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Zinc in PDB 3swc: Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide

Enzymatic activity of Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide

All present enzymatic activity of Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide:
2.1.1.37; 2.1.1.43;

Protein crystallography data

The structure of Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide, PDB code: 3swc was solved by Y.Chang, J.R.Horton, X.Zhang, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.78 / 2.33
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.090, 90.220, 95.400, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide (pdb code 3swc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide, PDB code: 3swc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3swc

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Zinc binding site 1 out of 8 in the Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:29.5
occ:1.00
 SG A:CYS1074 2.2 24.8 1.0
SG A:CYS1044 2.3 29.6 1.0
SG A:CYS1078 2.3 31.8 1.0
SG A:CYS1031 2.5 36.3 1.0
CB A:CYS1074 3.0 25.1 1.0
CB A:CYS1031 3.2 29.9 1.0
CB A:CYS1044 3.4 27.8 1.0
CB A:CYS1078 3.4 28.3 1.0
CA A:CYS1074 3.4 28.9 1.0
N A:CYS1031 3.5 32.9 1.0
ZN A:ZN303 3.8 29.9 1.0
ZN A:ZN302 3.8 30.2 1.0
CA A:CYS1031 3.9 28.6 1.0
SG A:CYS1080 4.0 26.1 1.0
SG A:CYS1042 4.2 36.4 1.0
N A:CYS1074 4.4 25.2 1.0
N A:ASN1075 4.5 28.1 1.0
C A:CYS1074 4.5 26.8 1.0
C A:TYR1030 4.5 33.5 1.0
CA A:CYS1044 4.6 35.9 1.0
CA A:CYS1078 4.7 29.9 1.0
N A:CYS1044 4.7 34.9 1.0
SG A:CYS1037 4.7 27.2 1.0
C A:CYS1031 4.8 34.4 1.0
CA A:TYR1030 4.8 33.9 1.0
ND2 A:ASN1086 4.8 24.5 1.0
O A:HOH6 4.8 35.1 1.0
O A:CYS1031 4.9 34.6 1.0

Zinc binding site 2 out of 8 in 3swc

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Zinc binding site 2 out of 8 in the Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:30.2
occ:1.00
 SG A:CYS1074 2.3 24.8 1.0
SG A:CYS1084 2.3 25.9 1.0
SG A:CYS1080 2.3 26.1 1.0
SG A:CYS1037 2.5 27.2 1.0
CB A:CYS1074 3.0 25.1 1.0
CB A:CYS1084 3.1 31.3 1.0
CB A:CYS1080 3.1 35.1 1.0
CB A:CYS1037 3.5 32.6 1.0
ZN A:ZN303 3.8 29.9 1.0
ZN A:ZN301 3.8 29.5 1.0
SG A:CYS1031 4.0 36.3 1.0
NH1 A:ARG1087 4.2 28.9 1.0
NE A:ARG1087 4.3 30.2 1.0
CB A:ASN1086 4.4 27.1 1.0
CA A:CYS1084 4.5 31.3 1.0
CA A:CYS1074 4.5 28.9 1.0
CA A:CYS1080 4.6 32.6 1.0
CZ A:ARG1087 4.7 33.6 1.0
O A:TRP1081 4.7 30.9 1.0
N A:ASN1086 4.8 27.1 1.0
CA A:CYS1037 4.9 29.8 1.0
CB A:CYS1078 4.9 28.3 1.0
C A:CYS1084 5.0 33.1 1.0

Zinc binding site 3 out of 8 in 3swc

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Zinc binding site 3 out of 8 in the Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:29.9
occ:1.00
 SG A:CYS1037 2.3 27.2 1.0
SG A:CYS1042 2.4 36.4 1.0
SG A:CYS1033 2.4 32.3 1.0
SG A:CYS1031 2.4 36.3 1.0
CB A:CYS1031 3.1 29.9 1.0
CB A:CYS1042 3.2 30.1 1.0
CB A:CYS1033 3.3 30.5 1.0
CB A:CYS1037 3.3 32.6 1.0
SG A:CYS1074 3.8 24.8 1.0
ZN A:ZN301 3.8 29.5 1.0
ZN A:ZN302 3.8 30.2 1.0
CA A:CYS1042 3.9 34.6 1.0
CA A:CYS1037 4.0 29.8 1.0
N A:CYS1033 4.3 30.7 1.0
CA A:CYS1033 4.4 31.9 1.0
CA A:CYS1031 4.5 28.6 1.0
C A:CYS1042 4.6 32.4 1.0
SG A:CYS1080 4.7 26.1 1.0
O A:HOH13 4.7 39.8 1.0
CB A:CYS1080 4.8 35.1 1.0
N A:MET1043 4.8 33.9 1.0
N A:CYS1037 4.8 33.7 1.0
O A:HOH11 4.9 34.8 1.0
O A:HOH12 4.9 32.1 1.0
C A:CYS1031 4.9 34.4 1.0

Zinc binding site 4 out of 8 in 3swc

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Zinc binding site 4 out of 8 in the Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:39.4
occ:1.00
 SG A:CYS1225 2.2 34.4 1.0
SG A:CYS1227 2.4 39.0 1.0
SG A:CYS1172 2.4 36.5 1.0
SG A:CYS1232 2.5 43.8 1.0
CB A:CYS1227 3.3 41.9 1.0
CB A:CYS1232 3.3 42.5 1.0
CB A:CYS1225 3.4 39.8 1.0
CB A:CYS1172 3.5 46.2 1.0
CA A:CYS1232 3.8 44.1 1.0
N A:CYS1227 4.0 39.9 1.0
N A:CYS1172 4.1 43.2 1.0
CA A:CYS1227 4.2 44.3 1.0
N A:ARG1233 4.2 45.6 1.0
NE2 A:HIS1170 4.3 39.0 1.0
CD2 A:HIS1170 4.4 39.2 1.0
CA A:CYS1172 4.4 41.2 1.0
C A:CYS1232 4.4 50.0 1.0
C A:CYS1225 4.6 45.6 1.0
O A:CYS1225 4.6 46.3 1.0
N A:HIS1234 4.6 45.7 1.0
CA A:CYS1225 4.6 40.3 1.0
N A:GLY1228 4.8 45.4 1.0
C A:CYS1227 4.9 42.4 1.0
CB A:HIS1234 5.0 44.0 1.0

Zinc binding site 5 out of 8 in 3swc

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Zinc binding site 5 out of 8 in the Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn305

b:31.6
occ:1.00
 SG B:CYS1044 2.2 30.5 1.0
SG B:CYS1074 2.3 27.6 1.0
SG B:CYS1078 2.4 27.9 1.0
SG B:CYS1031 2.4 37.3 1.0
CB B:CYS1074 3.1 26.5 1.0
CB B:CYS1031 3.2 30.4 1.0
CB B:CYS1078 3.3 28.1 1.0
CB B:CYS1044 3.3 25.1 1.0
CA B:CYS1074 3.5 27.6 1.0
N B:CYS1031 3.7 31.5 1.0
ZN B:ZN307 3.7 33.2 1.0
ZN B:ZN306 3.8 31.4 1.0
SG B:CYS1080 4.0 28.5 1.0
CA B:CYS1031 4.1 33.5 1.0
SG B:CYS1042 4.2 31.6 1.0
N B:CYS1074 4.5 25.5 1.0
N B:ASN1075 4.5 29.9 1.0
C B:CYS1074 4.6 31.5 1.0
CA B:CYS1044 4.6 27.9 1.0
CA B:CYS1078 4.6 33.1 1.0
N B:CYS1044 4.7 26.9 1.0
C B:TYR1030 4.7 33.4 1.0
SG B:CYS1037 4.8 36.7 1.0
O B:CYS1031 4.8 37.2 1.0
C B:CYS1031 4.8 33.9 1.0
CA B:TYR1030 4.9 32.1 1.0
ND2 B:ASN1086 4.9 28.0 1.0

Zinc binding site 6 out of 8 in 3swc

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Zinc binding site 6 out of 8 in the Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn306

b:31.4
occ:1.00
 SG B:CYS1084 2.3 29.3 1.0
SG B:CYS1074 2.3 27.6 1.0
SG B:CYS1080 2.4 28.5 1.0
SG B:CYS1037 2.4 36.7 1.0
CB B:CYS1080 3.1 29.1 1.0
CB B:CYS1074 3.2 26.5 1.0
CB B:CYS1084 3.2 33.0 1.0
CB B:CYS1037 3.5 34.8 1.0
ZN B:ZN307 3.7 33.2 1.0
ZN B:ZN305 3.8 31.6 1.0
SG B:CYS1031 4.1 37.3 1.0
NE B:ARG1087 4.3 31.0 1.0
NH1 B:ARG1087 4.4 30.8 1.0
CB B:ASN1086 4.5 30.8 1.0
CA B:CYS1080 4.6 30.9 1.0
CA B:CYS1074 4.6 27.6 1.0
CA B:CYS1084 4.7 32.0 1.0
CZ B:ARG1087 4.8 28.2 1.0
O B:TRP1081 4.8 32.0 1.0
CA B:CYS1037 4.8 37.2 1.0
N B:ASN1086 4.9 33.2 1.0
SG B:CYS1042 4.9 31.6 1.0
CB B:CYS1078 5.0 28.1 1.0

Zinc binding site 7 out of 8 in 3swc

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Zinc binding site 7 out of 8 in the Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn307

b:33.2
occ:1.00
 SG B:CYS1042 2.3 31.6 1.0
SG B:CYS1037 2.3 36.7 1.0
SG B:CYS1031 2.4 37.3 1.0
SG B:CYS1033 2.4 32.4 1.0
CB B:CYS1031 3.1 30.4 1.0
CB B:CYS1037 3.1 34.8 1.0
CB B:CYS1042 3.2 35.9 1.0
CB B:CYS1033 3.3 32.7 1.0
ZN B:ZN306 3.7 31.4 1.0
ZN B:ZN305 3.7 31.6 1.0
SG B:CYS1074 3.9 27.6 1.0
CA B:CYS1042 3.9 37.4 1.0
CA B:CYS1037 4.0 37.2 1.0
N B:CYS1033 4.4 37.1 1.0
CA B:CYS1033 4.5 37.2 1.0
CA B:CYS1031 4.5 33.5 1.0
SG B:CYS1080 4.6 28.5 1.0
O B:HOH92 4.7 38.5 1.0
C B:CYS1042 4.7 32.4 1.0
CB B:CYS1080 4.7 29.1 1.0
N B:CYS1037 4.9 35.4 1.0
C B:CYS1031 4.9 33.9 1.0
SG B:CYS1044 4.9 30.5 1.0
N B:MET1043 4.9 28.2 1.0

Zinc binding site 8 out of 8 in 3swc

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Zinc binding site 8 out of 8 in the Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME2 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn308

b:40.7
occ:1.00
 SG B:CYS1172 2.3 36.5 1.0
SG B:CYS1227 2.3 35.5 1.0
SG B:CYS1225 2.3 42.2 1.0
SG B:CYS1232 2.5 50.4 1.0
CB B:CYS1232 3.2 42.3 1.0
CB B:CYS1225 3.4 41.6 1.0
CB B:CYS1227 3.4 37.5 1.0
CB B:CYS1172 3.4 38.6 1.0
CA B:CYS1232 3.6 45.0 1.0
N B:CYS1172 4.0 38.2 1.0
N B:CYS1227 4.0 39.3 1.0
O B:HOH79 4.1 38.6 1.0
NE2 B:HIS1170 4.1 35.5 1.0
N B:ARG1233 4.2 46.6 1.0
CA B:CYS1227 4.3 44.6 1.0
CA B:CYS1172 4.3 33.5 1.0
CD2 B:HIS1170 4.3 35.6 1.0
C B:CYS1232 4.4 43.7 1.0
N B:HIS1234 4.6 44.7 1.0
CA B:CYS1225 4.6 46.5 1.0
C B:CYS1225 4.7 44.2 1.0
N B:CYS1232 4.8 44.8 1.0
N B:GLY1228 4.8 43.8 1.0
O B:CYS1225 4.9 47.7 1.0
C B:CYS1227 4.9 42.6 1.0
C B:HIS1171 5.0 36.4 1.0
CB B:HIS1234 5.0 44.0 1.0

Reference:

Y.Chang, L.Sun, K.Kokura, J.R.Horton, M.Fukuda, A.Espejo, V.Izumi, J.M.Koomen, M.T.Bedford, X.Zhang, Y.Shinkai, J.Fang, X.Cheng. MPP8 Mediates the Interactions Between Dna Methyltransferase DNMT3A and H3K9 Methyltransferase Glp/G9A. Nat Commun V. 2 533 2011.
ISSN: ESSN 2041-1723
PubMed: 22086334
DOI: 10.1038/NCOMMS1549
Page generated: Wed Aug 20 14:15:07 2025

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