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Zinc in PDB 8hfp: Crystal Structure of the Methyl-Cpg-Binding Domain of SETDB2 in Complex with the Cysteine-Rich Domain of C11ORF46 Protein

Enzymatic activity of Crystal Structure of the Methyl-Cpg-Binding Domain of SETDB2 in Complex with the Cysteine-Rich Domain of C11ORF46 Protein

All present enzymatic activity of Crystal Structure of the Methyl-Cpg-Binding Domain of SETDB2 in Complex with the Cysteine-Rich Domain of C11ORF46 Protein:
2.1.1.366;

Protein crystallography data

The structure of Crystal Structure of the Methyl-Cpg-Binding Domain of SETDB2 in Complex with the Cysteine-Rich Domain of C11ORF46 Protein, PDB code: 8hfp was solved by Y.Mahana, M.Ariyoshi, M.Shirakawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.06 / 1.82
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.97, 69.97, 116.88, 90, 90, 120
R / Rfree (%) 18.6 / 22.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Methyl-Cpg-Binding Domain of SETDB2 in Complex with the Cysteine-Rich Domain of C11ORF46 Protein (pdb code 8hfp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Methyl-Cpg-Binding Domain of SETDB2 in Complex with the Cysteine-Rich Domain of C11ORF46 Protein, PDB code: 8hfp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8hfp

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Zinc binding site 1 out of 6 in the Crystal Structure of the Methyl-Cpg-Binding Domain of SETDB2 in Complex with the Cysteine-Rich Domain of C11ORF46 Protein


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 the Methyl-Cpg-Binding Domain of SETDB2 in Complex with the Cysteine-Rich Domain of C11ORF46 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:26.4
occ:1.00
 SG A:CYS28 2.3 27.9 1.0
SG A:CYS26 2.3 22.7 1.0
SG A:CYS36 2.4 25.4 1.0
SG A:CYS33 2.4 26.5 1.0
CB A:CYS28 3.1 27.1 1.0
CB A:CYS33 3.2 29.2 1.0
CB A:CYS26 3.2 23.6 1.0
CB A:CYS36 3.3 23.8 1.0
N A:CYS36 3.5 21.5 1.0
CA A:CYS36 4.1 23.5 1.0
O C:HOH318 4.2 43.1 1.0
N A:CYS28 4.2 24.4 1.0
CA A:CYS28 4.2 24.8 1.0
O C:HOH322 4.3 44.8 1.0
CA A:GLY35 4.4 24.5 1.0
C A:GLY35 4.4 24.7 1.0
N A:GLY35 4.5 25.4 1.0
CA A:CYS26 4.6 24.2 1.0
CA A:CYS33 4.6 26.9 1.0
NZ C:LYS61 4.7 38.1 1.0
CE1 A:PHE37 4.8 24.2 1.0
C A:CYS26 4.9 23.5 1.0
CD1 A:PHE37 5.0 21.8 1.0

Zinc binding site 2 out of 6 in 8hfp

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Zinc binding site 2 out of 6 in the Crystal Structure of the Methyl-Cpg-Binding Domain of SETDB2 in Complex with the Cysteine-Rich Domain of C11ORF46 Protein


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 the Methyl-Cpg-Binding Domain of SETDB2 in Complex with the Cysteine-Rich Domain of C11ORF46 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:24.9
occ:1.00
 SG A:CYS43 2.3 25.6 1.0
SG A:CYS52 2.3 24.8 1.0
SG A:CYS40 2.4 23.9 1.0
SG A:CYS48 2.4 23.4 1.0
CB A:CYS40 3.2 24.8 1.0
CB A:CYS52 3.3 23.2 1.0
CB A:CYS48 3.3 24.8 1.0
CB A:CYS43 3.4 25.3 1.0
CA A:CYS52 3.5 23.2 1.0
N A:CYS43 3.8 25.1 1.0
N A:ARG53 4.0 23.8 1.0
CA A:CYS43 4.2 25.5 1.0
C A:CYS52 4.3 23.6 1.0
O A:HOH209 4.4 31.6 1.0
CB A:ALA42 4.6 27.4 1.0
SG A:CYS54 4.6 28.6 1.0
CA A:CYS40 4.6 24.0 1.0
C A:ALA42 4.7 30.0 1.0
CB A:SER45 4.7 27.3 1.0
CA A:CYS48 4.7 22.6 1.0
N A:CYS52 4.8 23.6 1.0
N A:SER45 4.8 26.6 1.0
O A:HOH214 4.8 30.0 1.0
C A:CYS43 4.8 24.8 1.0
N A:GLY44 4.9 24.5 1.0
N A:CYS54 4.9 25.3 1.0

Zinc binding site 3 out of 6 in 8hfp

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Zinc binding site 3 out of 6 in the Crystal Structure of the Methyl-Cpg-Binding Domain of SETDB2 in Complex with the Cysteine-Rich Domain of C11ORF46 Protein


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 the Methyl-Cpg-Binding Domain of SETDB2 in Complex with the Cysteine-Rich Domain of C11ORF46 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:31.4
occ:1.00
 NE2 C:HIS14 2.2 33.1 1.0
SG C:CYS64 2.2 30.6 1.0
SG C:CYS16 2.2 34.0 1.0
SG C:CYS20 2.3 33.4 1.0
CD2 C:HIS14 3.0 35.1 1.0
CB C:CYS64 3.2 29.1 1.0
CB C:CYS16 3.3 34.3 1.0
CE1 C:HIS14 3.3 35.0 1.0
CB C:CYS20 3.3 38.0 1.0
CA C:CYS16 3.5 37.1 1.0
CE1 C:TYR77 4.1 24.1 1.0
CG C:HIS14 4.2 38.8 1.0
ND1 C:HIS14 4.3 32.5 1.0
N C:CYS16 4.3 40.8 1.0
OH C:TYR77 4.4 25.6 1.0
NH2 C:ARG66 4.5 39.0 1.0
CA C:CYS20 4.6 42.5 1.0
CA C:CYS64 4.6 29.2 1.0
C C:CYS16 4.7 36.6 1.0
CZ C:TYR77 4.8 25.7 1.0
N C:SER17 4.8 37.4 1.0
O C:CYS64 4.9 28.7 1.0
C C:ASP15 5.0 44.5 1.0

Zinc binding site 4 out of 6 in 8hfp

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Zinc binding site 4 out of 6 in the Crystal Structure of the Methyl-Cpg-Binding Domain of SETDB2 in Complex with the Cysteine-Rich Domain of C11ORF46 Protein


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 the Methyl-Cpg-Binding Domain of SETDB2 in Complex with the Cysteine-Rich Domain of C11ORF46 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:26.5
occ:1.00
 SG B:CYS28 2.3 26.3 1.0
SG B:CYS26 2.4 25.5 1.0
SG B:CYS36 2.4 25.0 1.0
SG B:CYS33 2.4 26.1 1.0
CB B:CYS28 3.1 24.4 1.0
CB B:CYS33 3.2 26.1 1.0
CB B:CYS26 3.2 24.8 1.0
CB B:CYS36 3.4 28.3 1.0
N B:CYS36 3.5 25.9 1.0
CA B:CYS36 4.0 25.7 1.0
O D:HOH317 4.1 32.7 1.0
N B:CYS28 4.2 21.7 1.0
CA B:CYS28 4.2 23.8 1.0
C B:GLY35 4.3 29.4 1.0
CA B:GLY35 4.4 25.6 1.0
O D:HOH324 4.4 41.9 1.0
N B:GLY35 4.5 25.5 1.0
CA B:CYS26 4.6 24.4 1.0
CA B:CYS33 4.6 26.3 1.0
NZ D:LYS61 4.6 32.4 1.0
CE1 B:PHE37 4.9 21.3 1.0
C B:CYS26 4.9 25.5 1.0

Zinc binding site 5 out of 6 in 8hfp

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Zinc binding site 5 out of 6 in the Crystal Structure of the Methyl-Cpg-Binding Domain of SETDB2 in Complex with the Cysteine-Rich Domain of C11ORF46 Protein


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 the Methyl-Cpg-Binding Domain of SETDB2 in Complex with the Cysteine-Rich Domain of C11ORF46 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn102

b:25.0
occ:1.00
 SG B:CYS52 2.3 26.2 1.0
SG B:CYS43 2.3 25.0 1.0
SG B:CYS40 2.4 24.8 1.0
SG B:CYS48 2.4 23.4 1.0
CB B:CYS40 3.1 23.5 1.0
CB B:CYS52 3.2 24.8 1.0
CB B:CYS48 3.4 24.1 1.0
CB B:CYS43 3.4 26.7 1.0
CA B:CYS52 3.5 24.4 1.0
N B:CYS43 3.8 27.8 1.0
N B:ARG53 3.9 22.6 1.0
C B:CYS52 4.2 25.5 1.0
CA B:CYS43 4.2 27.8 1.0
O B:HOH221 4.2 32.7 1.0
CA B:CYS40 4.6 24.7 1.0
CB B:ALA42 4.6 28.8 1.0
SG B:CYS54 4.6 28.6 1.0
N B:CYS54 4.8 26.0 1.0
N B:CYS52 4.8 24.1 1.0
CA B:CYS48 4.8 22.2 1.0
CB B:SER45 4.8 28.1 1.0
C B:CYS43 4.8 27.7 1.0
C B:ALA42 4.8 28.2 1.0
N B:SER45 4.9 26.0 1.0
O B:HOH216 4.9 29.7 1.0
N B:GLY44 4.9 26.9 1.0

Zinc binding site 6 out of 6 in 8hfp

Go back to Zinc Binding Sites List in 8hfp
Zinc binding site 6 out of 6 in the Crystal Structure of the Methyl-Cpg-Binding Domain of SETDB2 in Complex with the Cysteine-Rich Domain of C11ORF46 Protein


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 the Methyl-Cpg-Binding Domain of SETDB2 in Complex with the Cysteine-Rich Domain of C11ORF46 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:37.8
occ:1.00
 SG D:CYS64 1.9 34.5 1.0
NE2 D:HIS14 2.2 44.0 1.0
SG D:CYS16 2.4 41.8 1.0
SG D:CYS20 2.4 41.6 1.0
CE1 D:HIS14 3.0 45.9 1.0
CB D:CYS64 3.1 37.6 1.0
CB D:CYS20 3.3 43.4 1.0
CD2 D:HIS14 3.3 47.6 1.0
CB D:CYS16 3.4 39.3 1.0
CA D:CYS16 3.6 41.3 1.0
CE1 D:TYR77 4.1 29.4 1.0
ND1 D:HIS14 4.2 41.5 1.0
CG D:HIS14 4.4 50.0 1.0
OH D:TYR77 4.4 35.1 1.0
N D:CYS16 4.4 41.9 1.0
CA D:CYS64 4.5 37.6 1.0
CA D:CYS20 4.6 46.2 1.0
NH2 D:ARG66 4.7 44.2 1.0
O D:CYS64 4.8 37.3 1.0
C D:CYS16 4.8 35.5 1.0
N D:SER17 4.8 45.0 1.0
CZ D:TYR77 4.8 34.2 1.0
C D:CYS64 4.9 32.9 1.0
NE D:ARG66 5.0 33.8 1.0
C D:ASP15 5.0 50.6 1.0

Reference:

Y.Mahana, M.Ariyoshi, K.Nagao, C.Obuse, M.Shirakawa. Structural Evidence For Protein Binding By the Methyl-Cpg-Binding Domain of Setdb Proteins To Be Published.
Page generated: Fri Aug 22 10:46:42 2025

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