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Zinc in PDB 5grq: Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide

Enzymatic activity of Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide

All present enzymatic activity of Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide:
3.6.4.12;

Protein crystallography data

The structure of Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide, PDB code: 5grq was solved by H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.34 / 1.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.428, 56.217, 102.917, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 17.9

Other elements in 5grq:

The structure of Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide (pdb code 5grq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide, PDB code: 5grq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 5grq

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Zinc binding site 1 out of 11 in the Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide


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 Dhb Domain of Daxx in Complex with An Atrx Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn207

b:11.2
occ:0.97
 OE1 A:GLU104 2.0 10.7 1.0
NE2 A:HIS137 2.1 11.3 1.0
CL A:CL204 2.2 12.1 1.0
CL A:CL205 2.3 12.0 1.0
CD A:GLU104 2.8 11.9 1.0
OE2 A:GLU104 3.0 12.4 1.0
CD2 A:HIS137 3.0 11.0 1.0
CE1 A:HIS137 3.1 9.0 1.0
O A:HOH388 3.9 22.6 1.0
CD1 A:PHE99 3.9 11.1 1.0
O B:HOH327 4.0 30.6 1.0
O1 A:GOL203 4.1 34.1 1.0
ND1 A:HIS137 4.1 10.0 1.0
CG A:HIS137 4.1 8.9 1.0
CG A:GLU104 4.2 9.2 1.0
C1 A:GOL203 4.4 32.3 1.0
CE1 A:PHE99 4.4 10.8 1.0
O A:HOH380 4.5 17.3 1.0
N B:LYS56 4.6 12.5 1.0
CB A:GLU104 4.7 9.1 1.0
CB B:LYS56 4.8 14.6 1.0
CG A:PHE99 4.8 9.8 1.0
O A:HOH401 4.9 19.4 1.0
CG B:LYS56 4.9 19.6 1.0
CB A:PHE99 4.9 10.0 1.0

Zinc binding site 2 out of 11 in 5grq

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Zinc binding site 2 out of 11 in the Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide


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 Dhb Domain of Daxx in Complex with An Atrx Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn208

b:11.7
occ:0.96
 OXT A:ACT201 2.0 10.9 1.0
ND1 A:HIS96 2.1 12.4 1.0
CL B:CL201 2.2 15.7 1.0
SG B:CYS58 2.3 10.7 1.0
C A:ACT201 2.9 20.6 1.0
CE1 A:HIS96 3.0 13.0 1.0
CB B:CYS58 3.1 10.2 1.0
CG A:HIS96 3.2 11.5 1.0
O A:ACT201 3.3 28.8 1.0
CB A:HIS96 3.6 10.0 1.0
CA A:HIS96 3.9 10.8 1.0
N A:SER97 3.9 9.5 1.0
CB B:LYS60 4.0 11.3 1.0
NE2 A:HIS96 4.1 14.5 1.0
CD2 A:HIS96 4.2 13.3 1.0
O B:CYS58 4.3 11.8 1.0
CH3 A:ACT201 4.3 22.2 1.0
CA B:CYS58 4.4 9.6 1.0
C B:CYS58 4.4 10.8 1.0
C A:HIS96 4.4 9.2 1.0
N B:LYS60 4.5 9.1 1.0
O B:HOH353 4.5 17.6 1.0
CB A:SER97 4.8 14.5 1.0
CA B:LYS60 4.8 9.2 1.0
CD B:LYS60 4.9 25.9 1.0
CA A:SER97 5.0 9.3 1.0
CB A:ALA139 5.0 15.5 1.0

Zinc binding site 3 out of 11 in 5grq

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Zinc binding site 3 out of 11 in the Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide


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 Dhb Domain of Daxx in Complex with An Atrx Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn209

b:13.8
occ:1.00
 OE2 A:GLU83 2.0 14.5 1.0
OXT A:ACT202 2.1 17.5 1.0
ND1 A:HIS81 2.1 14.8 1.0
CD A:GLU83 2.8 13.0 1.0
C A:ACT202 2.9 30.4 1.0
CE1 A:HIS81 3.0 15.3 1.0
OE1 A:GLU83 3.0 13.6 1.0
O A:ACT202 3.1 42.0 1.0
CG A:HIS81 3.2 11.3 1.0
CB A:HIS81 3.5 10.6 1.0
CA A:HIS81 4.0 12.5 1.0
NE2 A:HIS81 4.1 13.7 1.0
O A:HOH392 4.1 49.1 1.0
O A:HOH379 4.1 18.4 1.0
CD2 C:LEU1277 4.2 17.8 1.0
CD2 A:HIS81 4.2 12.0 1.0
CG A:GLU83 4.3 13.3 1.0
CH3 A:ACT202 4.3 35.6 1.0
CD1 C:LEU1277 4.5 16.0 1.0
O A:ASP80 4.5 14.0 1.0
O A:HOH428 4.8 36.5 1.0
CG C:LEU1277 4.8 15.5 1.0
C A:HIS81 4.9 10.4 1.0

Zinc binding site 4 out of 11 in 5grq

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Zinc binding site 4 out of 11 in the Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide


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 Dhb Domain of Daxx in Complex with An Atrx Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn212

b:12.7
occ:1.00
 ND1 B:HIS96 2.0 14.8 1.0
O A:ACT210 2.1 11.2 1.0
SG A:CYS58 2.3 10.5 1.0
CL A:CL206 2.3 18.9 1.0
CE1 B:HIS96 2.9 15.7 1.0
C A:ACT210 3.0 18.9 1.0
CG B:HIS96 3.1 12.2 1.0
CB A:CYS58 3.2 9.9 1.0
OXT A:ACT210 3.3 25.0 1.0
CB B:HIS96 3.5 11.1 1.0
CA B:HIS96 3.9 10.2 1.0
N B:SER97 3.9 10.2 1.0
CB A:LYS60 4.0 10.4 1.0
NE2 B:HIS96 4.1 15.4 1.0
O A:HOH400 4.1 40.0 1.0
CD2 B:HIS96 4.2 15.7 1.0
N A:LYS60 4.3 9.8 1.0
CH3 A:ACT210 4.4 21.8 1.0
CA A:CYS58 4.4 9.4 1.0
C B:HIS96 4.4 9.8 1.0
C A:CYS58 4.4 12.0 1.0
O A:CYS58 4.5 13.9 1.0
CA A:LYS60 4.8 9.1 1.0
O A:HOH341 4.8 28.5 1.0
CB B:ALA139 4.9 24.1 1.0
CB B:SER97 4.9 15.7 1.0
N A:TYR59 4.9 9.8 1.0
CA B:SER97 5.0 11.1 1.0

Zinc binding site 5 out of 11 in 5grq

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Zinc binding site 5 out of 11 in the Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide


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 Dhb Domain of Daxx in Complex with An Atrx Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn213

b:15.8
occ:1.00
 N A:GLY55 2.0 16.1 1.0
NE2 B:HIS137 2.0 15.6 1.0
OE2 B:GLU104 2.0 18.7 1.0
OXT A:ACT211 2.0 19.2 1.0
C A:ACT211 2.7 26.1 1.0
CD B:GLU104 2.7 16.7 1.0
OE1 B:GLU104 2.8 14.8 1.0
O A:ACT211 2.8 28.9 1.0
CA A:GLY55 2.9 18.4 1.0
CE1 B:HIS137 3.0 13.3 1.0
CD2 B:HIS137 3.1 14.1 1.0
O A:HOH378 3.9 29.9 1.0
O A:HOH304 4.1 45.3 1.0
ND1 B:HIS137 4.1 14.5 1.0
O B:HOH337 4.1 22.9 1.0
CG B:HIS137 4.2 11.9 1.0
CG B:GLU104 4.2 11.2 1.0
CH3 A:ACT211 4.2 31.9 1.0
O A:HOH396 4.2 36.9 1.0
C A:GLY55 4.3 18.8 1.0
O A:HOH335 4.4 14.5 1.0
CD1 B:PHE99 4.5 11.2 1.0
CE1 B:PHE99 4.5 14.2 1.0
O A:GLY55 4.7 20.0 1.0
O B:HOH317 4.8 14.8 1.0
O A:HOH340 4.9 48.2 1.0

Zinc binding site 6 out of 11 in 5grq

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Zinc binding site 6 out of 11 in the Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide


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 Dhb Domain of Daxx in Complex with An Atrx Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn214

b:18.8
occ:1.00
 OE1 C:GLU1279 2.1 19.2 1.0
O A:HOH307 2.1 26.3 1.0
O C:HOH1438 2.1 24.4 1.0
SG A:CYS131 2.2 16.2 1.0
OE2 C:GLU1279 2.6 18.0 1.0
CD C:GLU1279 2.7 16.5 1.0
CB A:CYS131 3.3 12.4 1.0
O C:HOH1427 3.8 30.6 1.0
O C:HOH1441 4.0 39.6 1.0
CG C:GLU1279 4.2 17.9 1.0
OD1 A:ASN128 4.2 33.4 1.0
C A:CYS131 4.3 11.1 1.0
N A:THR132 4.4 11.4 1.0
CA A:CYS131 4.4 10.7 1.0
NH2 A:ARG91 4.4 19.9 1.0
CD1 C:LEU1276 4.4 15.2 1.0
O A:CYS131 4.6 13.6 1.0
OG1 A:THR132 4.6 16.8 1.0
NE A:ARG91 4.6 13.7 1.0
CZ A:PHE87 4.8 16.6 1.0
CB C:GLU1279 4.8 16.4 1.0
CE2 A:PHE87 4.9 16.1 1.0
CA A:THR132 4.9 12.6 1.0
O A:ASN128 4.9 17.9 1.0

Zinc binding site 7 out of 11 in 5grq

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Zinc binding site 7 out of 11 in the Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:17.0
occ:1.00
 OE2 B:GLU83 2.0 17.1 1.0
ND1 B:HIS81 2.1 16.9 1.0
CD B:GLU83 2.8 13.3 1.0
OE1 B:GLU83 2.9 15.7 1.0
CE1 B:HIS81 3.0 14.2 1.0
CG B:HIS81 3.1 13.0 1.0
CB B:HIS81 3.5 11.3 1.0
CA B:HIS81 3.8 10.1 1.0
NE2 B:HIS81 4.1 14.1 1.0
CD2 B:HIS81 4.2 13.6 1.0
O B:HOH356 4.2 22.3 1.0
CG B:GLU83 4.3 11.9 1.0
CD2 D:LEU1277 4.3 19.3 1.0
O B:ASP80 4.5 14.1 1.0
CD1 D:LEU1277 4.5 19.9 1.0
C B:HIS81 4.7 11.8 1.0
N B:HIS81 4.9 11.3 1.0
CG D:LEU1277 4.9 19.2 1.0

Zinc binding site 8 out of 11 in 5grq

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Zinc binding site 8 out of 11 in the Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn203

b:20.2
occ:1.00
 O B:HOH329 2.0 20.3 1.0
OE1 D:GLU1279 2.1 17.9 1.0
SG B:CYS131 2.2 17.4 1.0
O D:HOH1419 2.3 23.9 1.0
OE2 D:GLU1279 2.5 18.4 1.0
CD D:GLU1279 2.6 16.9 1.0
CB B:CYS131 3.2 13.1 1.0
O D:HOH1405 3.9 25.8 1.0
C B:CYS131 3.9 11.9 1.0
N B:THR132 4.0 10.8 1.0
CG D:GLU1279 4.1 16.1 1.0
CA B:CYS131 4.2 12.4 1.0
OG1 B:THR132 4.2 18.4 1.0
O B:HOH358 4.2 48.8 1.0
O B:HOH374 4.2 32.5 1.0
NE B:ARG91 4.3 18.1 1.0
OD1 B:ASN128 4.3 21.9 1.0
O B:CYS131 4.3 13.7 1.0
CD1 D:LEU1276 4.5 12.9 1.0
CA B:THR132 4.5 12.3 1.0
NH2 B:ARG91 4.5 28.6 1.0
O B:ASN128 4.5 13.4 1.0
CE2 B:PHE87 4.7 19.1 1.0
CB D:GLU1279 4.8 18.2 1.0
CZ B:ARG91 4.9 30.1 1.0

Zinc binding site 9 out of 11 in 5grq

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Zinc binding site 9 out of 11 in the Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1302

b:21.8
occ:1.00
 OD2 C:ASP1264 2.0 27.2 1.0
OD2 C:ASP1259 2.0 22.4 1.0
OD2 C:ASP1261 2.0 21.0 1.0
O C:ACT1301 2.3 34.8 1.0
OXT C:ACT1301 2.6 43.6 1.0
C C:ACT1301 2.7 40.9 1.0
CG C:ASP1259 2.8 25.4 1.0
CG C:ASP1264 2.8 26.5 1.0
CG C:ASP1261 2.9 20.6 1.0
OD1 C:ASP1259 2.9 19.9 1.0
OD1 C:ASP1264 3.0 25.2 1.0
OD1 C:ASP1261 3.0 23.6 1.0
O C:HOH1414 3.6 24.5 1.0
O C:HOH1404 3.7 26.3 1.0
O C:HOH1423 3.8 27.8 1.0
O C:HOH1413 4.0 38.5 1.0
CB C:ASP1259 4.2 18.0 1.0
CB C:ASP1264 4.2 20.1 1.0
CB C:ASP1261 4.3 15.1 1.0
CH3 C:ACT1301 4.3 41.7 1.0
NH2 C:ARG1270 4.3 56.5 1.0
O C:HOH1430 4.3 50.6 1.0
CZ C:ARG1270 4.6 51.2 1.0
O C:HOH1411 4.6 36.1 1.0
NE C:ARG1270 4.7 45.9 1.0
N C:ASP1261 4.8 14.7 1.0
CA C:ASP1261 5.0 14.8 1.0
O C:ASP1261 5.0 15.8 1.0

Zinc binding site 10 out of 11 in 5grq

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Zinc binding site 10 out of 11 in the Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Dhb Domain of Daxx in Complex with An Atrx Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1303

b:13.9
occ:1.00
 OD1 C:ASP1262 2.0 16.2 1.0
O A:HOH319 2.1 14.0 1.0
O C:HOH1406 2.2 14.4 1.0
O C:HOH1408 2.2 17.4 1.0
CG C:ASP1262 3.0 21.0 1.0
OD2 C:ASP1262 3.3 21.6 1.0
O A:GLN77 3.9 14.9 1.0
OD1 C:ASP1263 4.0 19.1 1.0
OD2 A:ASP80 4.1 17.0 1.0
O A:HOH393 4.2 32.0 1.0
N C:ASP1262 4.2 15.5 1.0
OD2 C:ASP1263 4.3 18.9 1.0
CB C:ASP1262 4.3 17.5 1.0
OD1 A:ASP80 4.4 13.9 1.0
O A:HOH421 4.4 39.1 1.0
CG C:ASP1263 4.4 19.2 1.0
CG A:ASP80 4.5 15.1 1.0
O A:HOH320 4.5 15.6 1.0
CA C:ASP1262 4.6 16.3 1.0
O A:HOH353 4.7 12.2 1.0
C C:ASP1262 4.8 16.9 1.0
C A:GLN77 4.9 12.2 1.0

Reference:

H.Li, H.Li. N/A N/A.
Page generated: Sun Oct 27 17:10:00 2024

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