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Zinc in PDB 6h78: E1 Enzyme For Ubiquitin Like Protein Activation.

Protein crystallography data

The structure of E1 Enzyme For Ubiquitin Like Protein Activation., PDB code: 6h78 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) 107.98 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 143.860, 151.933, 153.543, 90.00, 93.07, 90.00
R / Rfree (%) 19 / 24.2

Other elements in 6h78:

The structure of E1 Enzyme For Ubiquitin Like Protein Activation. also contains other interesting chemical elements:

Magnesium (Mg) 32 atoms
Chlorine (Cl) 1 atom

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the E1 Enzyme For Ubiquitin Like Protein Activation. (pdb code 6h78). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the E1 Enzyme For Ubiquitin Like Protein Activation., PDB code: 6h78:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 6h78

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Zinc binding site 1 out of 16 in the E1 Enzyme For Ubiquitin Like Protein Activation.


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. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:45.0
occ:1.00
 SG A:CYS308 2.3 39.7 1.0
SG A:CYS303 2.3 48.6 1.0
SG A:CYS229 2.4 42.5 1.0
SG A:CYS226 2.4 40.7 1.0
CB A:CYS308 3.1 49.0 1.0
CB A:CYS303 3.2 54.9 1.0
CB A:CYS226 3.3 31.5 1.0
N A:CYS229 3.6 35.9 1.0
CB A:CYS229 3.6 28.3 1.0
N A:CYS226 3.7 30.5 1.0
CA A:CYS229 3.8 39.1 1.0
CA A:CYS226 3.9 39.8 1.0
O A:HOH528 4.2 47.6 1.0
C A:CYS226 4.3 35.9 1.0
C A:ALA228 4.4 48.8 1.0
O A:CYS226 4.5 32.8 1.0
N A:ALA228 4.5 43.2 1.0
CB A:ALA228 4.6 54.0 1.0
CA A:CYS303 4.6 55.8 1.0
CA A:CYS308 4.6 45.0 1.0
CA A:ALA228 4.7 50.9 1.0
OE1 A:GLN312 4.7 61.5 1.0
O A:ASN300 4.8 43.6 1.0
CB A:ASP305 4.9 55.3 1.0
C A:ALA225 4.9 35.6 1.0
ND2 A:ASN196 5.0 50.4 1.0

Zinc binding site 2 out of 16 in 6h78

Go back to Zinc Binding Sites List in 6h78
Zinc binding site 2 out of 16 in the E1 Enzyme For Ubiquitin Like Protein Activation.


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. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:44.8
occ:1.00
 SG B:CYS308 2.2 37.1 1.0
SG B:CYS303 2.3 47.6 1.0
SG B:CYS229 2.4 45.8 1.0
SG B:CYS226 2.4 49.6 1.0
CB B:CYS308 2.9 46.1 1.0
CB B:CYS303 3.2 57.2 1.0
CB B:CYS226 3.4 33.5 1.0
CB B:CYS229 3.6 33.3 1.0
N B:CYS229 3.7 38.9 1.0
CA B:CYS229 3.8 39.1 1.0
N B:CYS226 4.1 40.0 1.0
CA B:CYS226 4.2 44.9 1.0
O B:HOH506 4.3 53.8 1.0
CA B:CYS308 4.4 48.1 1.0
C B:ALA228 4.4 62.7 1.0
C B:CYS226 4.6 41.0 1.0
CA B:CYS303 4.6 43.1 1.0
ND2 B:ASN196 4.7 35.4 1.0
O B:CYS226 4.7 43.4 1.0
CB B:ALA228 4.7 50.8 1.0
CB B:ASP305 4.8 85.3 1.0
N B:ALA228 4.8 48.5 1.0
O B:ASN300 4.8 45.4 1.0
OE1 B:GLN312 4.9 57.7 1.0
CA B:ALA228 4.9 64.3 1.0
C B:CYS308 5.0 44.0 1.0

Zinc binding site 3 out of 16 in 6h78

Go back to Zinc Binding Sites List in 6h78
Zinc binding site 3 out of 16 in the E1 Enzyme For Ubiquitin Like Protein Activation.


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. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:70.9
occ:1.00
 SG C:CYS229 2.3 57.8 1.0
SG C:CYS308 2.3 52.6 1.0
SG C:CYS303 2.3 75.2 1.0
SG C:CYS226 2.4 71.9 1.0
CB C:CYS308 3.0 48.6 1.0
CB C:CYS303 3.2 0.6 1.0
CB C:CYS226 3.4 53.9 1.0
CB C:CYS229 3.5 52.2 1.0
N C:CYS229 3.5 59.4 1.0
CA C:CYS229 3.6 57.8 1.0
N C:CYS226 4.0 52.6 1.0
CA C:CYS226 4.2 47.4 1.0
C C:ALA228 4.4 66.3 1.0
CA C:CYS308 4.5 80.2 1.0
C C:CYS226 4.6 56.2 1.0
O C:HOH510 4.6 60.9 1.0
NE2 C:GLN312 4.6 66.4 1.0
CA C:CYS303 4.6 76.5 1.0
N C:ALA228 4.7 65.3 1.0
O C:CYS226 4.7 47.8 1.0
CB C:ALA228 4.7 59.3 1.0
CA C:ALA228 4.8 60.8 1.0
CB C:ASP305 4.8 84.6 1.0
O C:ASN300 4.9 73.7 1.0

Zinc binding site 4 out of 16 in 6h78

Go back to Zinc Binding Sites List in 6h78
Zinc binding site 4 out of 16 in the E1 Enzyme For Ubiquitin Like Protein Activation.


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. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn403

b:50.3
occ:1.00
 SG D:CYS226 2.3 40.3 1.0
SG D:CYS308 2.3 37.3 1.0
SG D:CYS229 2.3 53.2 1.0
SG D:CYS303 2.4 53.7 1.0
CB D:CYS308 3.1 56.1 1.0
CB D:CYS226 3.2 40.6 1.0
CB D:CYS303 3.4 59.4 1.0
CB D:CYS229 3.4 51.0 1.0
N D:CYS229 3.5 55.3 1.0
CA D:CYS229 3.6 49.6 1.0
N D:CYS226 3.8 30.2 1.0
CA D:CYS226 4.0 36.0 1.0
O D:HOH521 4.3 63.9 1.0
C D:ALA228 4.4 56.2 1.0
C D:CYS226 4.4 34.7 1.0
CB D:ALA228 4.5 62.0 1.0
O D:CYS226 4.5 41.7 1.0
CA D:CYS308 4.6 60.2 1.0
N D:ALA228 4.7 50.0 1.0
CA D:ALA228 4.8 51.3 1.0
CA D:CYS303 4.8 60.2 1.0
OE1 D:GLN312 4.8 41.0 1.0
CB D:ASP305 4.9 71.2 1.0
C D:ALA225 4.9 38.2 1.0
O D:ASN300 5.0 53.4 1.0

Zinc binding site 5 out of 16 in 6h78

Go back to Zinc Binding Sites List in 6h78
Zinc binding site 5 out of 16 in the E1 Enzyme For Ubiquitin Like Protein Activation.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of E1 Enzyme For Ubiquitin Like Protein Activation. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn403

b:59.0
occ:1.00
 SG E:CYS303 2.3 72.1 1.0
SG E:CYS229 2.3 58.0 1.0
SG E:CYS308 2.3 50.1 1.0
SG E:CYS226 2.4 56.8 1.0
CB E:CYS308 3.1 48.0 1.0
CB E:CYS303 3.2 78.3 1.0
CB E:CYS226 3.4 45.4 1.0
CB E:CYS229 3.4 57.9 1.0
N E:CYS229 3.4 51.9 1.0
CA E:CYS229 3.5 62.0 1.0
N E:CYS226 4.0 40.7 1.0
CA E:CYS226 4.2 36.8 1.0
C E:ALA228 4.3 59.5 1.0
C E:CYS226 4.5 44.1 1.0
CA E:CYS303 4.6 59.8 1.0
CA E:CYS308 4.6 57.6 1.0
CB E:ALA228 4.6 44.6 1.0
O E:CYS226 4.7 47.0 1.0
N E:ALA228 4.7 47.8 1.0
CA E:ALA228 4.8 52.5 1.0
CB E:ASP305 4.8 0.6 1.0
O E:ASN300 4.8 63.1 1.0
ND2 E:ASN196 4.9 40.7 1.0
C E:CYS229 5.0 64.5 1.0

Zinc binding site 6 out of 16 in 6h78

Go back to Zinc Binding Sites List in 6h78
Zinc binding site 6 out of 16 in the E1 Enzyme For Ubiquitin Like Protein Activation.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of E1 Enzyme For Ubiquitin Like Protein Activation. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn403

b:47.9
occ:1.00
 SG F:CYS308 2.3 35.9 1.0
SG F:CYS303 2.3 54.4 1.0
SG F:CYS229 2.4 50.3 1.0
SG F:CYS226 2.4 43.6 1.0
CB F:CYS308 3.0 35.8 1.0
CB F:CYS303 3.1 61.7 1.0
CB F:CYS226 3.5 32.6 1.0
N F:CYS229 3.6 48.8 1.0
CB F:CYS229 3.6 34.7 1.0
CA F:CYS229 3.7 55.6 1.0
N F:CYS226 4.1 32.6 1.0
CA F:CYS226 4.2 41.4 1.0
C F:ALA228 4.4 65.0 1.0
CA F:CYS308 4.4 42.2 1.0
O F:HOH512 4.4 46.5 1.0
C F:CYS226 4.5 35.5 1.0
CB F:ALA228 4.6 63.4 1.0
CA F:CYS303 4.6 50.9 1.0
O F:CYS226 4.6 34.5 1.0
O F:ASN300 4.7 79.3 1.0
N F:ALA228 4.7 42.2 1.0
CA F:ALA228 4.8 57.4 1.0
OE1 F:GLN312 4.8 78.4 1.0
CB F:ASP305 4.9 44.9 1.0
O F:ASP305 5.0 35.3 1.0

Zinc binding site 7 out of 16 in 6h78

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Zinc binding site 7 out of 16 in the E1 Enzyme For Ubiquitin Like Protein Activation.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of E1 Enzyme For Ubiquitin Like Protein Activation. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn403

b:46.2
occ:1.00
 SG G:CYS229 2.3 34.9 1.0
SG G:CYS303 2.3 43.9 1.0
SG G:CYS308 2.3 35.7 1.0
SG G:CYS226 2.3 45.3 1.0
CB G:CYS308 3.2 34.8 1.0
CB G:CYS226 3.3 39.6 1.0
CB G:CYS303 3.3 54.6 1.0
CB G:CYS229 3.4 30.0 1.0
N G:CYS229 3.4 38.1 1.0
CA G:CYS229 3.6 33.5 1.0
N G:CYS226 3.9 33.2 1.0
CA G:CYS226 4.1 39.3 1.0
O G:HOH544 4.2 54.2 1.0
C G:ALA228 4.3 47.1 1.0
C G:CYS226 4.5 43.2 1.0
N G:ALA228 4.6 44.7 1.0
O G:CYS226 4.6 43.7 1.0
CB G:ALA228 4.6 42.8 1.0
CA G:CYS308 4.6 48.4 1.0
CA G:ALA228 4.7 44.9 1.0
CB G:ASP305 4.7 59.3 1.0
CA G:CYS303 4.7 43.6 1.0
OE1 G:GLN312 4.8 36.7 1.0
OD1 G:ASN196 4.9 28.1 1.0

Zinc binding site 8 out of 16 in 6h78

Go back to Zinc Binding Sites List in 6h78
Zinc binding site 8 out of 16 in the E1 Enzyme For Ubiquitin Like Protein Activation.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of E1 Enzyme For Ubiquitin Like Protein Activation. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn403

b:47.1
occ:1.00
 SG H:CYS308 2.3 48.7 1.0
SG H:CYS229 2.3 51.0 1.0
SG H:CYS226 2.3 38.8 1.0
SG H:CYS303 2.3 41.7 1.0
CB H:CYS308 3.2 58.0 1.0
CB H:CYS226 3.3 43.1 1.0
CB H:CYS303 3.3 59.4 1.0
CB H:CYS229 3.5 45.6 1.0
N H:CYS229 3.6 34.3 1.0
CA H:CYS229 3.8 42.5 1.0
N H:CYS226 3.8 33.2 1.0
CA H:CYS226 4.0 43.1 1.0
C H:ALA228 4.3 47.1 1.0
C H:CYS226 4.4 28.6 1.0
O H:CYS226 4.5 30.7 1.0
CB H:ALA228 4.5 41.2 1.0
N H:ALA228 4.5 38.3 1.0
CA H:CYS308 4.7 42.5 1.0
CA H:CYS303 4.7 66.6 1.0
CA H:ALA228 4.7 39.9 1.0
OE1 H:GLN312 4.8 44.6 1.0
ND2 H:ASN196 4.9 29.6 1.0
O H:ASN300 4.9 56.6 1.0
CB H:ASP305 5.0 56.6 1.0

Zinc binding site 9 out of 16 in 6h78

Go back to Zinc Binding Sites List in 6h78
Zinc binding site 9 out of 16 in the E1 Enzyme For Ubiquitin Like Protein Activation.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of E1 Enzyme For Ubiquitin Like Protein Activation. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn402

b:44.9
occ:1.00
 SG I:CYS303 2.3 41.2 1.0
SG I:CYS226 2.3 41.9 1.0
SG I:CYS229 2.3 44.8 1.0
SG I:CYS308 2.3 39.8 1.0
CB I:CYS226 3.2 33.1 1.0
CB I:CYS303 3.2 45.5 1.0
CB I:CYS308 3.3 48.9 1.0
CB I:CYS229 3.5 27.9 1.0
N I:CYS229 3.6 30.6 1.0
N I:CYS226 3.8 41.6 1.0
CA I:CYS229 3.8 30.9 1.0
CA I:CYS226 3.9 41.8 1.0
C I:CYS226 4.3 41.1 1.0
O I:CYS226 4.3 46.5 1.0
O I:HOH527 4.3 42.5 1.0
C I:ALA228 4.3 41.4 1.0
N I:ALA228 4.4 40.1 1.0
CB I:ALA228 4.6 53.3 1.0
CA I:CYS303 4.6 47.0 1.0
CA I:ALA228 4.7 41.9 1.0
OE1 I:GLN312 4.7 47.3 1.0
CA I:CYS308 4.7 47.4 1.0
ND2 I:ASN196 4.9 31.9 1.0
CB I:ASP305 5.0 59.2 1.0
O I:ASN300 5.0 48.0 1.0
C I:ALA225 5.0 43.3 1.0

Zinc binding site 10 out of 16 in 6h78

Go back to Zinc Binding Sites List in 6h78
Zinc binding site 10 out of 16 in the E1 Enzyme For Ubiquitin Like Protein Activation.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of E1 Enzyme For Ubiquitin Like Protein Activation. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn403

b:40.1
occ:1.00
 SG J:CYS229 2.2 37.8 1.0
SG J:CYS308 2.3 35.4 1.0
SG J:CYS303 2.3 44.1 1.0
SG J:CYS226 2.4 43.6 1.0
CB J:CYS308 3.1 37.6 1.0
CB J:CYS303 3.2 51.8 1.0
N J:CYS229 3.4 35.9 1.0
CB J:CYS229 3.4 32.9 1.0
CB J:CYS226 3.5 36.8 1.0
CA J:CYS229 3.5 29.3 1.0
N J:CYS226 3.9 41.0 1.0
CA J:CYS226 4.1 42.1 1.0
O J:HOH519 4.3 51.6 1.0
C J:ALA228 4.3 38.6 1.0
C J:CYS226 4.6 44.0 1.0
CA J:CYS303 4.6 60.2 1.0
N J:ALA228 4.6 54.6 1.0
CA J:CYS308 4.6 46.4 1.0
O J:CYS226 4.6 42.5 1.0
CB J:ALA228 4.7 51.6 1.0
CA J:ALA228 4.7 43.3 1.0
OE1 J:GLN312 4.7 40.9 1.0
OD1 J:ASN196 4.8 30.4 1.0
CB J:ASP305 4.8 55.6 1.0
O J:ASN300 5.0 36.8 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: Mon Oct 28 22:40:52 2024

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