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Zinc in PDB 6h77: E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl

Protein crystallography data

The structure of E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl, PDB code: 6h77 was solved by N.Soudah, P.Padala, F.Hassouna, B.Mashahreh, A.A.Lebedev, M.N.Isupov, E.Cohen-Kfir, R.Wiener, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.76 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.110, 105.520, 93.880, 90.00, 102.29, 90.00
R / Rfree (%) 18.4 / 22.1

Other elements in 6h77:

The structure of E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl (pdb code 6h77). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl, PDB code: 6h77:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6h77

Go back to Zinc Binding Sites List in 6h77
Zinc binding site 1 out of 4 in the E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:42.8
occ:1.00
SG A:CYS229 2.3 46.9 1.0
SG A:CYS308 2.3 43.0 1.0
SG A:CYS303 2.3 48.1 1.0
SG A:CYS226 2.4 38.2 1.0
CB A:CYS303 3.1 42.7 1.0
CB A:CYS308 3.1 44.5 1.0
N A:CYS229 3.2 35.3 1.0
CB A:CYS226 3.4 37.1 1.0
CB A:CYS229 3.5 35.2 1.0
CA A:CYS229 3.5 45.5 1.0
N A:CYS226 4.0 49.1 1.0
C A:ALA228 4.1 54.5 1.0
CA A:CYS226 4.1 38.1 1.0
CB A:ALA228 4.5 39.8 1.0
C A:CYS226 4.5 44.3 1.0
O A:CYS226 4.5 45.2 1.0
O A:HOH557 4.5 47.8 1.0
CA A:CYS303 4.5 45.7 1.0
CA A:ALA228 4.6 48.1 1.0
N A:ALA228 4.6 33.3 1.0
NE2 A:GLN312 4.6 45.1 1.0
CA A:CYS308 4.6 46.4 1.0
ND2 A:ASN196 4.8 41.2 1.0
O A:ALA228 4.8 44.4 1.0
O A:ASN300 5.0 48.1 1.0

Zinc binding site 2 out of 4 in 6h77

Go back to Zinc Binding Sites List in 6h77
Zinc binding site 2 out of 4 in the E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:45.8
occ:1.00
SG B:CYS229 2.3 44.5 1.0
SG B:CYS308 2.3 43.6 1.0
SG B:CYS303 2.4 53.2 1.0
SG B:CYS226 2.4 45.7 1.0
N B:CYS229 3.2 38.8 1.0
CB B:CYS303 3.2 60.8 1.0
CB B:CYS308 3.2 45.7 1.0
CB B:CYS226 3.4 45.4 1.0
CB B:CYS229 3.5 37.4 1.0
CA B:CYS229 3.5 49.8 1.0
N B:CYS226 3.9 41.5 1.0
C B:ALA228 4.0 60.8 1.0
CA B:CYS226 4.1 40.0 1.0
CB B:ALA228 4.4 45.3 1.0
C B:CYS226 4.5 39.2 1.0
O B:CYS226 4.5 41.6 1.0
O B:HOH541 4.5 38.8 1.0
CA B:CYS303 4.6 53.6 1.0
NE2 B:GLN312 4.6 48.2 1.0
CA B:ALA228 4.6 53.8 1.0
N B:ALA228 4.6 42.1 1.0
CA B:CYS308 4.6 48.2 1.0
ND2 B:ASN196 4.8 36.2 1.0
O B:ALA228 4.8 53.5 1.0
O B:ASN300 5.0 50.8 1.0

Zinc binding site 3 out of 4 in 6h77

Go back to Zinc Binding Sites List in 6h77
Zinc binding site 3 out of 4 in the E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:47.4
occ:1.00
SG C:CYS308 2.3 39.6 1.0
SG C:CYS229 2.3 45.4 1.0
SG C:CYS303 2.4 55.8 1.0
SG C:CYS226 2.4 45.9 1.0
CB C:CYS308 3.1 39.4 1.0
CB C:CYS303 3.2 54.8 1.0
N C:CYS229 3.2 45.2 1.0
CB C:CYS226 3.4 51.8 1.0
CB C:CYS229 3.5 38.5 1.0
CA C:CYS229 3.6 44.0 1.0
N C:CYS226 3.9 47.4 1.0
CA C:CYS226 4.1 37.1 1.0
C C:ALA228 4.1 55.3 1.0
C C:CYS226 4.4 38.1 1.0
O C:HOH532 4.5 43.4 1.0
O C:CYS226 4.5 43.8 1.0
NE2 C:GLN312 4.5 51.0 1.0
CB C:ALA228 4.5 47.9 1.0
CA C:CYS303 4.6 53.3 1.0
CA C:CYS308 4.6 44.8 1.0
CA C:ALA228 4.7 52.1 1.0
N C:ALA228 4.7 43.6 1.0
ND2 C:ASN196 4.8 42.1 1.0
O C:ALA228 4.9 53.8 1.0
O C:ASN300 5.0 50.0 1.0

Zinc binding site 4 out of 4 in 6h77

Go back to Zinc Binding Sites List in 6h77
Zinc binding site 4 out of 4 in the E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn403

b:40.1
occ:1.00
SG D:CYS308 2.3 35.4 1.0
SG D:CYS229 2.3 40.3 1.0
SG D:CYS303 2.4 45.4 1.0
SG D:CYS226 2.4 38.4 1.0
CB D:CYS308 3.1 36.3 1.0
CB D:CYS303 3.1 35.8 1.0
N D:CYS229 3.2 36.7 1.0
CB D:CYS226 3.4 37.1 1.0
CB D:CYS229 3.5 33.7 1.0
CA D:CYS229 3.6 41.5 1.0
N D:CYS226 3.9 39.8 1.0
CA D:CYS226 4.1 34.5 1.0
C D:ALA228 4.1 51.4 1.0
C D:CYS226 4.5 36.9 1.0
O D:CYS226 4.5 41.0 1.0
CB D:ALA228 4.5 40.5 1.0
O D:HOH531 4.5 40.9 1.0
CA D:CYS303 4.6 40.4 1.0
NE2 D:GLN312 4.6 38.9 1.0
CA D:CYS308 4.6 38.5 1.0
CA D:ALA228 4.7 42.5 1.0
N D:ALA228 4.7 38.7 1.0
ND2 D:ASN196 4.8 40.6 1.0
O D:ALA228 4.9 35.5 1.0

Reference:

N.Soudah, P.Padala, F.Hassouna, M.Kumar, B.Mashahreh, A.A.Lebedev, M.N.Isupov, E.Cohen-Kfir, R.Wiener. An N-Terminal Extension to UBA5 Adenylation Domain Boosts UFM1 Activation: Isoform-Specific Differences in Ubiquitin-Like Protein Activation. J.Mol.Biol. V. 431 463 2019.
ISSN: ESSN 1089-8638
PubMed: 30412706
DOI: 10.1016/J.JMB.2018.10.007
Page generated: Wed Dec 16 11:55:58 2020

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