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Zinc in PDB 6fga: Crystal Structure of TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1

Enzymatic activity of Crystal Structure of TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1

All present enzymatic activity of Crystal Structure of TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1:
2.3.2.23; 2.3.2.24; 2.3.2.27;

Protein crystallography data

The structure of Crystal Structure of TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1, PDB code: 6fga was solved by M.Anandapadamanaban, M.Moche, M.Sunnerhagen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.90 / 2.82
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.835, 95.871, 235.097, 90.00, 93.15, 90.00
R / Rfree (%) 25.3 / 29.4

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1 (pdb code 6fga). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1, PDB code: 6fga:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 6fga

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Zinc binding site 1 out of 16 in the Crystal Structure of TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1


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 TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:66.7
occ:1.00
SG A:CYS51 2.2 89.4 1.0
SG A:CYS31 2.2 59.2 1.0
ND1 A:HIS33 2.3 85.7 1.0
SG A:CYS54 2.4 83.2 1.0
CG A:HIS33 3.1 83.6 1.0
CB A:CYS51 3.1 91.8 1.0
CE1 A:HIS33 3.2 83.4 1.0
CB A:CYS31 3.4 63.8 1.0
CB A:HIS33 3.4 85.4 1.0
CB A:CYS54 3.6 81.8 1.0
N A:CYS54 3.7 78.3 1.0
CD2 A:HIS33 4.1 85.6 1.0
NE2 A:HIS33 4.1 86.2 1.0
CA A:CYS54 4.2 86.4 1.0
CB A:VAL53 4.3 96.4 1.0
CD1 A:ILE29 4.5 0.0 1.0
N A:HIS33 4.5 71.7 1.0
CA A:CYS51 4.6 80.5 1.0
CA A:HIS33 4.6 82.0 1.0
C A:VAL53 4.7 87.4 1.0
CA A:CYS31 4.7 67.2 1.0
CA A:VAL53 4.8 93.8 1.0
N A:VAL53 4.8 94.1 1.0
C A:CYS54 4.9 92.2 1.0
N A:ARG55 4.9 93.4 1.0
CG1 A:VAL53 4.9 92.3 1.0
C A:CYS31 5.0 70.9 1.0

Zinc binding site 2 out of 16 in 6fga

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Zinc binding site 2 out of 16 in the Crystal Structure of TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1


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 TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:0.8
occ:1.00
SG A:CYS39 2.2 0.5 1.0
SG A:CYS16 2.2 0.2 1.0
SG A:CYS36 2.6 0.5 1.0
SG A:CYS19 2.8 0.2 1.0
CB A:CYS16 3.0 0.8 1.0
CB A:CYS36 3.0 0.7 1.0
CB A:CYS39 3.1 0.3 1.0
CB A:CYS19 3.6 100.0 1.0
N A:CYS36 3.7 1.0 1.0
N A:CYS19 3.8 0.4 1.0
CA A:CYS36 4.0 0.8 1.0
CA A:CYS19 4.3 0.9 1.0
CA A:CYS16 4.4 0.4 1.0
CA A:CYS39 4.5 0.5 1.0
CB A:ILE18 4.5 0.5 1.0
C A:ILE18 4.7 0.3 1.0
N A:CYS39 4.8 0.7 1.0
C A:CYS16 4.8 0.2 1.0
N A:ILE18 4.9 0.9 1.0
C A:CYS36 4.9 0.3 1.0
C A:PHE35 4.9 0.4 1.0
O A:CYS36 4.9 0.8 1.0
CA A:ILE18 4.9 0.1 1.0
O A:CYS16 4.9 0.7 1.0

Zinc binding site 3 out of 16 in 6fga

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Zinc binding site 3 out of 16 in the Crystal Structure of TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1


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 TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:93.2
occ:1.00
SG B:CYS54 2.2 0.9 1.0
SG B:CYS51 2.2 99.6 1.0
SG B:CYS31 2.3 79.0 1.0
ND1 B:HIS33 2.3 87.5 1.0
CB B:CYS51 3.1 0.2 1.0
CB B:CYS31 3.2 97.8 1.0
CE1 B:HIS33 3.2 86.7 1.0
CG B:HIS33 3.2 85.7 1.0
CB B:CYS54 3.5 0.7 1.0
CB B:HIS33 3.5 92.2 1.0
N B:CYS54 3.7 97.3 1.0
CA B:CYS54 4.1 99.5 1.0
NE2 B:HIS33 4.2 81.8 1.0
CD2 B:HIS33 4.3 84.5 1.0
CB B:VAL53 4.4 0.7 1.0
N B:HIS33 4.5 1.0 1.0
CA B:CYS31 4.5 0.3 1.0
CA B:CYS51 4.6 96.8 1.0
N B:ARG55 4.6 99.6 1.0
CD1 B:ILE29 4.7 99.9 1.0
CA B:HIS33 4.7 0.1 1.0
C B:CYS54 4.7 96.5 1.0
C B:VAL53 4.7 97.5 1.0
C B:CYS31 4.7 0.2 1.0
N B:VAL53 4.8 86.1 1.0
CA B:VAL53 4.9 99.0 1.0
N B:GLN56 4.9 97.2 1.0
O B:CYS31 5.0 0.8 1.0

Zinc binding site 4 out of 16 in 6fga

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Zinc binding site 4 out of 16 in the Crystal Structure of TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1


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 TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn102

b:89.7
occ:1.00
SG B:CYS19 2.3 90.0 1.0
SG B:CYS16 2.3 92.2 1.0
SG B:CYS39 2.5 96.4 1.0
SG B:CYS36 2.7 0.3 1.0
CB B:CYS16 2.8 96.5 1.0
CB B:CYS19 3.3 90.5 1.0
CB B:CYS36 3.4 94.2 1.0
CB B:CYS39 3.5 0.2 1.0
N B:CYS19 3.6 0.7 1.0
CA B:CYS19 4.0 99.6 1.0
N B:CYS36 4.1 93.0 1.0
CA B:CYS16 4.3 0.0 1.0
CA B:CYS36 4.4 95.8 1.0
CB B:ILE18 4.6 97.7 1.0
C B:ILE18 4.6 0.0 1.0
C B:CYS16 4.7 0.5 1.0
O B:CYS16 4.7 99.6 1.0
O B:ASP21 4.8 0.8 1.0
C B:CYS19 4.9 0.3 1.0
CA B:CYS39 4.9 0.7 1.0
N B:ILE18 4.9 91.3 1.0
N B:LEU20 4.9 0.1 1.0
CA B:ILE18 4.9 96.9 1.0

Zinc binding site 5 out of 16 in 6fga

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Zinc binding site 5 out of 16 in the Crystal Structure of TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1


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 TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn101

b:80.0
occ:1.00
ND1 C:HIS33 2.0 0.1 1.0
SG C:CYS54 2.3 77.2 1.0
SG C:CYS31 2.4 1.0 1.0
SG C:CYS51 2.5 87.5 1.0
CE1 C:HIS33 2.8 0.1 1.0
CG C:HIS33 2.9 0.4 1.0
CB C:CYS31 3.3 0.1 1.0
CB C:HIS33 3.3 0.4 1.0
CB C:CYS51 3.4 82.5 1.0
CB C:CYS54 3.5 82.7 1.0
N C:CYS54 3.7 80.0 1.0
NE2 C:HIS33 3.9 0.3 1.0
CD2 C:HIS33 3.9 0.9 1.0
CA C:CYS54 4.2 81.0 1.0
CB C:VAL53 4.2 76.9 1.0
N C:HIS33 4.4 0.5 1.0
CA C:HIS33 4.5 0.9 1.0
CA C:CYS31 4.7 98.9 1.0
C C:VAL53 4.7 78.0 1.0
CG1 C:VAL53 4.8 75.8 1.0
CD1 C:ILE29 4.8 99.4 1.0
CA C:VAL53 4.8 79.6 1.0
C C:CYS31 4.9 93.6 1.0
CA C:CYS51 4.9 82.9 1.0
N C:VAL53 4.9 82.1 1.0
C C:CYS54 4.9 78.9 1.0

Zinc binding site 6 out of 16 in 6fga

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Zinc binding site 6 out of 16 in the Crystal Structure of TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1


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 TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn102

b:87.7
occ:1.00
SG C:CYS19 2.2 79.2 1.0
SG C:CYS39 2.5 90.3 1.0
SG C:CYS36 2.5 0.1 1.0
SG C:CYS16 2.7 79.2 1.0
CB C:CYS16 3.0 84.3 1.0
CB C:CYS19 3.2 86.1 1.0
CB C:CYS36 3.2 0.5 1.0
CB C:CYS39 3.7 95.2 1.0
N C:CYS19 3.8 84.2 1.0
CA C:CYS19 4.1 85.4 1.0
N C:CYS36 4.2 97.3 1.0
CA C:CYS36 4.3 0.6 1.0
CA C:CYS16 4.5 85.2 1.0
O C:ASP21 4.8 0.8 1.0
C C:ILE18 4.9 94.5 1.0
C C:CYS19 4.9 89.8 1.0

Zinc binding site 7 out of 16 in 6fga

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Zinc binding site 7 out of 16 in the Crystal Structure of TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1


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 TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn101

b:51.6
occ:1.00
ND1 D:HIS33 2.1 68.1 1.0
SG D:CYS54 2.2 54.1 1.0
SG D:CYS31 2.3 57.1 1.0
SG D:CYS51 2.4 58.1 1.0
CE1 D:HIS33 3.0 69.2 1.0
CB D:CYS51 3.1 68.2 1.0
CG D:HIS33 3.2 69.4 1.0
CB D:CYS31 3.3 60.4 1.0
CB D:HIS33 3.6 77.1 1.0
CB D:CYS54 3.6 56.1 1.0
N D:CYS54 3.7 54.2 1.0
NE2 D:HIS33 4.1 73.8 1.0
CA D:CYS54 4.2 58.1 1.0
CD2 D:HIS33 4.2 72.3 1.0
CB D:VAL53 4.5 49.1 1.0
CD1 D:ILE29 4.6 71.7 1.0
CA D:CYS51 4.6 61.9 1.0
N D:HIS33 4.6 69.5 1.0
CA D:CYS31 4.6 66.6 1.0
CA D:HIS33 4.7 73.9 1.0
C D:CYS54 4.7 61.8 1.0
C D:VAL53 4.7 52.9 1.0
N D:ARG55 4.7 66.2 1.0
CB D:GLN56 4.8 83.6 1.0
C D:CYS31 4.8 69.6 1.0
N D:GLN56 4.9 87.0 1.0
N D:VAL53 5.0 51.3 1.0
CA D:VAL53 5.0 50.6 1.0

Zinc binding site 8 out of 16 in 6fga

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Zinc binding site 8 out of 16 in the Crystal Structure of TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1


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 TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn102

b:85.8
occ:1.00
SG D:CYS39 2.3 98.3 1.0
SG D:CYS16 2.3 64.4 1.0
SG D:CYS19 2.6 93.1 1.0
SG D:CYS36 2.7 97.2 1.0
CB D:CYS16 3.0 66.1 1.0
CB D:CYS36 3.1 88.1 1.0
CB D:CYS39 3.3 96.6 1.0
CB D:CYS19 3.5 0.2 1.0
N D:CYS19 3.9 0.7 1.0
N D:CYS36 3.9 81.9 1.0
CA D:CYS36 4.1 91.6 1.0
CA D:CYS19 4.3 0.9 1.0
CA D:CYS16 4.4 71.5 1.0
CA D:CYS39 4.6 99.3 1.0
CB D:ILE18 4.7 87.3 1.0
C D:ILE18 4.8 0.3 1.0
N D:CYS39 4.9 0.9 1.0
C D:CYS16 4.9 78.3 1.0

Zinc binding site 9 out of 16 in 6fga

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Zinc binding site 9 out of 16 in the Crystal Structure of TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1


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 TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn101

b:46.4
occ:1.00
SG E:CYS51 2.2 51.0 1.0
ND1 E:HIS33 2.2 66.1 1.0
SG E:CYS54 2.2 63.9 1.0
SG E:CYS31 2.5 89.3 1.0
CG E:HIS33 3.0 74.0 1.0
CE1 E:HIS33 3.1 72.7 1.0
CB E:CYS51 3.3 43.8 1.0
CB E:HIS33 3.4 76.2 1.0
CB E:CYS31 3.5 79.8 1.0
CB E:CYS54 3.5 61.5 1.0
N E:CYS54 3.6 55.7 1.0
CD2 E:HIS33 4.1 73.0 1.0
NE2 E:HIS33 4.1 74.0 1.0
CA E:CYS54 4.1 57.6 1.0
CB E:VAL53 4.1 46.4 1.0
C E:VAL53 4.5 51.5 1.0
N E:HIS33 4.6 76.2 1.0
CA E:HIS33 4.6 76.0 1.0
CA E:CYS51 4.7 48.0 1.0
CA E:VAL53 4.7 45.3 1.0
CG1 E:VAL53 4.7 48.3 1.0
CD1 E:ILE29 4.7 56.0 1.0
N E:VAL53 4.7 43.3 1.0
CA E:CYS31 4.8 75.5 1.0
C E:CYS54 4.8 49.8 1.0
N E:ARG55 4.9 51.5 1.0
CB E:GLN56 5.0 62.9 1.0

Zinc binding site 10 out of 16 in 6fga

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Zinc binding site 10 out of 16 in the Crystal Structure of TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1


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 TRIM21 E3 Ligase, Ring Domain in Complex with Its Cognate E2 Conjugating Enzyme UBE2E1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn102

b:49.3
occ:1.00
SG E:CYS16 2.2 51.1 1.0
SG E:CYS39 2.2 45.8 1.0
SG E:CYS36 2.6 61.0 1.0
SG E:CYS19 2.7 57.3 1.0
CB E:CYS16 3.1 47.5 1.0
CB E:CYS36 3.1 68.7 1.0
CB E:CYS39 3.1 62.8 1.0
CB E:CYS19 3.4 52.2 1.0
N E:CYS19 3.8 54.6 1.0
N E:CYS36 3.8 55.1 1.0
CA E:CYS36 4.1 59.8 1.0
CA E:CYS19 4.3 56.5 1.0
CA E:CYS16 4.5 50.1 1.0
CA E:CYS39 4.5 62.7 1.0
CB E:ILE18 4.6 58.6 1.0
O E:CYS36 4.7 54.6 1.0
C E:ILE18 4.8 55.4 1.0
N E:CYS39 4.8 55.3 1.0
C E:CYS16 4.9 53.9 1.0
C E:CYS36 4.9 59.4 1.0
N E:ILE18 5.0 50.8 1.0
O E:CYS16 5.0 59.6 1.0

Reference:

M.Anandapadamanaban, N.C.Kyriakidis, V.Csizmok, A.Wallenhammar, A.C.Espinosa, A.Ahlner, A.R.Round, J.Trewhella, M.Moche, M.Wahren-Herlenius, M.Sunnerhagen. E3 Ubiquitin-Protein Ligase TRIM21-Mediated Lysine Capture By UBE2E1 Reveals Substrate-Targeting Mode of A Ubiquitin-Conjugating E2. J.Biol.Chem. V. 294 11404 2019.
ISSN: ESSN 1083-351X
PubMed: 31160341
DOI: 10.1074/JBC.RA119.008485
Page generated: Wed Dec 16 11:48:06 2020

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