1.0 CB C:CYS56 3.2 0.8 1.0 CB C:CYS76 3.2 0.1 1.0 CB C:CYS53 3.4 0.0 1.0 CB C:CYS73 3.4 0.5 1.0 N C:CYS56 3.7 0.7 1.0 CA C:CYS56 4.0 0.4 1.0 CB C:SER58 4.1 0.7 1.0 N C:CYS73 4.1 0.8 1.0 CB C:CYS55 4.2 0.9 1.0 CA C:CYS73 4.3 0.9 1.0 CA C:CYS76 4.5 0.0 1.0 C C:CYS55 4.6 0.1 1.0 C C:CYS56 4.7 0.8 1.0 N C:CYS76 4.7 0.5 1.0 CA C:CYS53 4.8 0.3 1.0 SG C:CYS55 4.8 0.3 1.0 N C:GLY57 4.8 0.5 1.0 N C:SER58 4.9 0.1 1.0 C C:CYS73 4.9 0.8 1.0 CA C:CYS55 5.0 0.8 1.0 OG C:SER58 5.0 0.3 1.0

S.K.Ooi, C.Qiu, E.Bernstein, K.Li, D.Jia, Z.Yang, H.Erdjument-Bromage, P.Tempst, S.P.Lin, C.D.Allis, X.Cheng, T.H.Bestor. DNMT3L Connects Unmethylated Lysine 4 of Histone H3 to De Novo Methylation of Dna. Nature V. 448 714 2007.
ISSN: ISSN 0028-0836
PubMed: 17687327
DOI: 10.1038/NATURE05987