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Zinc in PDB 2pvc: DNMT3L Recognizes Unmethylated Histone H3 Lysine 4

Protein crystallography data

The structure of DNMT3L Recognizes Unmethylated Histone H3 Lysine 4, PDB code: 2pvc was solved by X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.41 / 3.69
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 267.700, 267.700, 150.000, 90.00, 90.00, 120.00
R / Rfree (%) 26.4 / 30.2

Zinc Binding Sites:

The binding sites of Zinc atom in the DNMT3L Recognizes Unmethylated Histone H3 Lysine 4 (pdb code 2pvc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the DNMT3L Recognizes Unmethylated Histone H3 Lysine 4, PDB code: 2pvc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 2pvc

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Zinc binding site 1 out of 9 in the DNMT3L Recognizes Unmethylated Histone H3 Lysine 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of DNMT3L Recognizes Unmethylated Histone H3 Lysine 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:58.3
occ:0.41
 SG A:CYS121 2.3 0.4 1.0
SG A:CYS99 2.4 85.5 1.0
SG A:CYS96 2.6 0.0 1.0
SG A:CYS118 2.6 0.1 1.0
CB A:CYS118 2.6 98.3 1.0
N A:CYS118 3.2 0.2 1.0
CB A:CYS121 3.2 0.7 1.0
CA A:CYS118 3.5 1.0 1.0
N A:CYS99 3.6 0.1 1.0
CB A:ILE98 3.7 0.3 1.0
CB A:CYS96 3.7 0.5 1.0
CB A:CYS99 3.9 0.4 1.0
N A:ILE98 4.2 0.8 1.0
CA A:ILE98 4.3 0.7 1.0
CA A:CYS99 4.4 0.4 1.0
C A:TYR117 4.4 0.2 1.0
CG1 A:ILE98 4.4 0.6 1.0
C A:ILE98 4.4 0.8 1.0
CA A:CYS121 4.5 0.3 1.0
C A:CYS118 4.6 0.2 1.0
N A:CYS121 4.6 0.9 1.0
CG2 A:ILE98 4.6 0.7 1.0
O A:CYS118 4.7 0.6 1.0
CD1 A:ILE98 4.7 92.6 1.0
CA A:TYR117 4.7 0.6 1.0
O A:SER101 4.9 0.6 1.0

Zinc binding site 2 out of 9 in 2pvc

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Zinc binding site 2 out of 9 in the DNMT3L Recognizes Unmethylated Histone H3 Lysine 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of DNMT3L Recognizes Unmethylated Histone H3 Lysine 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:0.0
occ:0.92
 SG A:CYS113 2.4 0.3 1.0
SG A:CYS108 2.4 88.6 1.0
SG A:CYS145 2.4 0.9 1.0
SG A:CYS142 2.5 96.7 1.0
CB A:CYS113 2.8 0.1 1.0
CB A:CYS142 3.5 0.7 1.0
CB A:CYS108 3.5 0.7 1.0
N A:CYS142 3.8 0.2 1.0
CB A:CYS145 3.8 0.8 1.0
CA A:CYS142 4.2 0.3 1.0
CB A:ASN110 4.3 0.3 1.0
CA A:CYS113 4.3 0.0 1.0
C A:VAL141 4.8 0.7 1.0
CA A:CYS145 4.9 0.9 1.0
N A:CYS145 4.9 0.5 1.0
CA A:CYS108 4.9 1.0 1.0
CA A:VAL141 5.0 0.3 1.0

Zinc binding site 3 out of 9 in 2pvc

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Zinc binding site 3 out of 9 in the DNMT3L Recognizes Unmethylated Histone H3 Lysine 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of DNMT3L Recognizes Unmethylated Histone H3 Lysine 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:0.5
occ:0.85
 SG A:CYS53 2.2 96.7 1.0
SG A:CYS73 2.5 0.5 1.0
SG A:CYS56 2.5 0.2 1.0
SG A:CYS76 2.6 0.6 1.0
CB A:CYS53 2.8 99.4 1.0
CB A:CYS73 2.9 0.5 1.0
CB A:CYS76 3.0 0.5 1.0
N A:CYS73 3.1 0.1 1.0
CA A:CYS73 3.6 0.7 1.0
CB A:CYS56 4.0 0.0 1.0
N A:CYS56 4.0 0.3 1.0
C A:ILE72 4.3 0.7 1.0
CA A:CYS53 4.3 0.4 1.0
CA A:CYS76 4.3 0.1 1.0
C A:CYS73 4.4 0.5 1.0
O A:CYS73 4.4 90.7 1.0
N A:CYS76 4.5 0.1 1.0
CB A:CYS55 4.5 0.5 1.0
CA A:CYS56 4.5 0.2 1.0
CA A:ILE72 4.6 0.2 1.0
CB A:SER58 4.6 0.3 1.0
O A:CYS53 4.8 0.1 1.0
N A:GLY57 4.8 0.2 1.0
C A:CYS53 4.9 0.1 1.0
CG2 A:ILE72 4.9 0.9 1.0
N A:SER58 5.0 0.8 1.0

Zinc binding site 4 out of 9 in 2pvc

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Zinc binding site 4 out of 9 in the DNMT3L Recognizes Unmethylated Histone H3 Lysine 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of DNMT3L Recognizes Unmethylated Histone H3 Lysine 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn605

b:14.4
occ:0.41
 SG B:CYS121 2.1 55.0 1.0
SG B:CYS99 2.2 59.1 1.0
SG B:CYS118 2.3 73.0 1.0
SG B:CYS96 2.3 72.8 1.0
CB B:CYS118 2.4 66.4 1.0
CB B:CYS121 2.7 56.5 1.0
CB B:CYS99 3.0 75.6 1.0
CB B:CYS96 3.2 68.7 1.0
CA B:CYS118 3.7 88.6 1.0
N B:CYS99 3.7 62.7 1.0
CA B:CYS121 3.9 64.9 1.0
CA B:CYS99 3.9 78.2 1.0
N B:CYS118 4.0 92.4 1.0
N B:CYS121 4.1 68.7 1.0
O B:CYS118 4.1 92.6 1.0
C B:CYS118 4.2 91.7 1.0
NH2 B:ARG35 4.3 0.8 1.0
CB B:SER101 4.5 0.7 1.0
CA B:CYS96 4.7 67.3 1.0
C B:CYS99 4.7 94.8 1.0
CB B:ILE98 4.7 64.5 1.0
C B:ILE98 4.8 66.5 1.0
N B:CYS100 4.9 0.4 1.0
N B:SER101 4.9 0.1 1.0

Zinc binding site 5 out of 9 in 2pvc

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Zinc binding site 5 out of 9 in the DNMT3L Recognizes Unmethylated Histone H3 Lysine 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of DNMT3L Recognizes Unmethylated Histone H3 Lysine 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn606

b:71.6
occ:0.92
 SG B:CYS113 2.2 70.0 1.0
SG B:CYS142 2.2 62.7 1.0
SG B:CYS145 2.2 58.3 1.0
SG B:CYS108 2.4 68.9 1.0
CB B:CYS113 2.7 65.7 1.0
CB B:CYS145 3.3 62.6 1.0
CB B:CYS108 3.4 63.3 1.0
CB B:CYS142 3.6 64.1 1.0
N B:CYS142 4.0 69.4 1.0
CA B:CYS113 4.1 77.0 1.0
CA B:CYS142 4.4 65.3 1.0
O B:LEU144 4.4 92.1 1.0
CA B:CYS145 4.5 76.3 1.0
CB B:ASN110 4.6 0.1 1.0
C B:LEU144 4.7 78.9 1.0
N B:CYS145 4.8 74.6 1.0
CA B:CYS108 4.8 67.7 1.0
N B:CYS113 4.9 93.7 1.0
C B:CYS113 5.0 77.7 1.0

Zinc binding site 6 out of 9 in 2pvc

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Zinc binding site 6 out of 9 in the DNMT3L Recognizes Unmethylated Histone H3 Lysine 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of DNMT3L Recognizes Unmethylated Histone H3 Lysine 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn604

b:61.6
occ:0.85
 SG B:CYS53 2.2 69.1 1.0
SG B:CYS56 2.3 100.0 1.0
SG B:CYS76 2.3 81.7 1.0
SG B:CYS73 2.7 0.3 1.0
CB B:CYS73 3.0 0.5 1.0
CB B:CYS53 3.1 40.2 1.0
CB B:CYS76 3.1 0.1 1.0
CB B:CYS56 3.4 99.5 1.0
N B:CYS56 3.5 1.0 1.0
N B:CYS73 3.7 86.6 1.0
CA B:CYS73 3.9 96.0 1.0
CA B:CYS56 4.0 99.2 1.0
CB B:CYS55 4.1 0.4 1.0
CB B:SER58 4.4 87.0 1.0
CA B:CYS76 4.4 0.7 1.0
C B:CYS56 4.4 0.5 1.0
O B:CYS53 4.4 64.5 1.0
CA B:CYS53 4.5 54.3 1.0
C B:CYS55 4.6 98.8 1.0
N B:CYS76 4.6 0.9 1.0
C B:CYS73 4.6 95.0 1.0
O B:CYS73 4.7 88.1 1.0
N B:SER58 4.8 98.7 1.0
CA B:CYS55 4.8 93.5 1.0
C B:CYS53 4.8 49.7 1.0
O B:CYS56 4.8 99.8 1.0
C B:ILE72 4.9 69.5 1.0
N B:GLY57 4.9 0.8 1.0
N B:CYS55 5.0 66.0 1.0

Zinc binding site 7 out of 9 in 2pvc

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Zinc binding site 7 out of 9 in the DNMT3L Recognizes Unmethylated Histone H3 Lysine 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of DNMT3L Recognizes Unmethylated Histone H3 Lysine 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn608

b:69.1
occ:0.41
 SG C:CYS96 2.4 0.5 1.0
SG C:CYS121 2.5 0.0 1.0
SG C:CYS99 2.6 59.1 1.0
CB C:CYS121 2.6 0.7 1.0
CB C:CYS118 3.2 0.3 1.0
SG C:CYS118 3.2 0.9 1.0
N C:CYS118 3.3 0.8 1.0
CB C:CYS96 3.6 0.5 1.0
CB C:ILE98 3.8 0.2 1.0
CA C:CYS118 3.9 0.4 1.0
N C:CYS99 4.0 62.7 1.0
CB C:CYS99 4.0 75.6 1.0
CA C:CYS121 4.1 0.8 1.0
N C:ILE98 4.4 0.8 1.0
C C:TYR117 4.4 0.4 1.0
NH2 C:ARG35 4.4 0.6 1.0
N C:CYS121 4.5 0.2 1.0
CA C:ILE98 4.5 1.0 1.0
CA C:TYR117 4.5 0.9 1.0
CD1 C:ILE98 4.5 0.3 1.0
CB C:TYR117 4.6 0.6 1.0
CG2 C:ILE98 4.6 0.7 1.0
CG1 C:ILE98 4.6 0.8 1.0
C C:ILE98 4.6 0.6 1.0
CA C:CYS99 4.6 78.2 1.0
C C:CYS118 4.8 0.5 1.0
CA C:CYS96 4.9 0.1 1.0

Zinc binding site 8 out of 9 in 2pvc

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Zinc binding site 8 out of 9 in the DNMT3L Recognizes Unmethylated Histone H3 Lysine 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of DNMT3L Recognizes Unmethylated Histone H3 Lysine 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn609

b:0.9
occ:0.92
 SG C:CYS113 2.4 1.0 1.0
SG C:CYS142 2.5 0.2 1.0
CB C:CYS145 2.8 0.2 1.0
SG C:CYS145 2.8 0.6 1.0
SG C:CYS108 3.0 0.9 1.0
CB C:CYS142 3.2 0.1 1.0
CB C:CYS113 3.3 0.9 1.0
CB C:CYS108 3.5 0.2 1.0
N C:CYS145 3.6 0.5 1.0
CA C:CYS145 3.7 0.1 1.0
OH C:TYR117 4.2 0.6 1.0
N C:CYS142 4.3 0.3 1.0
CA C:CYS142 4.3 0.2 1.0
CB C:ARG115 4.4 0.6 1.0
CG C:ARG115 4.5 0.2 1.0
CD C:ARG115 4.6 0.8 1.0
CA C:CYS113 4.7 0.1 1.0
C C:LEU144 4.8 0.8 1.0
N C:ARG115 4.9 0.9 1.0
C C:CYS142 5.0 0.1 1.0

Zinc binding site 9 out of 9 in 2pvc

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Zinc binding site 9 out of 9 in the DNMT3L Recognizes Unmethylated Histone H3 Lysine 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of DNMT3L Recognizes Unmethylated Histone H3 Lysine 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn607

b:0.3
occ:0.85
 SG C:CYS76 2.6 0.2 1.0
CB C:CYS56 2.7 0.1 1.0
SG C:CYS73 2.8 0.4 1.0
SG C:CYS53 3.2 0.2 1.0
SG C:CYS56 3.7 0.5 1.0
CB C:CYS76 3.9 0.6 1.0
CA C:CYS56 4.0 0.2 1.0
N C:CYS76 4.0 0.0 1.0
N C:CYS56 4.0 1.0 1.0
CB C:PRO75 4.3 0.0 1.0
CB C:CYS53 4.4 0.4 1.0
CB C:SER58 4.5 0.8 1.0
CA C:CYS76 4.5 0.7 1.0
CB C:CYS73 4.6 0.0 1.0
CD C:PRO75 4.6 0.0 1.0
CG C:PRO75 4.7 0.0 1.0
C C:CYS56 4.9 0.0 1.0

Reference:

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
Page generated: Thu Oct 17 03:14:17 2024

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