Zinc in PDB 7l3l: Structure of TRAF5 and TRAF6 Ring Hetero Dimer

Enzymatic activity of Structure of TRAF5 and TRAF6 Ring Hetero Dimer

All present enzymatic activity of Structure of TRAF5 and TRAF6 Ring Hetero Dimer:
2.3.2.27;

Protein crystallography data

The structure of Structure of TRAF5 and TRAF6 Ring Hetero Dimer, PDB code: 7l3l was solved by A.Das, A.J.Middleton, P.Padala, C.L.Day, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.25 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.597, 106.062, 94.427, 90, 102.64, 90
R / Rfree (%) 20.4 / 23.4

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Structure of TRAF5 and TRAF6 Ring Hetero Dimer (pdb code 7l3l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Structure of TRAF5 and TRAF6 Ring Hetero Dimer, PDB code: 7l3l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 7l3l

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Zinc binding site 1 out of 14 in the Structure of TRAF5 and TRAF6 Ring Hetero Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of TRAF5 and TRAF6 Ring Hetero Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:49.7
occ:1.00
SG A:CYS45 2.3 50.0 1.0
SG A:CYS48 2.4 53.6 1.0
SG A:CYS65 2.4 54.3 1.0
SG A:CYS68 2.7 55.2 1.0
CB A:CYS45 2.8 50.9 1.0
CB A:CYS48 2.9 50.0 1.0
CB A:CYS65 3.3 51.6 1.0
N A:CYS65 3.6 47.1 1.0
N A:CYS48 3.6 52.7 1.0
CB A:CYS68 3.6 58.1 1.0
CA A:CYS48 3.8 51.1 1.0
CA A:CYS65 4.0 49.7 1.0
CA A:CYS45 4.3 51.4 1.0
C A:CYS48 4.5 51.1 1.0
N A:HIS49 4.6 56.0 1.0
C A:PHE64 4.7 43.5 1.0
C A:PHE47 4.8 54.0 1.0
CA A:PHE64 4.9 44.6 1.0
C A:CYS45 4.9 52.0 1.0
N A:PHE47 5.0 52.7 1.0

Zinc binding site 2 out of 14 in 7l3l

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Zinc binding site 2 out of 14 in the Structure of TRAF5 and TRAF6 Ring Hetero Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of TRAF5 and TRAF6 Ring Hetero Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:55.7
occ:1.00
OD2 A:ASP84 1.8 60.5 1.0
ND1 A:HIS62 2.3 50.5 1.0
SG A:CYS81 2.4 53.5 1.0
SG A:CYS60 2.4 50.1 1.0
CB A:CYS60 2.7 49.5 1.0
CG A:ASP84 2.7 62.1 1.0
CE1 A:HIS62 3.1 53.2 1.0
CB A:CYS81 3.2 54.1 1.0
CG A:HIS62 3.3 49.2 1.0
OD1 A:ASP84 3.4 71.3 1.0
CB A:ASP84 3.6 56.8 1.0
CB A:HIS62 3.7 47.4 1.0
CA A:CYS60 4.0 50.2 1.0
N A:ASP84 4.0 50.2 1.0
C A:CYS60 4.1 51.7 1.0
O A:CYS60 4.2 53.5 1.0
NE2 A:HIS62 4.2 53.3 1.0
CD2 A:HIS62 4.3 52.1 1.0
CA A:ASP84 4.5 51.7 1.0
OG1 A:THR58 4.6 42.1 1.0
CA A:CYS81 4.7 53.4 1.0
N A:HIS62 4.7 45.7 1.0
N A:GLY61 4.8 46.7 1.0
CB A:VAL83 4.8 48.1 1.0
N A:CYS60 4.9 49.5 1.0
CA A:HIS62 4.9 45.1 1.0

Zinc binding site 3 out of 14 in 7l3l

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Zinc binding site 3 out of 14 in the Structure of TRAF5 and TRAF6 Ring Hetero Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of TRAF5 and TRAF6 Ring Hetero Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:75.3
occ:1.00
SG A:CYS110 2.1 74.8 1.0
SG A:CYS132 2.2 74.7 1.0
NE2 A:HIS128 2.2 74.9 1.0
SG A:CYS116 2.4 80.1 1.0
CB A:CYS116 3.0 79.1 1.0
CB A:CYS110 3.1 73.3 1.0
CD2 A:HIS128 3.1 72.5 1.0
CE1 A:HIS128 3.2 75.1 1.0
CB A:CYS132 3.3 78.0 1.0
ND2 A:ASN112 3.5 80.7 1.0
ND1 A:HIS128 4.3 73.3 1.0
CG A:HIS128 4.3 72.2 1.0
CB A:ASN112 4.4 79.5 1.0
CG A:ASN112 4.4 80.5 1.0
CA A:CYS110 4.5 72.5 1.0
CA A:CYS116 4.5 79.8 1.0
CB A:ALA118 4.5 65.7 1.0
CA A:CYS132 4.6 80.5 1.0
CD2 A:LEU129 4.7 74.9 1.0
N A:ASN112 4.9 80.8 1.0

Zinc binding site 4 out of 14 in 7l3l

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Zinc binding site 4 out of 14 in the Structure of TRAF5 and TRAF6 Ring Hetero Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of TRAF5 and TRAF6 Ring Hetero Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:118.1
occ:1.00
SG A:CYS144 2.3 127.6 1.0
SG A:CYS161 2.7 117.7 1.0
CB A:CYS161 2.9 113.1 1.0
OD1 A:ASN141 3.0 120.6 1.0
SG A:CYS139 3.6 114.6 1.0
CB A:CYS139 3.7 112.4 1.0
CD2 A:HIS156 3.7 109.5 1.0
CB A:CYS144 3.8 126.8 1.0
CB A:HIS156 3.9 108.3 1.0
CA A:CYS161 3.9 109.7 1.0
CG A:HIS156 4.1 108.7 1.0
CG A:ASN141 4.2 119.0 1.0
CB A:GLU146 4.4 130.8 1.0
CG A:GLU146 4.5 130.1 1.0
CG2 A:VAL148 4.8 105.8 1.0
N A:CYS161 4.8 108.8 1.0
ND2 A:ASN141 4.9 119.3 1.0
CD1 A:LEU153 4.9 98.3 1.0
NE2 A:HIS156 4.9 111.1 1.0
CA A:CYS144 5.0 126.2 1.0

Zinc binding site 5 out of 14 in 7l3l

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Zinc binding site 5 out of 14 in the Structure of TRAF5 and TRAF6 Ring Hetero Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of TRAF5 and TRAF6 Ring Hetero Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:45.5
occ:1.00
SG B:CYS90 2.3 45.8 1.0
SG B:CYS73 2.3 50.3 1.0
SG B:CYS93 2.3 51.4 1.0
SG B:CYS70 2.4 46.5 1.0
O B:GLN54 3.0 72.8 1.0
CB B:CYS70 3.1 45.3 1.0
CB B:CYS93 3.2 49.7 1.0
CB B:CYS90 3.2 48.2 1.0
CB B:CYS73 3.3 50.7 1.0
N B:CYS73 3.7 49.4 1.0
N B:CYS90 3.9 49.8 1.0
C B:GLN54 4.0 65.5 1.0
CA B:CYS73 4.1 50.2 1.0
CA B:CYS90 4.2 47.5 1.0
CB B:ILE72 4.5 46.9 1.0
CA B:GLN54 4.5 65.5 1.0
CA B:CYS93 4.6 48.1 1.0
CA B:CYS70 4.6 45.1 1.0
C B:ILE72 4.8 47.3 1.0
CG2 B:ILE72 4.8 46.9 1.0
N B:CYS93 4.9 47.2 1.0
C B:CYS73 4.9 50.1 1.0
N B:GLY55 4.9 63.3 1.0
CB B:GLN54 5.0 64.9 1.0

Zinc binding site 6 out of 14 in 7l3l

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Zinc binding site 6 out of 14 in the Structure of TRAF5 and TRAF6 Ring Hetero Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of TRAF5 and TRAF6 Ring Hetero Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:46.8
occ:1.00
OD2 B:ASP108 2.2 46.5 1.0
SG B:CYS105 2.2 44.2 1.0
CD2 B:HIS87 2.3 42.2 1.0
SG B:CYS85 2.5 47.0 1.0
OD1 B:ASP108 2.6 46.9 1.0
CG B:ASP108 2.6 43.9 1.0
NE2 B:HIS87 3.0 43.9 1.0
CG B:HIS87 3.1 41.9 1.0
CB B:CYS105 3.3 42.8 1.0
CB B:CYS85 3.5 46.0 1.0
CB B:HIS87 3.8 40.8 1.0
CB B:ASP108 3.9 41.8 1.0
CE1 B:HIS87 3.9 41.8 1.0
ND1 B:HIS87 4.0 43.8 1.0
OG1 B:THR83 4.0 44.2 1.0
N B:ASP108 4.1 37.9 1.0
CB B:VAL107 4.4 40.0 1.0
C B:CYS85 4.6 45.6 1.0
CA B:CYS85 4.6 44.4 1.0
CA B:ASP108 4.6 40.4 1.0
CA B:CYS105 4.6 43.2 1.0
O B:CYS85 4.7 49.9 1.0
C B:VAL107 4.8 40.1 1.0
N B:HIS87 4.8 40.5 1.0
O B:CYS105 4.9 42.8 1.0
N B:VAL107 4.9 40.1 1.0
C B:CYS105 4.9 42.5 1.0
CA B:VAL107 4.9 40.1 1.0
CG1 B:VAL107 4.9 39.2 1.0
CA B:HIS87 4.9 39.8 1.0
N B:GLY86 5.0 41.4 1.0

Zinc binding site 7 out of 14 in 7l3l

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Zinc binding site 7 out of 14 in the Structure of TRAF5 and TRAF6 Ring Hetero Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of TRAF5 and TRAF6 Ring Hetero Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn203

b:63.6
occ:1.00
NE2 B:HIS151 2.2 66.2 1.0
SG B:CYS155 2.3 70.5 1.0
SG B:CYS139 2.4 70.9 1.0
SG B:CYS134 2.5 72.3 1.0
CB B:CYS134 3.1 71.4 1.0
CB B:CYS139 3.1 73.2 1.0
CD2 B:HIS151 3.1 64.0 1.0
CE1 B:HIS151 3.3 65.4 1.0
CB B:CYS155 3.7 68.3 1.0
ND2 B:ASN136 3.9 77.7 1.0
CB B:ASN136 4.3 77.5 1.0
CG B:HIS151 4.3 64.3 1.0
CB B:HIS141 4.3 67.7 1.0
ND1 B:HIS151 4.4 64.4 1.0
CA B:CYS134 4.5 71.1 1.0
CG B:ASN136 4.5 76.7 1.0
CA B:CYS139 4.6 74.2 1.0
O B:CYS134 4.6 72.0 1.0
ND1 B:HIS141 4.7 65.2 1.0
C B:CYS134 4.7 72.4 1.0
CA B:CYS155 4.8 67.4 1.0
CG B:HIS141 5.0 66.9 1.0

Zinc binding site 8 out of 14 in 7l3l

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Zinc binding site 8 out of 14 in the Structure of TRAF5 and TRAF6 Ring Hetero Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of TRAF5 and TRAF6 Ring Hetero Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:47.3
occ:1.00
CB C:CYS48 2.2 52.3 1.0
SG C:CYS68 2.3 54.4 1.0
SG C:CYS45 2.3 48.2 1.0
SG C:CYS65 2.5 49.0 1.0
CB C:CYS45 2.7 46.2 1.0
SG C:CYS48 3.2 52.0 1.0
CB C:CYS65 3.2 49.4 1.0
CA C:CYS48 3.4 54.2 1.0
CB C:CYS68 3.5 53.5 1.0
N C:CYS48 3.5 51.8 1.0
N C:CYS65 3.6 49.1 1.0
CA C:CYS65 4.0 48.9 1.0
CA C:CYS45 4.2 46.7 1.0
C C:CYS48 4.5 58.7 1.0
C C:PHE64 4.7 48.1 1.0
C C:PHE47 4.8 50.1 1.0
C C:CYS45 4.8 49.6 1.0
CA C:CYS68 4.8 53.0 1.0
N C:HIS49 4.8 53.9 1.0
CE1 C:HIS67 4.8 58.4 1.0
O C:SER50 4.9 49.9 1.0
O C:CYS45 4.9 50.7 1.0
CA C:PHE64 5.0 47.7 1.0
NE2 C:HIS67 5.0 57.8 1.0
N C:CYS45 5.0 46.9 1.0
C C:CYS65 5.0 48.4 1.0

Zinc binding site 9 out of 14 in 7l3l

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Zinc binding site 9 out of 14 in the Structure of TRAF5 and TRAF6 Ring Hetero Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of TRAF5 and TRAF6 Ring Hetero Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:63.6
occ:1.00
OD2 C:ASP84 2.1 60.1 1.0
SG C:CYS81 2.2 58.5 1.0
ND1 C:HIS62 2.2 59.2 1.0
SG C:CYS60 2.4 55.0 1.0
CG C:ASP84 2.7 59.7 1.0
CE1 C:HIS62 2.8 60.8 1.0
OD1 C:ASP84 2.9 62.0 1.0
CB C:CYS81 3.1 57.5 1.0
CB C:CYS60 3.2 56.8 1.0
CG C:HIS62 3.2 58.5 1.0
CB C:HIS62 3.8 55.6 1.0
NE2 C:HIS62 3.9 58.7 1.0
CB C:ASP84 4.0 57.7 1.0
CG2 C:VAL83 4.0 58.7 1.0
CD2 C:HIS62 4.1 59.1 1.0
O C:CYS60 4.3 58.3 1.0
N C:ASP84 4.3 58.2 1.0
CA C:CYS60 4.5 57.2 1.0
C C:CYS60 4.6 57.9 1.0
CA C:CYS81 4.6 57.0 1.0
CA C:ASP84 4.8 57.8 1.0
CG2 C:THR58 4.8 53.5 1.0

Zinc binding site 10 out of 14 in 7l3l

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Zinc binding site 10 out of 14 in the Structure of TRAF5 and TRAF6 Ring Hetero Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of TRAF5 and TRAF6 Ring Hetero Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn203

b:51.5
occ:1.00
NE2 C:HIS128 2.1 53.2 1.0
SG C:CYS110 2.2 51.1 1.0
SG C:CYS132 2.3 53.5 1.0
SG C:CYS116 2.3 53.3 1.0
CE1 C:HIS128 2.9 52.4 1.0
CB C:CYS116 3.1 53.7 1.0
CD2 C:HIS128 3.2 53.1 1.0
CB C:CYS132 3.2 54.1 1.0
CB C:CYS110 3.4 50.3 1.0
ND1 C:HIS128 4.0 51.1 1.0
CA C:CYS132 4.2 54.5 1.0
CG C:HIS128 4.2 53.2 1.0
ND2 C:ASN112 4.3 55.3 1.0
CB C:ASN112 4.4 54.6 1.0
CA C:CYS116 4.5 55.2 1.0
CA C:CYS110 4.8 49.8 1.0
CB C:ALA118 4.8 48.4 1.0
CG C:ASN112 4.9 54.1 1.0
C C:CYS132 4.9 53.4 1.0
O C:CYS116 4.9 56.9 1.0
C C:CYS116 4.9 56.5 1.0

Reference:

A.Das, A.J.Middleton, P.Padala, E.C.Ledgerwood, P.D.Mace, C.L.Day. The Structure and Ubiquitin Binding Properties of Traf Ring Heterodimers. J.Mol.Biol. 66844 2021.
ISSN: ESSN 1089-8638
PubMed: 33539883
DOI: 10.1016/J.JMB.2021.166844
Page generated: Wed Mar 3 16:22:17 2021

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