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Zinc in PDB 4i51: Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A

Enzymatic activity of Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A

All present enzymatic activity of Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A:
2.1.1.43;

Protein crystallography data

The structure of Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A, PDB code: 4i51 was solved by A.Dong, H.Zeng, J.R.Walker, K.Islam, C.Bountra, C.H.Arrowsmith, A.M.Edwards, M.Lou, J.Min, H.Wu, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.78 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.497, 83.800, 95.052, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 19.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A (pdb code 4i51). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A, PDB code: 4i51:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4i51

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Zinc binding site 1 out of 8 in the Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3002

b:21.1
occ:1.00
 SG A:CYS1074 2.3 19.4 1.0
SG A:CYS1078 2.3 18.7 1.0
SG A:CYS1044 2.4 19.8 1.0
SG A:CYS1031 2.4 21.3 1.0
CB A:CYS1074 3.2 19.8 1.0
CB A:CYS1078 3.3 18.0 1.0
CB A:CYS1031 3.4 21.4 1.0
CB A:CYS1044 3.4 18.3 1.0
CA A:CYS1074 3.5 18.8 1.0
N A:CYS1031 3.6 20.0 1.0
ZN A:ZN3003 3.8 20.6 1.0
ZN A:ZN3004 3.8 22.3 1.0
CA A:CYS1031 4.0 21.9 1.0
SG A:CYS1080 4.1 21.2 1.0
SG A:CYS1042 4.3 21.1 1.0
N A:CYS1074 4.4 19.1 1.0
N A:ASN1075 4.5 18.8 1.0
CA A:CYS1078 4.6 18.9 1.0
C A:TYR1030 4.6 21.1 1.0
C A:CYS1074 4.6 18.9 1.0
SG A:CYS1037 4.7 20.6 1.0
CA A:CYS1044 4.7 20.3 1.0
N A:CYS1044 4.7 21.3 1.0
O A:HOH3204 4.8 21.3 1.0
C A:CYS1031 4.9 22.5 1.0
CA A:TYR1030 4.9 21.7 1.0
O A:CYS1031 4.9 21.9 1.0
ND2 A:ASN1086 4.9 17.1 1.0

Zinc binding site 2 out of 8 in 4i51

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Zinc binding site 2 out of 8 in the Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3003

b:20.6
occ:1.00
 SG A:CYS1084 2.3 20.3 1.0
SG A:CYS1037 2.3 20.6 1.0
SG A:CYS1080 2.3 21.2 1.0
SG A:CYS1074 2.3 19.4 1.0
CB A:CYS1074 3.2 19.8 1.0
CB A:CYS1080 3.2 21.5 1.0
CB A:CYS1084 3.2 20.0 1.0
CB A:CYS1037 3.4 21.3 1.0
ZN A:ZN3004 3.8 22.3 1.0
ZN A:ZN3002 3.8 21.1 1.0
SG A:CYS1031 4.0 21.3 1.0
NE A:ARG1087 4.3 19.8 1.0
NH2 A:ARG1087 4.4 21.2 1.0
CB A:ASN1086 4.6 20.1 1.0
CA A:CYS1080 4.6 23.0 1.0
CA A:CYS1074 4.6 18.8 1.0
CA A:CYS1084 4.7 21.6 1.0
CA A:CYS1037 4.8 23.3 1.0
CZ A:ARG1087 4.8 22.6 1.0
O A:TRP1081 4.9 20.1 1.0
N A:ASN1086 4.9 20.9 1.0
CB A:CYS1078 4.9 18.0 1.0

Zinc binding site 3 out of 8 in 4i51

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Zinc binding site 3 out of 8 in the Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3004

b:22.3
occ:1.00
 SG A:CYS1042 2.3 21.1 1.0
SG A:CYS1031 2.3 21.3 1.0
SG A:CYS1033 2.3 23.6 1.0
SG A:CYS1037 2.4 20.6 1.0
CB A:CYS1031 3.1 21.4 1.0
CB A:CYS1033 3.2 24.1 1.0
CB A:CYS1042 3.2 21.8 1.0
CB A:CYS1037 3.3 21.3 1.0
ZN A:ZN3003 3.8 20.6 1.0
ZN A:ZN3002 3.8 21.1 1.0
CA A:CYS1042 3.9 23.5 1.0
CA A:CYS1037 3.9 23.3 1.0
SG A:CYS1074 4.0 19.4 1.0
N A:CYS1033 4.4 22.7 1.0
CA A:CYS1033 4.4 24.9 1.0
CA A:CYS1031 4.5 21.9 1.0
C A:CYS1042 4.7 23.6 1.0
N A:CYS1037 4.7 24.8 1.0
O A:HOH3146 4.8 28.2 1.0
SG A:CYS1080 4.8 21.2 1.0
N A:MET1043 4.8 23.7 1.0
CB A:CYS1080 4.9 21.5 1.0
O A:HOH3300 4.9 22.4 1.0
C A:CYS1031 5.0 22.5 1.0

Zinc binding site 4 out of 8 in 4i51

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Zinc binding site 4 out of 8 in the Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3005

b:38.5
occ:1.00
 SG A:CYS1232 2.3 46.9 1.0
SG A:CYS1172 2.3 35.9 1.0
SG A:CYS1225 2.4 37.9 1.0
SG A:CYS1227 2.4 37.6 1.0
CB A:CYS1225 3.3 40.2 1.0
CB A:CYS1227 3.3 36.0 1.0
CB A:CYS1232 3.4 49.2 1.0
CB A:CYS1172 3.4 37.7 1.0
CA A:CYS1232 3.8 49.5 1.0
N A:CYS1227 4.0 39.0 1.0
N A:CYS1172 4.0 33.4 1.0
NE2 A:HIS1170 4.2 30.3 1.0
CA A:CYS1227 4.2 39.2 1.0
N A:ARG1233 4.2 47.5 1.0
CA A:CYS1172 4.3 36.5 1.0
CD2 A:HIS1170 4.3 30.5 1.0
O A:HOH3188 4.4 46.1 1.0
C A:CYS1232 4.4 49.3 1.0
CA A:CYS1225 4.6 41.6 1.0
N A:HIS1234 4.6 51.2 1.0
C A:CYS1225 4.6 41.9 1.0
N A:GLY1228 4.8 42.0 1.0
O A:CYS1225 4.8 42.0 1.0
C A:CYS1227 4.9 40.9 1.0
N A:ARG1226 4.9 40.7 1.0
CB A:HIS1234 4.9 46.5 1.0

Zinc binding site 5 out of 8 in 4i51

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Zinc binding site 5 out of 8 in the Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3002

b:22.5
occ:1.00
 SG B:CYS1078 2.3 20.1 1.0
SG B:CYS1044 2.3 21.6 1.0
SG B:CYS1074 2.4 20.5 1.0
SG B:CYS1031 2.4 22.8 1.0
CB B:CYS1074 3.2 19.2 1.0
CB B:CYS1031 3.2 23.3 1.0
CB B:CYS1078 3.3 18.9 1.0
CB B:CYS1044 3.4 20.8 1.0
CA B:CYS1074 3.6 19.7 1.0
N B:CYS1031 3.6 22.9 1.0
ZN B:ZN3004 3.8 24.7 1.0
ZN B:ZN3003 3.8 23.1 1.0
CA B:CYS1031 4.0 22.8 1.0
SG B:CYS1080 4.2 22.1 1.0
SG B:CYS1042 4.3 24.3 1.0
N B:ASN1075 4.5 18.0 1.0
C B:TYR1030 4.5 23.4 1.0
CA B:CYS1078 4.6 21.1 1.0
N B:CYS1074 4.6 18.5 1.0
C B:CYS1074 4.6 19.2 1.0
SG B:CYS1037 4.7 24.2 1.0
CA B:CYS1044 4.7 20.6 1.0
N B:CYS1044 4.7 21.7 1.0
CA B:TYR1030 4.8 22.9 1.0
C B:CYS1031 4.8 25.1 1.0
O B:CYS1031 4.9 21.6 1.0
O B:HOH3202 5.0 23.1 1.0

Zinc binding site 6 out of 8 in 4i51

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Zinc binding site 6 out of 8 in the Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3003

b:23.1
occ:1.00
 SG B:CYS1037 2.2 24.2 1.0
SG B:CYS1084 2.3 22.9 1.0
SG B:CYS1080 2.3 22.1 1.0
SG B:CYS1074 2.4 20.5 1.0
CB B:CYS1084 3.2 22.4 1.0
CB B:CYS1080 3.2 23.4 1.0
CB B:CYS1074 3.2 19.2 1.0
CB B:CYS1037 3.3 26.0 1.0
ZN B:ZN3004 3.8 24.7 1.0
ZN B:ZN3002 3.8 22.5 1.0
SG B:CYS1031 4.0 22.8 1.0
NE B:ARG1087 4.3 23.7 1.0
NH2 B:ARG1087 4.3 24.2 1.0
CB B:ASN1086 4.6 24.6 1.0
CA B:CYS1080 4.6 24.9 1.0
CA B:CYS1084 4.7 24.1 1.0
CA B:CYS1074 4.7 19.7 1.0
CA B:CYS1037 4.7 28.2 1.0
CZ B:ARG1087 4.7 23.1 1.0
O B:TRP1081 4.8 23.4 1.0
N B:ASN1086 4.9 23.3 1.0
CB B:CYS1078 5.0 18.9 1.0

Zinc binding site 7 out of 8 in 4i51

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Zinc binding site 7 out of 8 in the Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3004

b:24.7
occ:1.00
 SG B:CYS1033 2.3 28.9 1.0
SG B:CYS1042 2.3 24.3 1.0
SG B:CYS1031 2.3 22.8 1.0
SG B:CYS1037 2.4 24.2 1.0
CB B:CYS1031 3.1 23.3 1.0
CB B:CYS1033 3.2 32.0 1.0
CB B:CYS1042 3.2 25.2 1.0
CB B:CYS1037 3.3 26.0 1.0
ZN B:ZN3003 3.8 23.1 1.0
ZN B:ZN3002 3.8 22.5 1.0
CA B:CYS1037 3.9 28.2 1.0
CA B:CYS1042 3.9 27.0 1.0
SG B:CYS1074 4.1 20.5 1.0
N B:CYS1033 4.4 30.1 1.0
CA B:CYS1033 4.4 35.3 1.0
O B:HOH3123 4.5 30.1 1.0
CA B:CYS1031 4.6 22.8 1.0
C B:CYS1042 4.7 25.5 1.0
N B:CYS1037 4.7 30.3 1.0
SG B:CYS1080 4.8 22.1 1.0
CB B:CYS1080 4.8 23.4 1.0
N B:MET1043 4.8 25.3 1.0
O B:HOH3119 4.9 30.3 1.0
C B:CYS1031 5.0 25.1 1.0
C B:CYS1037 5.0 30.6 1.0

Zinc binding site 8 out of 8 in 4i51

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Zinc binding site 8 out of 8 in the Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Methyltransferase Domain of Human Euchromatic Histone Methyltransferase 1, Mutant Y1211A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3005

b:54.1
occ:1.00
 SG B:CYS1172 2.3 53.5 1.0
SG B:CYS1232 2.3 62.6 1.0
SG B:CYS1225 2.4 59.3 1.0
SG B:CYS1227 2.7 56.4 1.0
CB B:CYS1232 3.2 68.5 1.0
CB B:CYS1172 3.4 55.1 1.0
CB B:CYS1225 3.4 60.2 1.0
CB B:CYS1227 3.6 53.0 1.0
CA B:CYS1232 3.8 68.4 1.0
N B:CYS1172 4.0 47.8 1.0
N B:ARG1233 4.1 65.7 1.0
N B:CYS1227 4.2 56.9 1.0
NE2 B:HIS1170 4.2 45.6 1.0
CA B:CYS1172 4.3 52.1 1.0
CD2 B:HIS1170 4.3 45.2 1.0
CA B:CYS1227 4.4 55.9 1.0
C B:CYS1232 4.4 69.4 1.0
N B:HIS1234 4.6 64.5 1.0
CA B:CYS1225 4.7 60.1 1.0
C B:CYS1225 4.7 61.8 1.0
O B:CYS1225 4.9 60.4 1.0
N B:GLY1228 5.0 60.3 1.0

Reference:

K.Islam, Y.Chen, H.Wu, I.R.Bothwell, G.J.Blum, H.Zeng, A.Dong, W.Zheng, J.Min, H.Deng, M.Luo. Defining Efficient Enzyme-Cofactor Pairs For Bioorthogonal Profiling of Protein Methylation. Proc.Natl.Acad.Sci.Usa V. 110 16778 2013.
ISSN: ISSN 0027-8424
PubMed: 24082136
DOI: 10.1073/PNAS.1216365110
Page generated: Wed Dec 16 05:23:20 2020

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