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Zinc in PDB 4r8p: Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle

Enzymatic activity of Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle

All present enzymatic activity of Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle:
6.3.2.19;

Protein crystallography data

The structure of Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle, PDB code: 4r8p was solved by R.K.Mcginty, R.C.Henrici, S.Tan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 3.28
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 104.923, 180.049, 375.251, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle (pdb code 4r8p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle, PDB code: 4r8p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4r8p

Go back to Zinc Binding Sites List in 4r8p
Zinc binding site 1 out of 8 in the Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn201

b:81.7
occ:1.00
 SG K:CYS39 2.3 80.4 1.0
SG K:CYS18 2.4 79.6 1.0
SG K:CYS42 2.4 85.8 1.0
SG K:CYS21 2.4 86.8 1.0
CB K:CYS39 2.9 91.6 1.0
CB K:CYS18 3.1 80.3 1.0
CB K:CYS21 3.2 87.5 1.0
CB K:CYS42 3.4 79.7 1.0
N K:CYS39 3.7 75.4 1.0
N K:CYS21 3.7 91.2 1.0
CA K:CYS39 3.9 76.2 1.0
CA K:CYS21 4.1 96.1 1.0
NH1 L:ARG26 4.2 84.8 1.0
CA K:CYS18 4.5 80.3 1.0
CB K:LEU20 4.5 88.6 1.0
C K:LEU20 4.6 87.9 1.0
CA K:CYS42 4.8 84.9 1.0
C K:CYS39 4.9 79.6 1.0
N K:LEU20 4.9 82.1 1.0
C K:PHE38 4.9 73.4 1.0
CA K:LEU20 4.9 85.2 1.0
C K:CYS18 4.9 84.1 1.0

Zinc binding site 2 out of 8 in 4r8p

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Zinc binding site 2 out of 8 in the Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn202

b:66.8
occ:1.00
 ND1 K:HIS36 2.1 83.3 1.0
SG K:CYS34 2.3 85.0 1.0
SG K:CYS56 2.3 90.3 1.0
SG K:CYS53 2.4 86.2 1.0
CE1 K:HIS36 2.9 83.6 1.0
CG K:HIS36 3.0 85.0 1.0
CB K:CYS53 3.2 82.2 1.0
CB K:CYS34 3.3 95.4 1.0
CB K:HIS36 3.5 77.2 1.0
CD1 K:ILE31 3.7 91.1 1.0
CB K:CYS56 3.7 82.6 1.0
NE2 K:HIS36 3.9 76.4 1.0
N K:CYS56 3.9 88.6 1.0
CD2 K:HIS36 4.0 81.1 1.0
CA K:CYS56 4.4 88.9 1.0
CG1 K:ILE31 4.5 86.8 1.0
CB K:ILE55 4.6 74.2 1.0
CA K:CYS34 4.6 83.1 1.0
CA K:CYS53 4.7 76.5 1.0
O K:CYS34 4.8 75.9 1.0
C K:CYS34 4.8 70.3 1.0
CA K:HIS36 4.9 66.4 1.0
C K:CYS56 5.0 92.4 1.0
N K:HIS36 5.0 75.2 1.0

Zinc binding site 3 out of 8 in 4r8p

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Zinc binding site 3 out of 8 in the Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn401

b:88.9
occ:1.00
 SG L:CYS54 2.4 92.7 1.0
SG L:CYS72 2.4 85.4 1.0
SG L:CYS75 2.4 98.7 1.0
SG L:CYS51 2.4 79.9 1.0
CB L:CYS72 2.9 70.1 1.0
CB L:CYS51 3.2 74.8 1.0
CB L:CYS75 3.3 68.4 1.0
CB L:CYS54 3.4 98.7 1.0
N L:CYS54 3.9 84.9 1.0
N L:CYS72 4.0 69.8 1.0
CA L:CYS72 4.0 71.0 1.0
CA L:CYS54 4.3 90.3 1.0
NH1 L:ARG121 4.6 0.2 1.0
CB L:ILE53 4.6 85.7 1.0
CA L:CYS51 4.7 76.5 1.0
CD L:ARG121 4.7 0.5 1.0
CA L:CYS75 4.7 93.2 1.0
C L:ILE53 5.0 89.8 1.0

Zinc binding site 4 out of 8 in 4r8p

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Zinc binding site 4 out of 8 in the Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn402

b:58.5
occ:1.00
 ND1 L:HIS69 2.2 81.8 1.0
SG L:CYS67 2.3 83.6 1.0
SG L:CYS87 2.3 81.4 1.0
SG L:CYS90 2.3 66.5 1.0
CE1 L:HIS69 2.8 82.4 1.0
CB L:CYS67 2.9 62.3 1.0
CB L:CYS87 3.1 74.6 1.0
CG L:HIS69 3.2 70.9 1.0
OG1 L:THR89 3.3 99.5 1.0
CB L:CYS90 3.7 76.1 1.0
CB L:HIS69 3.8 60.8 1.0
NE2 L:HIS69 4.0 73.7 1.0
N L:CYS90 4.0 79.1 1.0
CD2 L:HIS69 4.2 71.7 1.0
OG1 L:THR64 4.3 59.5 1.0
CA L:CYS67 4.3 60.8 1.0
CA L:CYS90 4.4 77.9 1.0
CA L:CYS87 4.6 63.8 1.0
CB L:LYS92 4.7 86.1 1.0
CB L:THR89 4.7 86.3 1.0
C L:CYS67 4.7 66.5 1.0
O L:CYS67 4.8 59.9 1.0
C L:CYS90 4.9 81.9 1.0
N L:CYS67 4.9 56.1 1.0
C L:THR89 5.0 84.3 1.0

Zinc binding site 5 out of 8 in 4r8p

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Zinc binding site 5 out of 8 in the Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:0.8
occ:1.00
 SG M:CYS21 2.1 0.5 1.0
SG M:CYS18 2.2 0.3 1.0
SG M:CYS42 2.4 0.8 1.0
SG M:CYS39 2.4 0.4 1.0
CB M:CYS39 2.8 0.1 1.0
CB M:CYS18 3.1 0.7 1.0
CB M:CYS21 3.2 0.5 1.0
CB M:CYS42 3.4 0.9 1.0
N M:CYS21 3.6 0.2 1.0
N M:CYS39 3.8 97.9 1.0
CA M:CYS39 3.9 0.9 1.0
CA M:CYS21 4.0 0.5 1.0
CB M:LEU20 4.4 0.4 1.0
CA M:CYS18 4.5 0.8 1.0
C M:LEU20 4.5 0.5 1.0
N M:LEU20 4.8 0.2 1.0
CA M:LEU20 4.8 1.0 1.0
C M:CYS39 4.8 0.7 1.0
CA M:CYS42 4.8 0.5 1.0
C M:CYS18 4.9 0.8 1.0
C M:PHE38 5.0 0.0 1.0
O M:CYS39 5.0 0.9 1.0

Zinc binding site 6 out of 8 in 4r8p

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Zinc binding site 6 out of 8 in the Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn202

b:0.7
occ:1.00
 ND1 M:HIS36 2.2 0.1 1.0
SG M:CYS34 2.4 0.0 1.0
SG M:CYS53 2.4 0.3 1.0
SG M:CYS56 2.4 0.4 1.0
CG M:HIS36 2.8 1.0 1.0
CB M:CYS34 3.0 0.3 1.0
CE1 M:HIS36 3.1 0.2 1.0
CB M:HIS36 3.1 0.0 1.0
CB M:CYS53 3.5 0.5 1.0
CD2 M:HIS36 3.8 0.4 1.0
CB M:CYS56 3.8 0.9 1.0
NE2 M:HIS36 3.9 0.3 1.0
N M:CYS56 4.1 0.1 1.0
CA M:CYS34 4.4 0.6 1.0
CA M:HIS36 4.4 0.9 1.0
N M:HIS36 4.4 0.1 1.0
CB M:ILE55 4.5 0.9 1.0
CA M:CYS56 4.6 0.6 1.0
C M:CYS34 4.7 0.6 1.0
O M:CYS34 4.7 0.4 1.0
CD1 M:ILE31 4.9 93.8 1.0
CA M:CYS53 4.9 0.9 1.0

Zinc binding site 7 out of 8 in 4r8p

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Zinc binding site 7 out of 8 in the Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn401

b:94.0
occ:1.00
 SG N:CYS54 2.3 0.9 1.0
SG N:CYS51 2.4 0.2 1.0
SG N:CYS75 2.5 0.4 1.0
SG N:CYS72 2.6 0.5 1.0
CB N:CYS51 2.8 91.1 1.0
NH1 N:ARG121 3.1 0.7 1.0
CB N:CYS72 3.1 85.7 1.0
CB N:CYS54 3.3 0.8 1.0
CB N:CYS75 3.5 82.0 1.0
N N:CYS54 3.8 92.5 1.0
N N:CYS72 4.0 85.8 1.0
CA N:CYS72 4.1 92.0 1.0
CA N:CYS54 4.1 98.7 1.0
CZ N:ARG121 4.3 0.1 1.0
CA N:CYS51 4.3 96.0 1.0
CB N:ILE53 4.6 92.6 1.0
O N:CYS51 4.6 0.4 1.0
C N:CYS51 4.7 95.8 1.0
C N:ILE53 4.8 94.4 1.0
CA N:CYS75 4.9 97.9 1.0
NH2 N:ARG121 4.9 0.7 1.0
C N:CYS54 4.9 93.8 1.0

Zinc binding site 8 out of 8 in 4r8p

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Zinc binding site 8 out of 8 in the Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the RING1B/BMI1/UBCH5C PRC1 Ubiquitylation Module Bound to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn402

b:78.3
occ:1.00
 ND1 N:HIS69 2.2 93.0 1.0
SG N:CYS90 2.3 0.3 1.0
SG N:CYS87 2.5 80.7 1.0
SG N:CYS67 2.5 95.0 1.0
CE1 N:HIS69 2.7 94.0 1.0
CB N:CYS67 3.0 74.1 1.0
CB N:CYS90 3.2 82.2 1.0
CB N:CYS87 3.2 0.9 1.0
OG1 N:THR89 3.3 96.6 1.0
CG N:HIS69 3.5 91.8 1.0
N N:CYS90 3.7 88.3 1.0
CA N:CYS90 4.0 91.0 1.0
NE2 N:HIS69 4.0 0.8 1.0
CB N:HIS69 4.2 85.0 1.0
CD2 N:HIS69 4.4 0.2 1.0
CA N:CYS67 4.5 0.9 1.0
C N:CYS90 4.6 90.5 1.0
OG1 N:THR64 4.6 0.1 1.0
CA N:CYS87 4.6 0.5 1.0
CB N:THR89 4.7 81.3 1.0
C N:THR89 4.7 96.3 1.0
N N:ARG91 4.8 90.1 1.0
CB N:LYS92 4.9 0.7 1.0
C N:CYS67 4.9 99.5 1.0
O N:CYS87 4.9 99.1 1.0
C N:CYS87 5.0 95.5 1.0
O N:CYS67 5.0 0.5 1.0

Reference:

R.K.Mcginty, R.C.Henrici, S.Tan. Crystal Structure of the PRC1 Ubiquitylation Module Bound to the Nucleosome. Nature V. 514 591 2014.
ISSN: ISSN 0028-0836
PubMed: 25355358
DOI: 10.1038/NATURE13890
Page generated: Sun Oct 27 06:55:26 2024

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