Atomistry » Zinc » PDB 4rvh-4tpg » 4s3o
Atomistry »
  Zinc »
    PDB 4rvh-4tpg »
      4s3o »

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

Go back to Zinc Binding Sites List in 4s3o
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

Go back to Zinc Binding Sites List in 4s3o
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

Go back to Zinc Binding Sites List in 4s3o
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

Go back to Zinc Binding Sites List in 4s3o
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

Go back to Zinc Binding Sites List in 4s3o
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

Go back to Zinc Binding Sites List in 4s3o
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

Go back to Zinc Binding Sites List in 4s3o
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

Go back to Zinc Binding Sites List in 4s3o
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy