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Zinc in PDB 4s3o: PCGF5-RING1B-UBCH5C Complex

Enzymatic activity of PCGF5-RING1B-UBCH5C Complex

All present enzymatic activity of PCGF5-RING1B-UBCH5C Complex:
6.3.2.19;

Protein crystallography data

The structure of PCGF5-RING1B-UBCH5C Complex, PDB code: 4s3o was solved by A.M.Taherbhoy, A.G.Cochran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.92 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.392, 105.285, 132.417, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 23.7

Zinc Binding Sites:

The binding sites of Zinc atom in the PCGF5-RING1B-UBCH5C Complex (pdb code 4s3o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the PCGF5-RING1B-UBCH5C Complex, PDB code: 4s3o:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4s3o

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Zinc binding site 1 out of 8 in the PCGF5-RING1B-UBCH5C Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PCGF5-RING1B-UBCH5C Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn200

b:29.1
occ:1.00
 SG B:CYS54 2.3 27.5 1.0
SG B:CYS75 2.4 30.5 1.0
SG B:CYS72 2.4 27.6 1.0
SG B:CYS51 2.4 26.7 1.0
CB B:CYS51 3.0 20.7 1.0
CB B:CYS72 3.1 29.2 1.0
CB B:CYS54 3.3 28.2 1.0
CB B:CYS75 3.3 28.8 1.0
N B:CYS54 3.7 28.1 1.0
N B:CYS72 3.9 27.5 1.0
CA B:CYS54 4.1 25.2 1.0
CA B:CYS72 4.1 28.3 1.0
CA B:CYS51 4.5 26.1 1.0
CA B:CYS75 4.7 34.5 1.0
CB B:ILE53 4.8 26.7 1.0
C B:ILE53 4.8 29.5 1.0
C B:CYS54 4.9 24.3 1.0
C B:CYS51 5.0 24.6 1.0

Zinc binding site 2 out of 8 in 4s3o

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Zinc binding site 2 out of 8 in the PCGF5-RING1B-UBCH5C Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of PCGF5-RING1B-UBCH5C Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:34.5
occ:1.00
 ND1 B:HIS69 2.0 25.6 1.0
SG B:CYS67 2.3 33.1 1.0
SG B:CYS87 2.4 31.4 1.0
SG B:CYS90 2.4 35.5 1.0
CE1 B:HIS69 2.9 33.9 1.0
CG B:HIS69 3.1 27.8 1.0
CB B:CYS87 3.1 35.9 1.0
CB B:CYS67 3.2 36.2 1.0
CB B:CYS90 3.4 38.6 1.0
CB B:HIS69 3.6 27.0 1.0
N B:CYS90 3.7 34.6 1.0
NE2 B:HIS69 4.0 35.3 1.0
CA B:CYS90 4.1 36.4 1.0
CD2 B:HIS69 4.2 32.3 1.0
OG1 B:THR64 4.3 28.4 1.0
CB B:THR89 4.4 35.5 1.0
CA B:CYS67 4.5 35.4 1.0
CA B:CYS87 4.6 36.5 1.0
C B:THR89 4.7 36.1 1.0
C B:CYS90 4.8 37.8 1.0
C B:CYS67 4.8 30.9 1.0
O B:CYS67 4.9 31.4 1.0
CA B:HIS69 4.9 27.2 1.0
N B:HIS69 4.9 26.8 1.0
N B:ARG91 4.9 37.8 1.0
CA B:THR89 4.9 35.3 1.0
N B:THR89 4.9 32.1 1.0
CB B:LYS92 5.0 46.6 1.0

Zinc binding site 3 out of 8 in 4s3o

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Zinc binding site 3 out of 8 in the PCGF5-RING1B-UBCH5C Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of PCGF5-RING1B-UBCH5C Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:35.6
occ:1.00
 SG E:CYS72 2.3 36.0 1.0
SG E:CYS54 2.3 34.7 1.0
SG E:CYS75 2.3 38.5 1.0
SG E:CYS51 2.4 30.5 1.0
CB E:CYS51 3.0 27.2 1.0
CB E:CYS72 3.1 39.3 1.0
CB E:CYS54 3.2 33.4 1.0
CB E:CYS75 3.3 34.1 1.0
N E:CYS54 3.6 32.5 1.0
N E:CYS72 4.0 32.6 1.0
CA E:CYS54 4.0 32.4 1.0
CA E:CYS72 4.1 33.6 1.0
CA E:CYS51 4.5 36.5 1.0
CB E:ILE53 4.7 32.8 1.0
CA E:CYS75 4.7 35.5 1.0
C E:ILE53 4.7 38.1 1.0
C E:CYS54 4.9 32.3 1.0
C E:CYS51 4.9 34.6 1.0
O E:CYS51 5.0 36.4 1.0

Zinc binding site 4 out of 8 in 4s3o

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Zinc binding site 4 out of 8 in the PCGF5-RING1B-UBCH5C Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of PCGF5-RING1B-UBCH5C Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn202

b:39.0
occ:1.00
 ND1 E:HIS69 2.0 34.0 1.0
SG E:CYS67 2.3 40.5 1.0
SG E:CYS87 2.3 36.1 1.0
SG E:CYS90 2.4 40.6 1.0
CE1 E:HIS69 2.8 43.5 1.0
CB E:CYS67 3.0 42.1 1.0
CG E:HIS69 3.1 33.2 1.0
CB E:CYS87 3.2 47.2 1.0
CB E:CYS90 3.5 42.6 1.0
CB E:HIS69 3.5 35.4 1.0
N E:CYS90 3.7 39.8 1.0
NE2 E:HIS69 4.0 41.7 1.0
CA E:CYS90 4.1 42.9 1.0
CD2 E:HIS69 4.1 36.7 1.0
OG1 E:THR64 4.3 38.3 1.0
CB E:THR89 4.4 41.2 1.0
CA E:CYS67 4.4 41.1 1.0
CA E:CYS87 4.6 40.5 1.0
C E:THR89 4.7 43.6 1.0
C E:CYS90 4.8 47.5 1.0
CA E:HIS69 4.8 36.8 1.0
C E:CYS67 4.9 38.8 1.0
N E:HIS69 4.9 37.2 1.0
CA E:THR89 4.9 41.6 1.0
CG2 E:THR89 4.9 43.0 1.0
N E:ARG91 4.9 48.2 1.0
N E:THR89 4.9 37.6 1.0
O E:CYS67 5.0 36.4 1.0
CB E:LYS92 5.0 61.5 1.0

Zinc binding site 5 out of 8 in 4s3o

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Zinc binding site 5 out of 8 in the PCGF5-RING1B-UBCH5C Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of PCGF5-RING1B-UBCH5C Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:33.2
occ:1.00
 SG C:CYS21 2.2 36.0 1.0
SG C:CYS42 2.3 31.6 1.0
SG C:CYS18 2.4 31.3 1.0
SG C:CYS39 2.5 30.8 1.0
CB C:CYS18 3.0 27.5 1.0
CB C:CYS39 3.1 27.9 1.0
CB C:CYS21 3.2 37.2 1.0
CB C:CYS42 3.3 39.5 1.0
N C:CYS21 3.8 32.4 1.0
N C:CYS39 3.9 32.8 1.0
CA C:CYS21 4.1 37.9 1.0
CA C:CYS39 4.1 30.0 1.0
O C:HOH311 4.3 33.6 1.0
NH1 B:ARG26 4.4 38.0 1.0
CA C:CYS18 4.5 34.1 1.0
CB C:ILE20 4.7 36.5 1.0
CA C:CYS42 4.7 35.8 1.0
C C:CYS21 4.9 38.6 1.0
C C:ILE20 4.9 34.6 1.0
N C:CYS42 5.0 29.7 1.0

Zinc binding site 6 out of 8 in 4s3o

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Zinc binding site 6 out of 8 in the PCGF5-RING1B-UBCH5C Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of PCGF5-RING1B-UBCH5C Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:31.5
occ:1.00
 ND1 C:HIS36 2.1 31.5 1.0
SG C:CYS34 2.3 34.9 1.0
SG C:CYS53 2.3 34.0 1.0
SG C:CYS56 2.4 38.1 1.0
CE1 C:HIS36 2.9 33.4 1.0
CB C:CYS53 3.1 40.6 1.0
CG C:HIS36 3.2 30.3 1.0
CB C:CYS34 3.3 36.4 1.0
CB C:CYS56 3.5 46.8 1.0
CB C:HIS36 3.6 28.6 1.0
N C:CYS56 3.8 36.7 1.0
NE2 C:HIS36 4.1 35.2 1.0
CA C:CYS56 4.2 46.9 1.0
CD2 C:HIS36 4.2 31.4 1.0
CA C:CYS53 4.5 41.2 1.0
O C:HOH313 4.5 37.5 1.0
CA C:CYS34 4.6 37.8 1.0
O C:CYS34 4.7 31.3 1.0
CB C:ARG55 4.7 31.9 1.0
C C:CYS34 4.7 35.3 1.0
N C:HIS36 4.8 27.8 1.0
CA C:HIS36 4.8 29.0 1.0
C C:ARG55 4.8 41.0 1.0
C C:CYS56 4.9 43.4 1.0
CB C:ASN58 5.0 52.4 1.0
N C:GLY57 5.0 43.0 1.0
N C:ARG55 5.0 34.9 1.0
C C:CYS53 5.0 37.6 1.0

Zinc binding site 7 out of 8 in 4s3o

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Zinc binding site 7 out of 8 in the PCGF5-RING1B-UBCH5C Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of PCGF5-RING1B-UBCH5C Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:29.5
occ:1.00
 SG F:CYS18 2.3 28.3 1.0
SG F:CYS21 2.3 32.0 1.0
SG F:CYS42 2.4 29.0 1.0
SG F:CYS39 2.5 27.1 1.0
CB F:CYS18 2.9 27.8 1.0
CB F:CYS39 3.1 24.2 1.0
CB F:CYS21 3.3 26.2 1.0
CB F:CYS42 3.3 26.8 1.0
N F:CYS21 3.8 30.7 1.0
N F:CYS39 3.9 26.9 1.0
CA F:CYS39 4.1 25.7 1.0
CA F:CYS21 4.1 30.5 1.0
NH1 E:ARG26 4.3 29.0 1.0
CA F:CYS18 4.4 32.3 1.0
O F:HOH303 4.6 26.7 1.0
CB F:ILE20 4.7 33.3 1.0
CA F:CYS42 4.7 26.4 1.0
O F:HOH335 4.7 44.5 1.0
C F:ILE20 4.9 32.6 1.0
C F:CYS21 4.9 33.2 1.0
C F:CYS18 5.0 31.6 1.0
N F:CYS42 5.0 24.7 1.0

Zinc binding site 8 out of 8 in 4s3o

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Zinc binding site 8 out of 8 in the PCGF5-RING1B-UBCH5C Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of PCGF5-RING1B-UBCH5C Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn202

b:36.9
occ:1.00
 ND1 F:HIS36 2.0 34.6 1.0
SG F:CYS34 2.2 37.3 1.0
SG F:CYS53 2.4 38.7 1.0
SG F:CYS56 2.4 43.4 1.0
CE1 F:HIS36 3.0 40.0 1.0
CB F:CYS53 3.1 38.2 1.0
CG F:HIS36 3.1 36.7 1.0
CB F:CYS34 3.2 47.2 1.0
CB F:CYS56 3.4 44.2 1.0
CB F:HIS36 3.5 32.2 1.0
N F:CYS56 3.8 43.7 1.0
NE2 F:HIS36 4.1 42.1 1.0
CA F:CYS56 4.2 47.9 1.0
CD2 F:HIS36 4.2 39.9 1.0
CA F:CYS34 4.5 46.1 1.0
CA F:CYS53 4.6 37.3 1.0
O F:CYS34 4.7 38.5 1.0
C F:CYS34 4.7 43.0 1.0
N F:HIS36 4.7 35.0 1.0
CA F:HIS36 4.7 32.0 1.0
CB F:ARG55 4.8 46.7 1.0
CB F:ASN58 4.8 51.8 1.0
C F:CYS56 4.8 48.8 1.0
C F:ARG55 4.9 49.0 1.0
N F:GLY57 5.0 42.7 1.0

Reference:

A.M.Taherbhoy, O.W.Huang, A.G.Cochran. BMI1-RING1B Is An Autoinhibited Ring E3 Ubiquitin Ligase. Nat Commun V. 6 7621 2015.
ISSN: ESSN 2041-1723
PubMed: 26151332
DOI: 10.1038/NCOMMS8621
Page generated: Sun Oct 27 08:23:04 2024

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