Zinc in PDB 8hz2: Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain

Enzymatic activity of Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain

All present enzymatic activity of Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain:
2.3.2.27;

Protein crystallography data

The structure of Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain, PDB code: 8hz2 was solved by O.Guven, H.Ciftci, H.Demirci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 45.885, 51.705, 54.3, 91.04, 112.15, 108.43
R / Rfree (%) 34.8 / 40.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain (pdb code 8hz2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain, PDB code: 8hz2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 8hz2

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Zinc binding site 1 out of 10 in the Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:64.9
occ:0.00
 SG A:CYS93 2.3 50.2 1.0
SG A:CYS70 2.3 65.6 1.0
SG A:CYS90 2.3 50.6 1.0
SG A:CYS73 2.3 87.0 1.0
CB A:CYS70 2.8 65.8 1.0
CB A:CYS90 3.0 52.4 1.0
CB A:CYS93 3.4 51.2 1.0
CB A:CYS73 3.6 86.0 1.0
N A:CYS90 3.9 50.5 1.0
N A:CYS73 4.0 81.8 1.0
CA A:CYS90 4.1 47.6 1.0
CA A:CYS70 4.3 65.3 1.0
CA A:CYS73 4.4 87.0 1.0
O A:GLN54 4.7 78.6 1.0
CB A:ILE72 4.7 78.7 1.0
CA A:GLY55 4.8 65.4 1.0
CA A:CYS93 4.8 49.8 1.0
C A:CYS70 4.9 72.4 1.0
O A:MET75 4.9 62.2 1.0
C A:GLN54 4.9 79.2 1.0
N A:GLY55 5.0 68.1 1.0

Zinc binding site 2 out of 10 in 8hz2

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Zinc binding site 2 out of 10 in the Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:52.0
occ:0.00
 OD2 A:ASP108 2.0 64.2 1.0
SG A:CYS105 2.3 51.0 1.0
SG A:CYS85 2.3 38.1 1.0
ND1 A:HIS87 2.3 47.7 1.0
CG A:ASP108 2.8 76.2 1.0
OD1 A:ASP108 3.1 82.9 1.0
CG A:HIS87 3.2 45.0 1.0
CE1 A:HIS87 3.3 47.4 1.0
CB A:CYS105 3.4 74.5 1.0
CB A:HIS87 3.5 47.3 1.0
CB A:CYS85 3.5 45.2 1.0
OG1 A:THR83 3.8 41.8 1.0
CG1 A:VAL107 3.9 64.8 1.0
CB A:ASP108 4.1 79.0 1.0
N A:HIS87 4.4 47.0 1.0
CD2 A:HIS87 4.4 38.2 1.0
NE2 A:HIS87 4.4 48.0 1.0
O A:HOH412 4.5 40.5 1.0
CA A:HIS87 4.5 44.8 1.0
CA A:CYS85 4.6 33.7 1.0
C A:CYS85 4.6 32.9 1.0
N A:ASP108 4.6 79.9 1.0
CB A:THR83 4.6 43.8 1.0
CA A:CYS105 4.8 87.3 1.0
N A:GLY86 4.8 38.9 1.0
O A:CYS85 4.9 41.3 1.0
CE2 A:PHE89 4.9 56.3 1.0
CZ A:PHE89 4.9 59.3 1.0
CG2 A:THR83 5.0 46.1 1.0
CA A:ASP108 5.0 85.3 1.0

Zinc binding site 3 out of 10 in 8hz2

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Zinc binding site 3 out of 10 in the Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:78.5
occ:0.00
 NE2 A:HIS151 2.1 86.4 1.0
SG A:CYS155 2.3 67.0 1.0
SG A:CYS134 2.3 59.9 1.0
SG A:CYS139 2.3 91.4 1.0
CD2 A:HIS151 2.5 80.1 1.0
CB A:CYS134 2.7 74.3 1.0
CB A:CYS139 3.2 79.9 1.0
CE1 A:HIS151 3.3 112.7 1.0
CB A:CYS155 3.8 67.5 1.0
CG A:HIS151 3.8 83.6 1.0
ND1 A:HIS151 4.2 108.8 1.0
CA A:CYS134 4.2 71.7 1.0
ND2 A:ASN136 4.4 60.7 1.0
CA A:CYS139 4.7 83.5 1.0
CB A:ASN136 4.9 60.5 1.0
CA A:CYS155 4.9 70.5 1.0
C A:CYS134 5.0 67.0 1.0

Zinc binding site 4 out of 10 in 8hz2

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Zinc binding site 4 out of 10 in the Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:72.9
occ:0.00
 NE2 A:HIS177 2.1 61.9 1.0
SG A:CYS182 2.3 74.9 1.0
SG A:CYS165 2.3 72.3 1.0
SG A:CYS162 2.3 75.6 1.0
CD2 A:HIS177 3.0 62.0 1.0
CE1 A:HIS177 3.1 62.3 1.0
CB A:CYS162 3.3 75.1 1.0
CB A:CYS182 3.6 71.3 1.0
CB A:CYS165 3.9 77.6 1.0
N A:CYS165 4.0 78.3 1.0
CG A:HIS177 4.2 60.6 1.0
ND1 A:HIS177 4.2 60.7 1.0
CB A:GLN164 4.2 69.5 1.0
CA A:CYS182 4.3 69.3 1.0
CE2 A:PHE169 4.5 67.7 1.0
OE1 A:GLN164 4.5 71.3 1.0
CA A:CYS165 4.5 83.8 1.0
CD A:PRO183 4.7 64.1 1.0
CA A:CYS162 4.7 74.2 1.0
CB A:ARG167 4.8 78.7 1.0
N A:GLN164 4.8 72.2 1.0
C A:GLN164 4.8 72.8 1.0
CA A:GLN164 4.9 72.6 1.0
CD A:ARG167 4.9 67.7 1.0

Zinc binding site 5 out of 10 in 8hz2

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Zinc binding site 5 out of 10 in the Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:181.4
occ:0.00
 NE2 A:HIS204 2.1 158.2 1.0
SG A:CYS192 2.3 208.1 1.0
SG A:CYS208 2.3 249.1 1.0
SG A:CYS189 2.3 154.1 1.0
CD2 A:HIS204 2.5 145.4 1.0
CB A:CYS189 2.7 155.8 1.0
CE1 A:HIS204 3.4 152.6 1.0
CB A:CYS192 3.6 210.4 1.0
CB A:CYS208 3.6 239.8 1.0
CG A:HIS204 3.8 133.3 1.0
N A:CYS192 3.9 207.2 1.0
CA A:CYS189 4.2 144.1 1.0
ND1 A:HIS204 4.2 133.5 1.0
OD1 A:ASP205 4.2 93.9 1.0
CA A:CYS192 4.3 209.7 1.0
CB A:ASN191 4.4 181.5 1.0
O A:HIS204 4.5 135.1 1.0
C A:CYS189 4.5 152.6 1.0
O A:CYS189 4.5 163.6 1.0
CA A:CYS208 4.6 241.9 1.0
C A:ASN191 4.7 200.5 1.0
CE A:MET196 4.7 107.8 1.0
ND2 A:ASN191 4.8 174.8 1.0
N A:ASN191 4.8 168.9 1.0
CA A:ASN191 4.9 182.8 1.0
N A:CYS189 5.0 130.8 1.0
C A:HIS204 5.0 117.7 1.0

Zinc binding site 6 out of 10 in 8hz2

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Zinc binding site 6 out of 10 in the Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:48.7
occ:0.00
 SG B:CYS90 2.3 43.3 1.0
SG B:CYS73 2.3 40.5 1.0
SG B:CYS70 2.3 51.4 1.0
SG B:CYS93 2.3 54.9 1.0
CB B:CYS70 2.8 49.4 1.0
CB B:CYS90 3.0 52.0 1.0
CB B:CYS93 3.4 60.4 1.0
CB B:CYS73 3.6 46.0 1.0
N B:CYS90 3.9 51.7 1.0
N B:CYS73 3.9 38.6 1.0
CA B:CYS90 4.0 50.6 1.0
CA B:CYS70 4.3 51.1 1.0
CA B:CYS73 4.3 43.0 1.0
N B:GLY55 4.4 51.5 1.0
N B:GLN54 4.5 55.8 1.0
CB B:ILE72 4.6 54.9 1.0
CA B:GLY55 4.8 54.8 1.0
CA B:CYS93 4.8 63.6 1.0
C B:CYS70 4.9 55.9 1.0
O B:MET75 4.9 42.3 1.0
O B:CYS70 4.9 50.0 1.0
C B:GLN54 5.0 50.4 1.0
C B:ILE72 5.0 42.3 1.0

Zinc binding site 7 out of 10 in 8hz2

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Zinc binding site 7 out of 10 in the Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:50.0
occ:0.00
 OD2 B:ASP108 2.2 44.1 1.0
SG B:CYS85 2.3 42.9 1.0
SG B:CYS105 2.3 40.5 1.0
ND1 B:HIS87 2.3 55.0 1.0
CG B:ASP108 3.1 46.6 1.0
CG B:HIS87 3.2 52.8 1.0
OD1 B:ASP108 3.3 49.5 1.0
CE1 B:HIS87 3.3 55.7 1.0
CB B:HIS87 3.5 58.1 1.0
CB B:CYS105 3.6 56.3 1.0
OG1 B:THR83 3.8 46.4 1.0
CB B:CYS85 3.8 46.3 1.0
NE2 B:HIS87 4.4 52.1 1.0
CD2 B:HIS87 4.4 53.3 1.0
CB B:ASP108 4.4 47.1 1.0
CZ B:PHE89 4.5 46.0 1.0
N B:ASP108 4.5 52.6 1.0
CB B:THR83 4.6 48.2 1.0
CE2 B:PHE89 4.6 42.4 1.0
O B:CYS85 4.6 43.6 1.0
CB B:VAL107 4.6 50.0 1.0
C B:CYS85 4.7 45.2 1.0
CA B:HIS87 4.7 57.4 1.0
N B:HIS87 4.8 56.3 1.0
CA B:CYS85 4.8 46.8 1.0
CA B:CYS105 4.9 59.4 1.0
CG2 B:THR83 4.9 54.7 1.0

Zinc binding site 8 out of 10 in 8hz2

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Zinc binding site 8 out of 10 in the Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:102.5
occ:0.00
 NE2 B:HIS151 2.1 100.0 1.0
SG B:CYS134 2.3 87.4 1.0
SG B:CYS139 2.3 123.5 1.0
SG B:CYS155 2.3 147.0 1.0
CE1 B:HIS151 2.6 105.4 1.0
CB B:CYS134 3.0 79.6 1.0
CD2 B:HIS151 3.3 93.8 1.0
CB B:CYS139 3.7 137.1 1.0
CB B:CYS155 3.8 147.4 1.0
ND1 B:HIS151 3.8 99.6 1.0
CG B:HIS151 4.2 92.7 1.0
CB B:PHE157 4.4 188.6 1.0
CA B:CYS134 4.5 67.7 1.0
ND2 B:ASN136 4.5 120.3 1.0
CB B:ASN136 4.5 111.9 1.0
CA B:CYS155 4.7 162.4 1.0
O B:ASN136 4.9 107.4 1.0
CE B:MET143 4.9 76.1 1.0
CG B:ASN136 4.9 104.8 1.0

Zinc binding site 9 out of 10 in 8hz2

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Zinc binding site 9 out of 10 in the Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:274.8
occ:0.00
 O B:HOH401 1.9 30.0 1.0
NE2 B:HIS177 2.1 301.4 1.0
SG B:CYS165 2.3 252.9 1.0
SG B:CYS182 2.3 373.0 1.0
SG B:CYS162 2.3 263.3 1.0
CD2 B:HIS177 2.8 307.8 1.0
CE1 B:HIS177 3.3 291.2 1.0
CB B:CYS162 3.5 252.4 1.0
CD B:ARG167 3.7 197.9 1.0
CB B:CYS182 3.7 368.4 1.0
O B:HOH419 3.7 315.6 1.0
CG B:ARG167 4.0 220.0 1.0
CB B:CYS165 4.0 246.0 1.0
CE2 B:PHE169 4.0 254.5 1.0
CG B:HIS177 4.0 302.5 1.0
O B:HOH412 4.1 30.0 1.0
ND1 B:HIS177 4.2 287.2 1.0
N B:CYS165 4.2 243.3 1.0
CZ B:PHE169 4.3 231.0 1.0
CB B:GLN164 4.4 249.5 1.0
O B:CYS162 4.5 242.9 1.0
CA B:CYS182 4.7 368.8 1.0
CG1 B:ILE178 4.7 320.8 1.0
CA B:CYS165 4.7 242.8 1.0
CA B:ILE178 4.8 347.6 1.0
C B:GLN164 4.8 284.5 1.0
CA B:CYS162 4.9 244.3 1.0
C B:CYS162 5.0 239.1 1.0

Zinc binding site 10 out of 10 in 8hz2

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Zinc binding site 10 out of 10 in the Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn305

b:284.7
occ:0.00
 NE2 B:HIS204 2.1 280.0 1.0
CD2 B:HIS204 2.3 284.1 1.0
SG B:CYS192 2.3 282.6 1.0
SG B:CYS189 2.3 239.5 1.0
SG B:CYS208 2.3 232.8 1.0
CB B:CYS189 2.4 244.3 1.0
CB B:CYS192 3.0 276.7 1.0
CE1 B:HIS204 3.4 280.9 1.0
CG B:HIS204 3.6 288.5 1.0
OD1 B:ASP205 3.7 294.3 1.0
N B:CYS192 3.8 277.3 1.0
CB B:CYS208 3.9 238.7 1.0
CA B:CYS189 3.9 236.6 1.0
CA B:CYS192 4.0 276.7 1.0
ND1 B:HIS204 4.1 285.2 1.0
N B:CYS189 4.6 251.0 1.0
C B:CYS189 4.6 236.3 1.0
CB B:HIS204 4.8 308.2 1.0
CG B:ASP205 4.9 308.9 1.0
C B:CYS192 4.9 276.0 1.0
C B:ASN191 5.0 254.4 1.0
CA B:CYS208 5.0 252.8 1.0

Reference:

O.Guven, H.Ciftci, H.Demirci. Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-Terminal Domain To Be Published.
Page generated: Sat Apr 8 09:25:52 2023

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