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Zinc in PDB 2igq: Human Euchromatic Histone Methyltransferase 1

Enzymatic activity of Human Euchromatic Histone Methyltransferase 1

All present enzymatic activity of Human Euchromatic Histone Methyltransferase 1:
2.1.1.43;

Protein crystallography data

The structure of Human Euchromatic Histone Methyltransferase 1, PDB code: 2igq was solved by J.Min, H.Wu, T.Antoshenko, P.Loppnau, J.Weigelt, 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) 42.11 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.520, 95.863, 102.124, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 23.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Euchromatic Histone Methyltransferase 1 (pdb code 2igq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Human Euchromatic Histone Methyltransferase 1, PDB code: 2igq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2igq

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Zinc binding site 1 out of 8 in the Human Euchromatic Histone Methyltransferase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Euchromatic Histone Methyltransferase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:24.2
occ:1.00
 SG A:CYS1074 2.2 21.8 1.0
SG A:CYS1078 2.3 23.4 1.0
SG A:CYS1044 2.3 23.1 1.0
SG A:CYS1031 2.4 23.8 1.0
CB A:CYS1074 3.2 18.8 1.0
CB A:CYS1031 3.2 26.0 1.0
CB A:CYS1044 3.3 22.6 1.0
CB A:CYS1078 3.4 26.6 1.0
CA A:CYS1074 3.6 21.0 1.0
N A:CYS1031 3.6 26.4 1.0
ZN A:ZN503 3.7 25.7 1.0
ZN A:ZN502 3.7 23.4 1.0
CA A:CYS1031 4.0 26.2 1.0
SG A:CYS1080 4.0 22.4 1.0
SG A:CYS1042 4.2 25.4 1.0
N A:ASN1075 4.5 22.4 1.0
N A:CYS1074 4.5 19.4 1.0
CA A:CYS1044 4.6 23.7 1.0
C A:TYR1030 4.6 25.9 1.0
C A:CYS1074 4.6 21.4 1.0
N A:CYS1044 4.7 24.7 1.0
CA A:CYS1078 4.7 25.9 1.0
SG A:CYS1037 4.7 28.2 1.0
C A:CYS1031 4.8 27.0 1.0
CA A:TYR1030 4.9 26.2 1.0
O A:HOH1323 4.9 25.9 1.0
O A:CYS1031 4.9 26.2 1.0

Zinc binding site 2 out of 8 in 2igq

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Zinc binding site 2 out of 8 in the Human Euchromatic Histone Methyltransferase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Euchromatic Histone Methyltransferase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:23.4
occ:1.00
 SG A:CYS1080 2.2 22.4 1.0
SG A:CYS1084 2.3 22.8 1.0
SG A:CYS1074 2.3 21.8 1.0
SG A:CYS1037 2.3 28.2 1.0
CB A:CYS1074 3.1 18.8 1.0
CB A:CYS1080 3.2 25.0 1.0
CB A:CYS1084 3.2 22.2 1.0
CB A:CYS1037 3.3 27.8 1.0
ZN A:ZN503 3.7 25.7 1.0
ZN A:ZN501 3.7 24.2 1.0
SG A:CYS1031 4.0 23.8 1.0
NE A:ARG1087 4.3 24.3 1.0
NH1 A:ARG1087 4.3 23.3 1.0
CA A:CYS1074 4.6 21.0 1.0
CB A:ASN1086 4.6 23.1 1.0
CA A:CYS1080 4.7 25.4 1.0
CA A:CYS1084 4.7 24.2 1.0
CZ A:ARG1087 4.7 24.1 1.0
CA A:CYS1037 4.7 28.8 1.0
O A:TRP1081 4.8 26.4 1.0
SG A:CYS1042 4.9 25.4 1.0
N A:ASN1086 5.0 23.9 1.0

Zinc binding site 3 out of 8 in 2igq

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Zinc binding site 3 out of 8 in the Human Euchromatic Histone Methyltransferase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Euchromatic Histone Methyltransferase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:25.7
occ:1.00
 SG A:CYS1042 2.2 25.4 1.0
SG A:CYS1031 2.2 23.8 1.0
SG A:CYS1037 2.4 28.2 1.0
SG A:CYS1033 2.4 29.5 1.0
CB A:CYS1031 3.1 26.0 1.0
CB A:CYS1037 3.2 27.8 1.0
CB A:CYS1042 3.3 26.7 1.0
CB A:CYS1033 3.3 30.5 1.0
ZN A:ZN502 3.7 23.4 1.0
ZN A:ZN501 3.7 24.2 1.0
CA A:CYS1037 3.9 28.8 1.0
CA A:CYS1042 3.9 26.6 1.0
SG A:CYS1074 3.9 21.8 1.0
N A:CYS1033 4.5 30.2 1.0
CA A:CYS1033 4.5 31.6 1.0
O A:HOH1282 4.5 24.8 1.0
CA A:CYS1031 4.6 26.2 1.0
SG A:CYS1080 4.6 22.4 1.0
O A:HOH1287 4.6 29.1 1.0
N A:CYS1037 4.7 28.8 1.0
C A:CYS1042 4.7 25.9 1.0
CB A:CYS1080 4.8 25.0 1.0
N A:MET1043 4.9 25.4 1.0
C A:CYS1037 5.0 29.6 1.0
C A:CYS1031 5.0 27.0 1.0

Zinc binding site 4 out of 8 in 2igq

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Zinc binding site 4 out of 8 in the Human Euchromatic Histone Methyltransferase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Euchromatic Histone Methyltransferase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:43.0
occ:1.00
 SG A:CYS1227 2.2 40.5 1.0
SG A:CYS1225 2.3 51.6 1.0
SG A:CYS1172 2.5 37.4 1.0
SG A:CYS1232 2.6 52.7 1.0
CB A:CYS1232 3.2 53.0 1.0
CB A:CYS1227 3.2 45.4 1.0
CB A:CYS1172 3.3 34.4 1.0
CB A:CYS1225 3.6 51.3 1.0
CA A:CYS1232 3.8 53.4 1.0
N A:CYS1227 4.0 47.0 1.0
N A:CYS1172 4.1 32.6 1.0
CA A:CYS1227 4.2 45.7 1.0
CA A:CYS1172 4.3 34.0 1.0
N A:ARG1233 4.3 53.9 1.0
CE1 A:HIS1170 4.4 34.9 1.0
C A:CYS1232 4.5 53.8 1.0
ND1 A:HIS1170 4.6 34.6 1.0
CB A:SER1229 4.7 48.2 1.0
N A:HIS1234 4.7 55.0 1.0
CA A:CYS1225 4.8 51.3 1.0
C A:CYS1225 4.8 50.6 1.0
N A:GLY1228 4.8 46.3 1.0
C A:CYS1227 4.9 46.1 1.0
N A:SER1229 4.9 48.3 1.0
CB A:HIS1234 5.0 55.5 1.0

Zinc binding site 5 out of 8 in 2igq

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Zinc binding site 5 out of 8 in the Human Euchromatic Histone Methyltransferase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Euchromatic Histone Methyltransferase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:26.1
occ:1.00
 SG B:CYS1074 2.3 21.5 1.0
SG B:CYS1044 2.3 25.9 1.0
SG B:CYS1078 2.4 23.6 1.0
SG B:CYS1031 2.4 22.3 1.0
CB B:CYS1074 3.3 19.4 1.0
CB B:CYS1031 3.3 23.1 1.0
CB B:CYS1078 3.3 23.1 1.0
CB B:CYS1044 3.4 26.7 1.0
N B:CYS1031 3.6 23.8 1.0
CA B:CYS1074 3.6 21.7 1.0
ZN B:ZN503 3.8 25.5 1.0
ZN B:ZN502 3.8 23.7 1.0
CA B:CYS1031 4.0 24.1 1.0
SG B:CYS1080 4.1 22.2 1.0
SG B:CYS1042 4.3 23.5 1.0
C B:TYR1030 4.5 26.4 1.0
N B:ASN1075 4.6 24.1 1.0
N B:CYS1074 4.6 20.4 1.0
CA B:CYS1078 4.6 24.1 1.0
CA B:CYS1044 4.6 27.8 1.0
N B:CYS1044 4.6 28.1 1.0
C B:CYS1074 4.7 22.9 1.0
CA B:TYR1030 4.7 27.1 1.0
O B:HOH1269 4.7 22.9 1.0
SG B:CYS1037 4.7 23.4 1.0
C B:CYS1031 4.8 24.0 1.0
ND2 B:ASN1086 4.9 20.8 1.0

Zinc binding site 6 out of 8 in 2igq

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Zinc binding site 6 out of 8 in the Human Euchromatic Histone Methyltransferase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human Euchromatic Histone Methyltransferase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:23.7
occ:1.00
 SG B:CYS1080 2.2 22.2 1.0
SG B:CYS1084 2.3 22.0 1.0
SG B:CYS1074 2.3 21.5 1.0
SG B:CYS1037 2.4 23.4 1.0
CB B:CYS1074 3.2 19.4 1.0
CB B:CYS1080 3.3 22.8 1.0
CB B:CYS1084 3.3 24.6 1.0
CB B:CYS1037 3.4 26.1 1.0
ZN B:ZN503 3.7 25.5 1.0
ZN B:ZN501 3.8 26.1 1.0
SG B:CYS1031 4.0 22.3 1.0
NH2 B:ARG1087 4.3 23.3 1.0
NE B:ARG1087 4.3 23.5 1.0
CB B:ASN1086 4.6 22.6 1.0
CA B:CYS1074 4.6 21.7 1.0
O B:TRP1081 4.7 23.9 1.0
CA B:CYS1080 4.7 23.8 1.0
CZ B:ARG1087 4.7 22.3 1.0
CA B:CYS1084 4.8 25.1 1.0
CA B:CYS1037 4.8 26.7 1.0
CB B:CYS1078 4.9 23.1 1.0

Zinc binding site 7 out of 8 in 2igq

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Zinc binding site 7 out of 8 in the Human Euchromatic Histone Methyltransferase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human Euchromatic Histone Methyltransferase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:25.5
occ:1.00
 SG B:CYS1031 2.3 22.3 1.0
SG B:CYS1042 2.3 23.5 1.0
SG B:CYS1037 2.3 23.4 1.0
SG B:CYS1033 2.4 23.0 1.0
CB B:CYS1031 3.2 23.1 1.0
CB B:CYS1033 3.2 24.6 1.0
CB B:CYS1037 3.3 26.1 1.0
CB B:CYS1042 3.3 24.4 1.0
ZN B:ZN502 3.7 23.7 1.0
ZN B:ZN501 3.8 26.1 1.0
CA B:CYS1042 3.9 24.4 1.0
SG B:CYS1074 3.9 21.5 1.0
CA B:CYS1037 4.0 26.7 1.0
N B:CYS1033 4.4 26.2 1.0
CA B:CYS1033 4.4 25.6 1.0
CA B:CYS1031 4.6 24.1 1.0
C B:CYS1042 4.6 25.0 1.0
O B:HOH1483 4.6 27.7 1.0
SG B:CYS1080 4.6 22.2 1.0
N B:MET1043 4.7 26.1 1.0
O B:HOH1254 4.7 24.7 1.0
CB B:CYS1080 4.8 22.8 1.0
N B:CYS1037 4.8 26.8 1.0
O B:HOH1336 4.9 41.2 1.0

Zinc binding site 8 out of 8 in 2igq

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Zinc binding site 8 out of 8 in the Human Euchromatic Histone Methyltransferase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human Euchromatic Histone Methyltransferase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:29.7
occ:1.00
 SG B:CYS1227 2.2 27.3 1.0
SG B:CYS1172 2.4 29.4 1.0
SG B:CYS1232 2.4 27.5 1.0
SG B:CYS1225 2.5 32.8 1.0
CB B:CYS1232 3.2 27.8 1.0
CB B:CYS1172 3.4 27.3 1.0
CB B:CYS1227 3.4 28.2 1.0
CB B:CYS1225 3.4 33.9 1.0
CA B:CYS1232 3.7 28.3 1.0
O B:HOH1297 4.0 25.7 1.0
N B:CYS1227 4.1 30.4 1.0
N B:CYS1172 4.1 26.0 1.0
CE1 B:HIS1170 4.2 25.5 1.0
N B:ARG1233 4.2 30.2 1.0
CA B:CYS1227 4.3 29.0 1.0
CA B:CYS1172 4.4 27.1 1.0
C B:CYS1232 4.4 29.2 1.0
ND1 B:HIS1170 4.5 29.0 1.0
N B:HIS1234 4.6 34.0 1.0
CA B:CYS1225 4.7 33.8 1.0
C B:CYS1225 4.7 33.3 1.0
N B:GLY1228 4.8 29.1 1.0
C B:CYS1227 4.9 29.0 1.0
CB B:SER1229 4.9 26.9 1.0
O B:CYS1225 4.9 33.6 1.0
N B:CYS1232 5.0 27.7 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: Thu Oct 17 00:54:11 2024

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