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

Go back to Zinc Binding Sites List in 8hfp
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

Go back to Zinc Binding Sites List in 8hfp
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

Go back to Zinc Binding Sites List in 8hfp
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

Go back to Zinc Binding Sites List in 8hfp
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

Go back to Zinc Binding Sites List in 8hfp
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: Thu Oct 31 07:14:03 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy