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Zinc in PDB 3sw9: Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME0 Peptide

Enzymatic activity of Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME0 Peptide

All present enzymatic activity of Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME0 Peptide:
2.1.1.37; 2.1.1.43;

Protein crystallography data

The structure of Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME0 Peptide, PDB code: 3sw9 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) 28.69 / 3.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.140, 91.140, 95.070, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 24.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME0 Peptide (pdb code 3sw9). 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 DNMT3AK44ME0 Peptide, PDB code: 3sw9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3sw9

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Zinc binding site 1 out of 8 in the Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME0 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 DNMT3AK44ME0 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:26.8
occ:1.00
 SG A:CYS1031 2.4 32.7 1.0
SG A:CYS1074 2.4 18.5 1.0
SG A:CYS1078 2.4 23.0 1.0
SG A:CYS1044 2.5 32.5 1.0
CB A:CYS1074 2.9 25.4 1.0
CB A:CYS1031 3.2 27.6 1.0
CB A:CYS1078 3.2 28.2 1.0
CA A:CYS1074 3.4 25.6 1.0
SG A:CYS1080 3.5 27.5 1.0
N A:CYS1031 3.6 36.6 1.0
CB A:CYS1044 3.7 27.9 1.0
ZN A:ZN3 3.7 30.8 1.0
ZN A:ZN2 3.7 25.7 1.0
CA A:CYS1031 4.0 32.7 1.0
N A:ASN1075 4.4 27.8 1.0
SG A:CYS1042 4.4 31.2 1.0
N A:CYS1074 4.4 25.0 1.0
C A:CYS1074 4.5 29.3 1.0
CA A:CYS1078 4.6 31.4 1.0
SG A:CYS1037 4.7 26.8 1.0
O A:CYS1031 4.7 32.0 1.0
C A:CYS1031 4.7 32.7 1.0
C A:TYR1030 4.7 37.9 1.0
N A:CYS1044 4.8 37.7 1.0
ND2 A:ASN1086 4.8 24.6 1.0
CA A:CYS1044 4.9 32.5 1.0
CA A:TYR1030 5.0 36.0 1.0

Zinc binding site 2 out of 8 in 3sw9

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Zinc binding site 2 out of 8 in the Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME0 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 DNMT3AK44ME0 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:25.7
occ:1.00
 SG A:CYS1080 2.3 27.5 1.0
SG A:CYS1084 2.3 25.8 1.0
SG A:CYS1074 2.4 18.5 1.0
SG A:CYS1037 2.7 26.8 1.0
CB A:CYS1084 2.9 26.0 1.0
CB A:CYS1080 3.0 34.3 1.0
CB A:CYS1074 3.1 25.4 1.0
CB A:CYS1037 3.6 32.2 1.0
ZN A:ZN1 3.7 26.8 1.0
ZN A:ZN3 3.8 30.8 1.0
SG A:CYS1031 4.1 32.7 1.0
NH1 A:ARG1087 4.3 24.9 1.0
NE A:ARG1087 4.3 24.2 1.0
CA A:CYS1084 4.4 25.7 1.0
CA A:CYS1080 4.5 31.5 1.0
CB A:ASN1086 4.5 28.9 1.0
CA A:CYS1074 4.6 25.6 1.0
CZ A:ARG1087 4.7 25.1 1.0
O A:TRP1081 4.9 28.4 1.0
C A:CYS1084 4.9 25.8 1.0
CB A:CYS1078 4.9 28.2 1.0
CA A:CYS1037 5.0 38.4 1.0
N A:ASN1086 5.0 27.8 1.0

Zinc binding site 3 out of 8 in 3sw9

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Zinc binding site 3 out of 8 in the Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME0 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 DNMT3AK44ME0 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:30.8
occ:1.00
 SG A:CYS1037 2.3 26.8 1.0
SG A:CYS1033 2.4 39.4 1.0
SG A:CYS1042 2.5 31.2 1.0
SG A:CYS1031 2.6 32.7 1.0
CB A:CYS1031 2.8 27.6 1.0
CB A:CYS1037 3.2 32.2 1.0
CB A:CYS1033 3.2 33.1 1.0
CB A:CYS1042 3.3 34.6 1.0
ZN A:ZN1 3.7 26.8 1.0
CA A:CYS1042 3.8 33.8 1.0
ZN A:ZN2 3.8 25.7 1.0
SG A:CYS1074 3.9 18.5 1.0
CA A:CYS1037 4.0 38.4 1.0
N A:CYS1033 4.2 29.6 1.0
SG A:CYS1080 4.3 27.5 1.0
CA A:CYS1031 4.3 32.7 1.0
CA A:CYS1033 4.4 30.2 1.0
C A:CYS1042 4.5 32.6 1.0
N A:MET1043 4.5 32.1 1.0
N A:CYS1037 4.6 36.4 1.0
C A:CYS1031 4.7 32.7 1.0
CB A:CYS1080 4.8 34.3 1.0
N A:VAL1032 4.9 35.1 1.0
SG A:CYS1044 4.9 32.5 1.0
N A:CYS1042 5.0 40.1 1.0

Zinc binding site 4 out of 8 in 3sw9

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Zinc binding site 4 out of 8 in the Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME0 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 DNMT3AK44ME0 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4

b:43.4
occ:1.00
 SG A:CYS1225 2.3 37.2 1.0
SG A:CYS1172 2.5 45.9 1.0
SG A:CYS1232 2.6 44.3 1.0
SG A:CYS1227 2.6 37.6 1.0
CB A:CYS1227 3.0 39.2 1.0
CB A:CYS1232 3.4 46.2 1.0
CB A:CYS1172 3.4 40.9 1.0
CB A:CYS1225 3.5 43.6 1.0
CA A:CYS1232 3.8 44.5 1.0
N A:CYS1172 4.0 44.3 1.0
CA A:CYS1227 4.1 45.0 1.0
NE2 A:HIS1170 4.1 41.3 1.0
N A:ARG1233 4.2 46.7 1.0
N A:CYS1227 4.2 45.5 1.0
O A:CYS1225 4.3 54.5 1.0
CD2 A:HIS1170 4.3 40.9 1.0
CA A:CYS1172 4.3 41.7 1.0
C A:CYS1232 4.4 45.8 1.0
N A:HIS1234 4.6 43.3 1.0
C A:CYS1225 4.7 47.8 1.0
CA A:CYS1225 4.7 44.6 1.0
C A:CYS1227 4.8 47.9 1.0
N A:GLY1228 4.9 53.7 1.0
C A:HIS1171 5.0 41.5 1.0
CB A:HIS1234 5.0 43.6 1.0
CD2 A:HIS1234 5.0 47.6 1.0

Zinc binding site 5 out of 8 in 3sw9

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Zinc binding site 5 out of 8 in the Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME0 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 DNMT3AK44ME0 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn5

b:31.9
occ:1.00
 SG B:CYS1044 2.3 41.2 1.0
SG B:CYS1074 2.4 29.6 1.0
SG B:CYS1031 2.5 36.0 1.0
SG B:CYS1078 2.6 30.8 1.0
CB B:CYS1074 3.2 30.1 1.0
CB B:CYS1078 3.3 29.8 1.0
CB B:CYS1044 3.4 32.6 1.0
CB B:CYS1031 3.4 32.7 1.0
SG B:CYS1080 3.5 37.1 1.0
CA B:CYS1074 3.5 27.5 1.0
ZN B:ZN6 3.6 32.3 1.0
ZN B:ZN7 3.7 36.8 1.0
N B:CYS1031 3.9 36.9 1.0
SG B:CYS1042 4.2 40.6 1.0
CA B:CYS1031 4.3 35.0 1.0
N B:CYS1074 4.5 26.0 1.0
N B:ASN1075 4.5 30.3 1.0
SG B:CYS1037 4.5 37.9 1.0
C B:CYS1074 4.6 30.5 1.0
CA B:CYS1078 4.7 33.8 1.0
CA B:CYS1044 4.7 30.8 1.0
ND2 B:ASN1086 4.7 29.8 1.0
N B:CYS1044 4.8 33.5 1.0
C B:TYR1030 4.9 36.4 1.0
C B:CYS1031 4.9 35.5 1.0

Zinc binding site 6 out of 8 in 3sw9

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Zinc binding site 6 out of 8 in the Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME0 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 DNMT3AK44ME0 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn6

b:32.3
occ:1.00
 SG B:CYS1037 2.2 37.9 1.0
SG B:CYS1074 2.4 29.6 1.0
SG B:CYS1080 2.4 37.1 1.0
SG B:CYS1084 2.5 33.4 1.0
CB B:CYS1080 2.9 38.6 1.0
CB B:CYS1084 3.1 32.6 1.0
CB B:CYS1074 3.3 30.1 1.0
CB B:CYS1037 3.5 37.4 1.0
ZN B:ZN5 3.6 31.9 1.0
ZN B:ZN7 3.7 36.8 1.0
SG B:CYS1031 4.1 36.0 1.0
CA B:CYS1080 4.4 35.4 1.0
NH1 B:ARG1087 4.4 33.9 1.0
NE B:ARG1087 4.4 33.5 1.0
CB B:ASN1086 4.5 30.2 1.0
CA B:CYS1084 4.7 35.6 1.0
O B:TRP1081 4.7 31.2 1.0
CA B:CYS1074 4.7 27.5 1.0
CZ B:ARG1087 4.8 31.4 1.0
CA B:CYS1037 4.8 39.3 1.0
O B:ASP1036 4.9 39.5 1.0
CB B:CYS1078 4.9 29.8 1.0
N B:ASN1086 5.0 35.1 1.0
C B:CYS1080 5.0 38.9 1.0

Zinc binding site 7 out of 8 in 3sw9

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Zinc binding site 7 out of 8 in the Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME0 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 DNMT3AK44ME0 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn7

b:36.8
occ:1.00
 SG B:CYS1031 2.3 36.0 1.0
SG B:CYS1037 2.4 37.9 1.0
SG B:CYS1042 2.5 40.6 1.0
SG B:CYS1033 2.6 36.6 1.0
CB B:CYS1042 3.1 43.9 1.0
CB B:CYS1031 3.1 32.7 1.0
CB B:CYS1037 3.2 37.4 1.0
CB B:CYS1033 3.4 40.8 1.0
ZN B:ZN6 3.7 32.3 1.0
ZN B:ZN5 3.7 31.9 1.0
CA B:CYS1042 3.8 46.1 1.0
CA B:CYS1037 3.9 39.3 1.0
SG B:CYS1074 4.1 29.6 1.0
SG B:CYS1080 4.4 37.1 1.0
N B:CYS1033 4.5 39.2 1.0
CA B:CYS1031 4.5 35.0 1.0
CA B:CYS1033 4.6 44.8 1.0
CB B:CYS1080 4.6 38.6 1.0
C B:CYS1042 4.6 37.3 1.0
N B:CYS1037 4.7 41.5 1.0
N B:MET1043 4.8 36.2 1.0
N B:VAL1032 4.8 36.9 1.0
SG B:CYS1044 4.9 41.2 1.0
C B:CYS1031 4.9 35.5 1.0
N B:CYS1042 4.9 50.0 1.0

Zinc binding site 8 out of 8 in 3sw9

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Zinc binding site 8 out of 8 in the Glp (G9A-Like Protein) Set Domain in Complex with DNMT3AK44ME0 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 DNMT3AK44ME0 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8

b:42.5
occ:1.00
 SG B:CYS1225 2.4 40.8 1.0
SG B:CYS1227 2.4 37.5 1.0
SG B:CYS1232 2.6 51.7 1.0
SG B:CYS1172 2.8 49.0 1.0
CB B:CYS1225 3.4 44.9 1.0
CB B:CYS1232 3.5 48.5 1.0
CA B:CYS1232 3.6 47.6 1.0
CB B:CYS1172 3.6 39.4 1.0
CB B:CYS1227 3.7 41.5 1.0
N B:CYS1172 4.1 42.7 1.0
NE2 B:HIS1170 4.1 40.3 1.0
N B:ARG1233 4.2 50.3 1.0
C B:CYS1232 4.4 50.6 1.0
CA B:CYS1172 4.5 38.6 1.0
CD2 B:HIS1170 4.5 37.6 1.0
N B:CYS1227 4.5 43.7 1.0
O B:CYS1225 4.5 56.5 1.0
N B:HIS1234 4.6 52.5 1.0
CA B:CYS1227 4.6 44.4 1.0
CA B:CYS1225 4.7 51.6 1.0
C B:CYS1225 4.7 48.1 1.0
N B:CYS1232 4.7 49.6 1.0
CD2 B:HIS1234 4.9 47.1 1.0
C B:HIS1171 4.9 37.6 1.0
CB B:HIS1234 4.9 52.4 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: Sat Oct 26 16:09:20 2024

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