Atomistry » Zinc » PDB 2pop-2q1q » 2pvc
Atomistry »
  Zinc »
    PDB 2pop-2q1q »
      2pvc »

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

Go back to Zinc Binding Sites List in 2pvc
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

Go back to Zinc Binding Sites List in 2pvc
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

Go back to Zinc Binding Sites List in 2pvc
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

Go back to Zinc Binding Sites List in 2pvc
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

Go back to Zinc Binding Sites List in 2pvc
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

Go back to Zinc Binding Sites List in 2pvc
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

Go back to Zinc Binding Sites List in 2pvc
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

Go back to Zinc Binding Sites List in 2pvc
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

Go back to Zinc Binding Sites List in 2pvc
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

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