Zinc in PDB 7t02: Cryo-Em Structure of DNMT5 Pseudo-Ternary Complex Solved By Incubation with Hemimethylated Dna and Sam

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of DNMT5 Pseudo-Ternary Complex Solved By Incubation with Hemimethylated Dna and Sam (pdb code 7t02). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Cryo-Em Structure of DNMT5 Pseudo-Ternary Complex Solved By Incubation with Hemimethylated Dna and Sam, PDB code: 7t02:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 7t02

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Zinc binding site 1 out of 5 in the Cryo-Em Structure of DNMT5 Pseudo-Ternary Complex Solved By Incubation with Hemimethylated Dna and Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of DNMT5 Pseudo-Ternary Complex Solved By Incubation with Hemimethylated Dna and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2401

b:68.6
occ:1.00
SG A:CYS817 2.3 19.3 1.0
SG A:CYS840 2.3 21.6 1.0
SG A:CYS819 2.3 21.7 1.0
SG A:CYS843 2.3 22.6 1.0
CB A:CYS843 3.1 22.6 1.0
CB A:CYS819 3.5 21.7 1.0
CB A:CYS817 3.5 19.3 1.0
CB A:CYS840 3.9 21.6 1.0
N A:CYS843 4.1 22.6 1.0
CA A:CYS843 4.2 22.6 1.0
N A:CYS819 4.2 21.7 1.0
N A:CYS840 4.2 21.6 1.0
CA A:CYS819 4.5 21.7 1.0
CA A:CYS840 4.7 21.6 1.0
CA A:CYS817 4.8 19.3 1.0
C A:CYS817 4.8 19.3 1.0
N A:GLN818 4.9 20.6 1.0

Zinc binding site 2 out of 5 in 7t02

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Zinc binding site 2 out of 5 in the Cryo-Em Structure of DNMT5 Pseudo-Ternary Complex Solved By Incubation with Hemimethylated Dna and Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of DNMT5 Pseudo-Ternary Complex Solved By Incubation with Hemimethylated Dna and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2402

b:81.7
occ:1.00
ND1 A:HIS1348 2.0 37.4 1.0
SG A:CYS1274 2.3 51.1 1.0
SG A:CYS1271 2.3 58.7 1.0
SG A:CYS1200 2.3 59.0 1.0
CE1 A:HIS1348 2.7 37.4 1.0
CB A:CYS1271 3.1 58.7 1.0
CG A:HIS1348 3.2 37.4 1.0
CB A:CYS1274 3.3 51.1 1.0
CB A:CYS1200 3.4 59.0 1.0
CB A:HIS1348 3.7 37.4 1.0
NE2 A:HIS1348 3.9 37.4 1.0
N A:CYS1274 4.1 51.1 1.0
CD2 A:HIS1348 4.2 37.4 1.0
CA A:CYS1274 4.4 51.1 1.0
CG1 A:VAL1344 4.5 34.6 1.0
CA A:CYS1271 4.6 58.7 1.0
NH2 A:ARG1273 4.7 56.4 1.0
CA A:CYS1200 4.7 59.0 1.0
O A:VAL1344 4.7 34.6 1.0

Zinc binding site 3 out of 5 in 7t02

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Zinc binding site 3 out of 5 in the Cryo-Em Structure of DNMT5 Pseudo-Ternary Complex Solved By Incubation with Hemimethylated Dna and Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of DNMT5 Pseudo-Ternary Complex Solved By Incubation with Hemimethylated Dna and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2403

b:54.6
occ:1.00
O A:GLU834 2.0 27.7 1.0
ND1 A:HIS849 2.1 25.0 1.0
SG A:CYS835 2.3 27.4 1.0
SG A:CYS832 2.3 26.0 1.0
SG A:CYS1065 2.4 24.9 1.0
CE1 A:HIS849 2.7 25.0 1.0
C A:GLU834 3.2 27.7 1.0
CG A:HIS849 3.3 25.0 1.0
CG A:GLU834 3.7 27.7 1.0
CB A:CYS1065 3.7 24.9 1.0
CB A:CYS832 3.9 26.0 1.0
CB A:HIS849 3.9 25.0 1.0
CB A:CYS835 3.9 27.4 1.0
NE2 A:HIS849 4.0 25.0 1.0
O A:CYS835 4.0 27.4 1.0
CA A:GLU834 4.1 27.7 1.0
N A:GLU834 4.2 27.7 1.0
N A:CYS835 4.2 27.4 1.0
CD2 A:HIS849 4.3 25.0 1.0
CD2 A:LEU1062 4.3 20.2 1.0
CD A:GLU834 4.4 27.7 1.0
CA A:CYS835 4.4 27.4 1.0
CB A:GLU834 4.4 27.7 1.0
C A:CYS835 4.4 27.4 1.0
OE2 A:GLU834 4.7 27.7 1.0
CA A:CYS1065 4.7 24.9 1.0
CA A:HIS849 4.8 25.0 1.0
N A:GLN833 5.0 26.7 1.0

Zinc binding site 4 out of 5 in 7t02

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Zinc binding site 4 out of 5 in the Cryo-Em Structure of DNMT5 Pseudo-Ternary Complex Solved By Incubation with Hemimethylated Dna and Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of DNMT5 Pseudo-Ternary Complex Solved By Incubation with Hemimethylated Dna and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2404

b:158.8
occ:1.00
CB A:CYS2107 1.9 63.4 1.0
SG A:CYS2081 2.3 67.7 1.0
SG A:CYS2107 2.4 63.4 1.0
SG A:CYS2104 2.4 67.9 1.0
ND1 A:HIS2083 2.5 75.6 1.0
CB A:CYS2104 2.7 67.9 1.0
CE1 A:HIS2083 3.2 75.6 1.0
CA A:CYS2107 3.4 63.4 1.0
CG A:HIS2083 3.6 75.6 1.0
N A:CYS2107 3.8 63.4 1.0
CB A:CYS2081 3.9 67.7 1.0
CB A:HIS2083 4.1 75.6 1.0
CA A:CYS2104 4.1 67.9 1.0
C A:CYS2107 4.3 63.4 1.0
O A:CYS2104 4.4 67.9 1.0
NE2 A:HIS2083 4.4 75.6 1.0
C A:CYS2104 4.6 67.9 1.0
CD2 A:HIS2083 4.6 75.6 1.0
O A:CYS2107 4.7 63.4 1.0
N A:CYS2104 4.7 67.9 1.0
CA A:CYS2081 4.8 67.7 1.0
N A:HIS2083 5.0 75.6 1.0

Zinc binding site 5 out of 5 in 7t02

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Zinc binding site 5 out of 5 in the Cryo-Em Structure of DNMT5 Pseudo-Ternary Complex Solved By Incubation with Hemimethylated Dna and Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of DNMT5 Pseudo-Ternary Complex Solved By Incubation with Hemimethylated Dna and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2405

b:72.1
occ:1.00
SG A:CYS2123 2.3 38.2 1.0
SG A:CYS2099 2.3 37.8 1.0
CB A:CYS2099 2.3 37.8 1.0
SG A:CYS2117 2.3 40.6 1.0
ND1 A:HIS2101 2.6 38.3 1.0
CE1 A:HIS2101 2.9 38.3 1.0
CB A:CYS2123 3.3 38.2 1.0
CB A:CYS2117 3.6 40.6 1.0
CA A:CYS2099 3.8 37.8 1.0
CG A:HIS2101 3.9 38.3 1.0
CB A:ALA2125 4.0 26.4 1.0
NE2 A:HIS2101 4.2 38.3 1.0
N A:CYS2099 4.5 37.8 1.0
N A:GLY2100 4.6 37.2 1.0
CB A:HIS2101 4.7 38.3 1.0
C A:CYS2099 4.7 37.8 1.0
CA A:CYS2123 4.7 38.2 1.0
CD2 A:HIS2101 4.7 38.3 1.0
N A:HIS2101 4.9 38.3 1.0
CA A:CYS2117 4.9 40.6 1.0
CA A:ALA2125 4.9 26.4 1.0

Reference:

J.Wang, S.Catania, C.Wang, M.J.De La Cruz, B.Rao, H.D.Madhani, D.J.Patel. Structural Insights Into DNMT5-Mediated Atp-Dependent High-Fidelity Epigenome Maintenance. Mol.Cell V. 82 1186 2022.
ISSN: ISSN 1097-2765
PubMed: 35202575
DOI: 10.1016/J.MOLCEL.2022.01.028
Page generated: Sat Apr 8 03:24:09 2023

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