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Zinc in PDB 3hna: Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Mono-Methylated H3K9 Peptide

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

All present enzymatic activity of Crystal Structure of Catalytic Domain of Human Euchromatic Histone Methyltransferase 1 in Complex with Sah and Mono-Methylated 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 Mono-Methylated H3K9 Peptide, PDB code: 3hna was solved by J.Min, H.Wu, P.Loppnau, J.Wleigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, A.N.Plotnikov, Structural Genomics Consortium(Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.75 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.526, 83.372, 95.130, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 19.3

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 Mono-Methylated H3K9 Peptide (pdb code 3hna). 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 Mono-Methylated H3K9 Peptide, PDB code: 3hna:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3hna

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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 Mono-Methylated 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 Mono-Methylated H3K9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:9.2
occ:1.00
 SG A:CYS1044 2.3 9.7 1.0
SG A:CYS1078 2.3 8.4 1.0
SG A:CYS1074 2.4 8.3 1.0
SG A:CYS1031 2.4 9.2 1.0
CB A:CYS1074 3.2 9.0 1.0
CB A:CYS1031 3.2 9.3 1.0
CB A:CYS1078 3.3 9.2 1.0
CB A:CYS1044 3.4 9.1 1.0
N A:CYS1031 3.6 9.2 1.0
CA A:CYS1074 3.6 8.0 1.0
ZN A:ZN502 3.8 8.9 1.0
ZN A:ZN503 3.8 9.7 1.0
CA A:CYS1031 4.0 9.5 1.0
SG A:CYS1080 4.1 9.2 1.0
SG A:CYS1042 4.2 9.9 1.0
N A:ASN1075 4.5 7.9 1.0
N A:CYS1074 4.5 7.8 1.0
C A:TYR1030 4.6 10.1 1.0
CA A:CYS1078 4.6 9.8 1.0
CA A:CYS1044 4.6 9.6 1.0
C A:CYS1074 4.7 8.2 1.0
N A:CYS1044 4.7 9.7 1.0
SG A:CYS1037 4.7 8.7 1.0
C A:CYS1031 4.8 9.7 1.0
CA A:TYR1030 4.8 9.7 1.0
O A:CYS1031 4.9 9.2 1.0
O A:HOH51 4.9 13.7 1.0

Zinc binding site 2 out of 8 in 3hna

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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 Mono-Methylated 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 Mono-Methylated H3K9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:8.9
occ:1.00
 SG A:CYS1080 2.3 9.2 1.0
SG A:CYS1037 2.3 8.7 1.0
SG A:CYS1084 2.4 8.4 1.0
SG A:CYS1074 2.4 8.3 1.0
CB A:CYS1074 3.2 9.0 1.0
CB A:CYS1080 3.2 9.3 1.0
CB A:CYS1084 3.2 9.2 1.0
CB A:CYS1037 3.4 11.7 1.0
ZN A:ZN503 3.8 9.7 1.0
ZN A:ZN501 3.8 9.2 1.0
SG A:CYS1031 4.0 9.2 1.0
NE A:ARG1087 4.3 10.2 1.0
NH2 A:ARG1087 4.4 11.6 1.0
CB A:ASN1086 4.6 8.4 1.0
CA A:CYS1080 4.6 9.3 1.0
CA A:CYS1074 4.6 8.0 1.0
CA A:CYS1084 4.7 9.7 1.0
CA A:CYS1037 4.7 12.5 1.0
CZ A:ARG1087 4.8 11.1 1.0
O A:TRP1081 4.8 8.9 1.0
CB A:CYS1078 5.0 9.2 1.0
N A:ASN1086 5.0 9.8 1.0
SG A:CYS1042 5.0 9.9 1.0

Zinc binding site 3 out of 8 in 3hna

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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 Mono-Methylated 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 Mono-Methylated H3K9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:9.7
occ:1.00
 SG A:CYS1042 2.3 9.9 1.0
SG A:CYS1033 2.3 11.1 1.0
SG A:CYS1037 2.3 8.7 1.0
SG A:CYS1031 2.4 9.2 1.0
CB A:CYS1031 3.1 9.3 1.0
CB A:CYS1042 3.2 11.6 1.0
CB A:CYS1037 3.2 11.7 1.0
CB A:CYS1033 3.3 12.2 1.0
ZN A:ZN502 3.8 8.9 1.0
ZN A:ZN501 3.8 9.2 1.0
CA A:CYS1037 3.9 12.5 1.0
CA A:CYS1042 3.9 12.4 1.0
SG A:CYS1074 4.1 8.3 1.0
N A:CYS1033 4.4 11.9 1.0
CA A:CYS1033 4.4 12.3 1.0
CA A:CYS1031 4.6 9.5 1.0
O A:HOH48 4.6 13.7 1.0
N A:CYS1037 4.7 12.6 1.0
C A:CYS1042 4.7 11.4 1.0
SG A:CYS1080 4.7 9.2 1.0
CB A:CYS1080 4.7 9.3 1.0
O A:HOH78 4.8 15.5 1.0
N A:MET1043 4.9 10.9 1.0
C A:CYS1031 4.9 9.7 1.0
N A:CYS1042 5.0 14.3 1.0

Zinc binding site 4 out of 8 in 3hna

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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 Mono-Methylated 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 Mono-Methylated H3K9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:15.3
occ:1.00
 SG A:CYS1232 2.3 18.4 1.0
SG A:CYS1225 2.3 14.8 1.0
SG A:CYS1227 2.4 16.7 1.0
SG A:CYS1172 2.5 15.4 1.0
CB A:CYS1232 3.3 21.1 1.0
CB A:CYS1225 3.3 16.5 1.0
CB A:CYS1227 3.4 17.1 1.0
CB A:CYS1172 3.4 16.0 1.0
CA A:CYS1232 3.7 21.4 1.0
N A:CYS1227 4.0 17.4 1.0
O A:HOH185 4.1 21.1 1.0
N A:CYS1172 4.1 14.3 1.0
CE1 A:HIS1170 4.2 10.6 1.0
CA A:CYS1227 4.2 17.4 1.0
N A:ARG1233 4.2 21.5 1.0
CA A:CYS1172 4.4 16.0 1.0
C A:CYS1232 4.4 22.0 1.0
ND1 A:HIS1170 4.5 13.8 1.0
CA A:CYS1225 4.6 16.7 1.0
N A:HIS1234 4.6 20.8 1.0
C A:CYS1225 4.6 17.8 1.0
O A:CYS1225 4.8 18.6 1.0
N A:GLY1228 4.8 18.9 1.0
CB A:HIS1234 4.9 20.1 1.0
C A:CYS1227 4.9 18.1 1.0
N A:CYS1232 5.0 21.9 1.0

Zinc binding site 5 out of 8 in 3hna

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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 Mono-Methylated 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 Mono-Methylated H3K9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:9.4
occ:1.00
 SG B:CYS1044 2.3 9.9 1.0
SG B:CYS1078 2.3 8.5 1.0
SG B:CYS1074 2.4 8.6 1.0
SG B:CYS1031 2.4 8.5 1.0
CB B:CYS1074 3.2 8.8 1.0
CB B:CYS1031 3.3 9.8 1.0
CB B:CYS1078 3.3 10.0 1.0
CB B:CYS1044 3.4 8.9 1.0
N B:CYS1031 3.6 9.5 1.0
CA B:CYS1074 3.6 7.9 1.0
ZN B:ZN502 3.8 9.0 1.0
ZN B:ZN503 3.8 9.4 1.0
CA B:CYS1031 4.0 9.4 1.0
SG B:CYS1080 4.2 8.9 1.0
SG B:CYS1042 4.3 9.4 1.0
N B:ASN1075 4.5 8.7 1.0
N B:CYS1074 4.5 7.7 1.0
CA B:CYS1078 4.6 9.7 1.0
C B:TYR1030 4.6 10.8 1.0
C B:CYS1074 4.6 9.1 1.0
N B:CYS1044 4.7 10.9 1.0
CA B:CYS1044 4.7 10.3 1.0
SG B:CYS1037 4.7 9.1 1.0
C B:CYS1031 4.8 9.7 1.0
O B:HOH68 4.8 15.0 1.0
CA B:TYR1030 4.8 11.2 1.0
O B:CYS1031 4.9 10.0 1.0

Zinc binding site 6 out of 8 in 3hna

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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 Mono-Methylated 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 Mono-Methylated H3K9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:9.0
occ:1.00
 SG B:CYS1080 2.3 8.9 1.0
SG B:CYS1084 2.3 9.2 1.0
SG B:CYS1037 2.3 9.1 1.0
SG B:CYS1074 2.4 8.6 1.0
CB B:CYS1074 3.2 8.8 1.0
CB B:CYS1080 3.2 9.7 1.0
CB B:CYS1084 3.2 9.5 1.0
CB B:CYS1037 3.3 9.8 1.0
ZN B:ZN503 3.8 9.4 1.0
ZN B:ZN501 3.8 9.4 1.0
SG B:CYS1031 4.0 8.5 1.0
NE B:ARG1087 4.3 9.6 1.0
NH2 B:ARG1087 4.4 12.0 1.0
CB B:ASN1086 4.6 8.1 1.0
CA B:CYS1074 4.6 7.9 1.0
CA B:CYS1080 4.7 9.8 1.0
CA B:CYS1084 4.7 10.0 1.0
CA B:CYS1037 4.7 10.8 1.0
CZ B:ARG1087 4.7 10.7 1.0
N B:ASN1086 4.9 10.0 1.0
O B:TRP1081 4.9 10.4 1.0
CB B:CYS1078 4.9 10.0 1.0

Zinc binding site 7 out of 8 in 3hna

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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 Mono-Methylated 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 Mono-Methylated H3K9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:9.4
occ:1.00
 SG B:CYS1033 2.3 10.3 1.0
SG B:CYS1042 2.3 9.4 1.0
SG B:CYS1031 2.4 8.5 1.0
SG B:CYS1037 2.4 9.1 1.0
CB B:CYS1031 3.1 9.8 1.0
CB B:CYS1033 3.2 10.5 1.0
CB B:CYS1042 3.3 10.6 1.0
CB B:CYS1037 3.3 9.8 1.0
ZN B:ZN502 3.8 9.0 1.0
ZN B:ZN501 3.8 9.4 1.0
CA B:CYS1037 3.9 10.8 1.0
CA B:CYS1042 3.9 10.8 1.0
SG B:CYS1074 4.1 8.6 1.0
N B:CYS1033 4.4 10.3 1.0
CA B:CYS1033 4.4 11.0 1.0
O B:HOH38 4.5 13.0 1.0
CA B:CYS1031 4.6 9.4 1.0
C B:CYS1042 4.7 11.0 1.0
N B:CYS1037 4.7 11.1 1.0
N B:MET1043 4.8 11.4 1.0
SG B:CYS1080 4.8 8.9 1.0
O B:HOH59 4.8 14.4 1.0
CB B:CYS1080 4.9 9.7 1.0
O B:HOH94 5.0 16.2 1.0

Zinc binding site 8 out of 8 in 3hna

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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 Mono-Methylated 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 Mono-Methylated H3K9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:14.3
occ:1.00
 SG B:CYS1232 2.3 15.5 1.0
SG B:CYS1225 2.4 14.1 1.0
SG B:CYS1227 2.4 14.5 1.0
SG B:CYS1172 2.4 13.3 1.0
CB B:CYS1225 3.3 17.4 1.0
CB B:CYS1232 3.3 16.7 1.0
CB B:CYS1227 3.4 15.4 1.0
CB B:CYS1172 3.4 14.6 1.0
CA B:CYS1232 3.7 16.9 1.0
N B:CYS1172 4.1 12.6 1.0
O B:HOH162 4.1 20.1 1.0
N B:CYS1227 4.1 16.6 1.0
CA B:CYS1227 4.3 16.0 1.0
N B:ARG1233 4.3 18.9 1.0
CE1 B:HIS1170 4.3 9.1 1.0
CA B:CYS1172 4.3 13.7 1.0
ND1 B:HIS1170 4.4 13.8 1.0
C B:CYS1232 4.4 18.2 1.0
CA B:CYS1225 4.6 17.3 1.0
N B:HIS1234 4.6 20.8 1.0
C B:CYS1225 4.7 17.8 1.0
N B:GLY1228 4.8 16.5 1.0
O B:CYS1225 4.9 18.8 1.0
C B:CYS1227 4.9 16.2 1.0
CB B:HIS1234 4.9 20.6 1.0
N B:CYS1232 5.0 16.8 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: Sat Oct 26 06:26:27 2024

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