Zinc in PDB 6y75: BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A)

Enzymatic activity of BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A)

All present enzymatic activity of BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A):
2.4.2.31;

Protein crystallography data

The structure of BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A), PDB code: 6y75 was solved by A.Ilari, V.Chiarini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.57 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.821, 67.605, 82.445, 90, 114.58, 90
R / Rfree (%) 25.4 / 30.2

Zinc Binding Sites:

The binding sites of Zinc atom in the BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A) (pdb code 6y75). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A), PDB code: 6y75:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6y75

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Zinc binding site 1 out of 4 in the BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:29.8
occ:1.00
NE2 A:HIS48 2.1 29.9 1.0
NE2 A:HIS125 2.1 24.5 1.0
N A:ASN-4 2.2 35.8 1.0
O A:ASN-4 2.2 31.4 1.0
C A:ASN-4 3.0 33.2 1.0
CD2 A:HIS48 3.0 30.6 1.0
CE1 A:HIS48 3.1 30.6 1.0
CE1 A:HIS125 3.1 23.8 1.0
CD2 A:HIS125 3.1 23.7 1.0
CA A:ASN-4 3.1 36.1 1.0
ND2 A:ASN-4 3.8 43.4 1.0
ND1 A:HIS48 4.1 32.2 1.0
CG A:HIS48 4.2 30.9 1.0
ND1 A:HIS125 4.2 24.2 1.0
CG A:HIS125 4.2 24.3 1.0
N A:LEU-3 4.3 31.3 1.0
CG1 A:VAL46 4.3 28.0 1.0
CB A:ASN-4 4.4 38.1 1.0
SD A:MET144 4.4 55.0 1.0
CG A:ASN-4 4.6 41.4 1.0
CB A:VAL46 4.7 28.0 1.0
O A:HOH627 4.9 30.4 1.0
CA A:LEU-3 5.0 30.8 1.0

Zinc binding site 2 out of 4 in 6y75

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Zinc binding site 2 out of 4 in the BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:36.4
occ:1.00
NE2 B:HIS125 2.1 33.5 1.0
NE2 B:HIS48 2.1 34.7 1.0
N B:ASN-4 2.2 46.0 1.0
O B:HOH657 2.4 41.2 1.0
O B:ASN-4 2.4 42.0 1.0
CE1 B:HIS125 3.1 33.0 1.0
CD2 B:HIS48 3.1 35.1 1.0
CE1 B:HIS48 3.1 34.5 1.0
CD2 B:HIS125 3.1 32.2 1.0
C B:ASN-4 3.2 43.6 1.0
CA B:ASN-4 3.2 45.0 1.0
ND2 B:ASN-4 3.8 50.3 1.0
CG1 B:VAL46 4.1 29.8 1.0
ND1 B:HIS125 4.2 32.5 1.0
ND1 B:HIS48 4.2 34.1 1.0
CG B:HIS48 4.2 34.6 1.0
CG B:HIS125 4.3 31.9 1.0
SD B:MET144 4.4 90.7 1.0
CB B:ASN-4 4.4 46.9 1.0
N B:LEU-3 4.5 41.0 1.0
CB B:VAL46 4.6 30.3 1.0
CG B:ASN-4 4.6 48.9 1.0
CG2 B:VAL46 5.0 29.6 1.0
O B:HOH630 5.0 52.5 1.0

Zinc binding site 3 out of 4 in 6y75

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Zinc binding site 3 out of 4 in the BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:33.3
occ:1.00
NE2 C:HIS48 1.9 34.0 1.0
NE2 C:HIS125 2.1 32.5 1.0
N C:ASN-4 2.2 40.8 1.0
O C:ASN-4 2.3 38.4 1.0
CD2 C:HIS48 2.9 34.9 1.0
CE1 C:HIS48 2.9 35.8 1.0
CD2 C:HIS125 3.1 31.0 1.0
C C:ASN-4 3.1 38.4 1.0
CE1 C:HIS125 3.1 32.1 1.0
CA C:ASN-4 3.2 40.3 1.0
ND2 C:ASN-4 4.0 42.8 1.0
ND1 C:HIS48 4.0 36.5 1.0
CG C:HIS48 4.0 34.8 1.0
CG1 C:VAL46 4.1 31.6 1.0
ND1 C:HIS125 4.2 31.6 1.0
CG C:HIS125 4.2 30.5 1.0
O C:HOH414 4.4 35.5 1.0
N C:LEU-3 4.4 37.1 1.0
CB C:ASN-4 4.5 41.2 1.0
SD C:MET144 4.5 63.7 1.0
CB C:VAL46 4.6 34.2 1.0
CG C:ASN-4 4.7 42.2 1.0

Zinc binding site 4 out of 4 in 6y75

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Zinc binding site 4 out of 4 in the BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:33.8
occ:1.00
NE2 D:HIS48 2.0 38.0 1.0
N D:ASN-4 2.1 45.7 1.0
NE2 D:HIS125 2.2 29.6 1.0
O D:ASN-4 2.4 40.5 1.0
O D:HOH429 2.4 31.2 1.0
CD2 D:HIS48 3.0 39.1 1.0
CE1 D:HIS48 3.0 38.6 1.0
C D:ASN-4 3.1 43.3 1.0
CE1 D:HIS125 3.1 31.3 1.0
CA D:ASN-4 3.2 46.1 1.0
CD2 D:HIS125 3.2 29.4 1.0
ND2 D:ASN-4 3.7 55.0 1.0
ND1 D:HIS48 4.1 38.9 1.0
CG D:HIS48 4.1 38.1 1.0
CG1 D:VAL46 4.1 29.1 1.0
ND1 D:HIS125 4.3 30.0 1.0
CG D:HIS125 4.3 29.0 1.0
CB D:ASN-4 4.3 49.5 1.0
N D:LEU-3 4.5 40.7 1.0
SD D:MET144 4.5 77.5 1.0
CG D:ASN-4 4.5 53.5 1.0
CB D:VAL46 4.6 29.8 1.0

Reference:

V.Chiarini, A.Fiorillo, S.Camerini, M.Crescenzi, S.Nakamura, T.Battista, L.Guidoni, G.Colotti, A.Ilari. Structural Basis of Ubiquitination Mediated By Protein Splicing in Early Eukarya Biochim.Biophys.Acta 2021.
ISSN: ISSN 0006-3002
DOI: HTTPS://DOI.ORG/10.1016/J.BBAGEN.2021.129844
Page generated: Wed Mar 3 16:14:10 2021

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