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Zinc in PDB 2rfi: Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide

Enzymatic activity of Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide

All present enzymatic activity of Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide, PDB code: 2rfi was solved by J.Min, H.Wu, P.Loppnau, J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, A.N.Plotnikov, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.80 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.593, 85.627, 95.670, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 22

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide (pdb code 2rfi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide, PDB code: 2rfi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2rfi

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Zinc binding site 1 out of 8 in the Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:17.5
occ:1.00
 SG A:CYS1044 2.3 17.8 1.0
SG A:CYS1031 2.4 16.2 1.0
SG A:CYS1078 2.4 16.7 1.0
SG A:CYS1074 2.4 15.6 1.0
CB A:CYS1031 3.2 17.0 1.0
CB A:CYS1074 3.3 15.8 1.0
CB A:CYS1078 3.3 16.2 1.0
CB A:CYS1044 3.4 18.5 1.0
N A:CYS1031 3.6 17.0 1.0
CA A:CYS1074 3.6 14.9 1.0
ZN A:ZN502 3.8 16.8 1.0
ZN A:ZN503 3.9 17.1 1.0
CA A:CYS1031 4.0 15.9 1.0
SG A:CYS1080 4.2 16.7 1.0
SG A:CYS1042 4.4 17.5 1.0
N A:ASN1075 4.5 15.3 1.0
N A:CYS1074 4.6 14.0 1.0
C A:TYR1030 4.6 17.6 1.0
CA A:CYS1078 4.6 16.6 1.0
CA A:CYS1044 4.6 18.5 1.0
N A:CYS1044 4.7 18.9 1.0
C A:CYS1074 4.7 15.3 1.0
SG A:CYS1037 4.7 16.8 1.0
C A:CYS1031 4.8 16.4 1.0
O A:HOH1270 4.8 20.7 1.0
O A:CYS1031 4.8 16.0 1.0
CA A:TYR1030 4.8 18.4 1.0

Zinc binding site 2 out of 8 in 2rfi

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Zinc binding site 2 out of 8 in the Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:16.8
occ:1.00
 SG A:CYS1037 2.3 16.8 1.0
SG A:CYS1080 2.3 16.7 1.0
SG A:CYS1084 2.3 16.7 1.0
SG A:CYS1074 2.4 15.6 1.0
CB A:CYS1080 3.2 17.1 1.0
CB A:CYS1084 3.2 17.7 1.0
CB A:CYS1074 3.2 15.8 1.0
CB A:CYS1037 3.3 18.0 1.0
ZN A:ZN503 3.8 17.1 1.0
ZN A:ZN501 3.8 17.5 1.0
SG A:CYS1031 4.0 16.2 1.0
NE A:ARG1087 4.3 16.0 1.0
NH2 A:ARG1087 4.4 18.2 1.0
CB A:ASN1086 4.6 16.8 1.0
CA A:CYS1080 4.6 17.5 1.0
CA A:CYS1074 4.7 14.9 1.0
CA A:CYS1084 4.7 17.8 1.0
CA A:CYS1037 4.7 18.5 1.0
CZ A:ARG1087 4.8 18.3 1.0
O A:TRP1081 4.8 18.1 1.0
N A:ASN1086 4.9 17.2 1.0
CB A:CYS1078 4.9 16.2 1.0

Zinc binding site 3 out of 8 in 2rfi

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Zinc binding site 3 out of 8 in the Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:17.1
occ:1.00
 SG A:CYS1033 2.3 16.9 1.0
SG A:CYS1042 2.4 17.5 1.0
SG A:CYS1037 2.4 16.8 1.0
SG A:CYS1031 2.4 16.2 1.0
CB A:CYS1031 3.1 17.0 1.0
CB A:CYS1033 3.2 18.1 1.0
CB A:CYS1037 3.2 18.0 1.0
CB A:CYS1042 3.3 18.3 1.0
ZN A:ZN502 3.8 16.8 1.0
ZN A:ZN501 3.9 17.5 1.0
CA A:CYS1037 3.9 18.5 1.0
CA A:CYS1042 3.9 18.8 1.0
SG A:CYS1074 4.1 15.6 1.0
CA A:CYS1033 4.4 18.0 1.0
N A:CYS1033 4.4 17.4 1.0
O A:HOH1269 4.4 20.5 1.0
O A:HOH1279 4.5 22.0 1.0
CA A:CYS1031 4.6 15.9 1.0
C A:CYS1042 4.6 18.5 1.0
N A:MET1043 4.7 18.7 1.0
N A:CYS1037 4.7 18.6 1.0
O A:HOH1315 4.8 25.0 1.0
SG A:CYS1080 4.8 16.7 1.0
CB A:CYS1080 4.9 17.1 1.0
C A:CYS1031 4.9 16.4 1.0
C A:CYS1037 5.0 19.6 1.0

Zinc binding site 4 out of 8 in 2rfi

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Zinc binding site 4 out of 8 in the Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:25.0
occ:1.00
 SG A:CYS1227 2.3 26.9 1.0
SG A:CYS1225 2.4 28.1 1.0
SG A:CYS1232 2.4 26.9 1.0
SG A:CYS1172 2.5 23.5 1.0
CB A:CYS1232 3.3 29.2 1.0
CB A:CYS1225 3.4 29.8 1.0
CB A:CYS1227 3.4 28.8 1.0
CB A:CYS1172 3.4 22.6 1.0
CA A:CYS1232 3.7 29.4 1.0
O A:HOH1352 4.1 28.5 1.0
N A:CYS1172 4.1 21.8 1.0
N A:CYS1227 4.1 29.7 1.0
CE1 A:HIS1170 4.3 18.2 1.0
N A:ARG1233 4.3 30.3 1.0
CA A:CYS1227 4.3 29.1 1.0
CA A:CYS1172 4.3 23.0 1.0
ND1 A:HIS1170 4.4 21.0 1.0
C A:CYS1232 4.5 30.0 1.0
N A:HIS1234 4.6 31.5 1.0
CA A:CYS1225 4.6 30.0 1.0
C A:CYS1225 4.7 30.4 1.0
N A:GLY1228 4.8 29.9 1.0
O A:CYS1225 4.8 30.5 1.0
CB A:HIS1234 4.9 31.5 1.0
C A:CYS1227 4.9 29.4 1.0
N A:CYS1232 4.9 29.4 1.0

Zinc binding site 5 out of 8 in 2rfi

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Zinc binding site 5 out of 8 in the Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:16.8
occ:1.00
 SG B:CYS1078 2.3 14.6 1.0
SG B:CYS1044 2.3 17.6 1.0
SG B:CYS1074 2.4 15.2 1.0
SG B:CYS1031 2.4 16.3 1.0
CB B:CYS1074 3.3 14.9 1.0
CB B:CYS1031 3.3 17.5 1.0
CB B:CYS1078 3.3 15.7 1.0
CB B:CYS1044 3.4 15.8 1.0
CA B:CYS1074 3.6 14.3 1.0
N B:CYS1031 3.6 18.0 1.0
ZN B:ZN502 3.8 16.5 1.0
ZN B:ZN503 3.8 17.4 1.0
CA B:CYS1031 4.0 17.7 1.0
SG B:CYS1080 4.1 16.9 1.0
SG B:CYS1042 4.3 18.9 1.0
N B:ASN1075 4.5 14.5 1.0
N B:CYS1074 4.5 14.5 1.0
C B:TYR1030 4.6 17.9 1.0
C B:CYS1074 4.6 14.8 1.0
N B:CYS1044 4.6 16.0 1.0
CA B:CYS1078 4.6 15.0 1.0
CA B:CYS1044 4.7 15.7 1.0
SG B:CYS1037 4.7 17.7 1.0
C B:CYS1031 4.8 18.8 1.0
CA B:TYR1030 4.8 18.0 1.0
O B:CYS1031 4.8 18.1 1.0
O B:HOH1256 4.9 21.6 1.0

Zinc binding site 6 out of 8 in 2rfi

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Zinc binding site 6 out of 8 in the Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:16.5
occ:1.00
 SG B:CYS1084 2.3 16.5 1.0
SG B:CYS1080 2.3 16.9 1.0
SG B:CYS1037 2.3 17.7 1.0
SG B:CYS1074 2.4 15.2 1.0
CB B:CYS1080 3.2 16.4 1.0
CB B:CYS1074 3.2 14.9 1.0
CB B:CYS1084 3.2 18.7 1.0
CB B:CYS1037 3.3 22.1 1.0
ZN B:ZN503 3.8 17.4 1.0
ZN B:ZN501 3.8 16.8 1.0
SG B:CYS1031 4.0 16.3 1.0
NE B:ARG1087 4.3 19.4 1.0
NH1 B:ARG1087 4.4 18.3 1.0
CB B:ASN1086 4.6 17.0 1.0
CA B:CYS1080 4.6 16.1 1.0
CA B:CYS1074 4.6 14.3 1.0
CA B:CYS1084 4.6 18.8 1.0
CA B:CYS1037 4.7 22.7 1.0
CZ B:ARG1087 4.7 17.4 1.0
O B:TRP1081 4.8 18.9 1.0
N B:ASN1086 4.9 17.9 1.0
CB B:CYS1078 5.0 15.7 1.0

Zinc binding site 7 out of 8 in 2rfi

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Zinc binding site 7 out of 8 in the Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:17.4
occ:1.00
 SG B:CYS1042 2.3 18.9 1.0
SG B:CYS1033 2.3 19.2 1.0
SG B:CYS1037 2.4 17.7 1.0
SG B:CYS1031 2.4 16.3 1.0
CB B:CYS1031 3.1 17.5 1.0
CB B:CYS1033 3.2 24.4 1.0
CB B:CYS1042 3.3 19.9 1.0
CB B:CYS1037 3.3 22.1 1.0
ZN B:ZN502 3.8 16.5 1.0
ZN B:ZN501 3.8 16.8 1.0
CA B:CYS1037 3.9 22.7 1.0
CA B:CYS1042 3.9 20.1 1.0
SG B:CYS1074 4.1 15.2 1.0
N B:CYS1033 4.4 24.3 1.0
CA B:CYS1033 4.4 24.9 1.0
CA B:CYS1031 4.5 17.7 1.0
O B:HOH1283 4.6 26.3 1.0
C B:CYS1042 4.7 18.9 1.0
N B:CYS1037 4.7 24.3 1.0
SG B:CYS1080 4.7 16.9 1.0
O B:HOH1260 4.8 22.0 1.0
N B:MET1043 4.8 18.0 1.0
CB B:CYS1080 4.8 16.4 1.0
C B:CYS1031 4.9 18.8 1.0
C B:CYS1037 5.0 23.8 1.0

Zinc binding site 8 out of 8 in 2rfi

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Zinc binding site 8 out of 8 in the Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Dimethylated H3K9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:43.7
occ:1.00
 SG B:CYS1227 2.0 53.3 1.0
SG B:CYS1225 2.4 54.9 1.0
SG B:CYS1172 2.5 38.8 1.0
SG B:CYS1232 2.8 56.4 1.0
CB B:CYS1227 3.2 54.5 1.0
CB B:CYS1172 3.4 35.6 1.0
CB B:CYS1225 3.5 55.3 1.0
CB B:CYS1232 3.5 56.0 1.0
N B:CYS1172 3.9 35.1 1.0
CA B:CYS1232 4.0 56.1 1.0
N B:CYS1227 4.1 54.8 1.0
CA B:CYS1227 4.2 54.5 1.0
CA B:CYS1172 4.3 35.5 1.0
CE1 B:HIS1170 4.4 34.8 1.0
ND1 B:HIS1170 4.5 34.5 1.0
N B:ARG1233 4.6 55.9 1.0
N B:GLY1228 4.6 55.0 1.0
CA B:CYS1225 4.8 55.3 1.0
C B:CYS1225 4.8 55.3 1.0
C B:CYS1227 4.8 54.7 1.0
C B:CYS1232 4.8 56.0 1.0
C B:HIS1171 4.9 34.9 1.0
CB B:SER1229 4.9 55.6 1.0
N B:HIS1234 4.9 55.9 1.0
O B:CYS1225 5.0 55.5 1.0
N B:SER1229 5.0 55.5 1.0

Reference:

H.Wu, J.Min, V.V.Lunin, T.Antoshenko, L.Dombrovski, H.Zeng, A.Allali-Hassani, V.Campagna-Slater, M.Vedadi, C.H.Arrowsmith, A.N.Plotnikov, M.Schapira. Structural Biology of Human H3K9 Methyltransferases Plos One V. 5 E8570 2010.
ISSN: ESSN 1932-6203
PubMed: 20084102
DOI: 10.1371/JOURNAL.PONE.0008570
Page generated: Wed Aug 20 05:37:55 2025

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