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Chlorine in PDB 4v3k: RNF38-UBCH5B-Ub Complex

Enzymatic activity of RNF38-UBCH5B-Ub Complex

All present enzymatic activity of RNF38-UBCH5B-Ub Complex:
6.3.2.19;

Protein crystallography data

The structure of RNF38-UBCH5B-Ub Complex, PDB code: 4v3k was solved by L.Buetow, M.Gabrielsen, N.G.Anthony, H.Dou, A.Patel, H.Aitkenhead, G.J.Sibbet, B.O.Smith, D.T.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.905 / 2.04
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 139.620, 139.620, 70.690, 90.00, 90.00, 90.00
R / Rfree (%) 18.07 / 22.34

Other elements in 4v3k:

The structure of RNF38-UBCH5B-Ub Complex also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the RNF38-UBCH5B-Ub Complex (pdb code 4v3k). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the RNF38-UBCH5B-Ub Complex, PDB code: 4v3k:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4v3k

Go back to Chlorine Binding Sites List in 4v3k
Chlorine binding site 1 out of 6 in the RNF38-UBCH5B-Ub Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of RNF38-UBCH5B-Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1148

b:50.4
occ:1.00
 O A:HOH2003 3.3 36.8 1.0
O A:HOH2001 3.4 32.1 1.0
N A:ALA2 3.5 30.3 1.0
N A:LEU3 3.6 27.9 1.0
N A:LYS4 3.6 23.9 1.0
CB A:LEU3 4.1 29.8 1.0
CB A:LYS4 4.2 25.3 1.0
CA A:LEU3 4.3 27.8 1.0
C A:ALA2 4.3 27.7 1.0
C A:LEU3 4.5 28.4 1.0
CA A:ALA2 4.5 27.9 1.0
CA A:LYS4 4.5 27.7 1.0

Chlorine binding site 2 out of 6 in 4v3k

Go back to Chlorine Binding Sites List in 4v3k
Chlorine binding site 2 out of 6 in the RNF38-UBCH5B-Ub Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of RNF38-UBCH5B-Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1149

b:48.0
occ:1.00
 NE A:ARG90 3.3 42.2 1.0
CG A:ARG90 3.5 32.0 1.0
OG A:SER91 3.6 28.6 1.0
O A:HOH2076 3.9 41.7 1.0
CZ A:ARG90 4.0 56.2 1.0
CD A:ARG90 4.0 41.5 1.0
NH2 A:ARG90 4.0 50.6 1.0
CB A:ASP87 4.2 21.6 1.0
CB A:SER91 4.2 29.5 1.0
CA A:ASP87 4.3 17.8 1.0
N A:SER91 4.3 24.6 1.0
CB A:ARG90 4.5 30.6 1.0
CA A:SER91 4.9 27.7 1.0
O A:ASP87 4.9 26.3 1.0

Chlorine binding site 3 out of 6 in 4v3k

Go back to Chlorine Binding Sites List in 4v3k
Chlorine binding site 3 out of 6 in the RNF38-UBCH5B-Ub Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of RNF38-UBCH5B-Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1150

b:49.1
occ:1.00
 ND2 A:ASN81 3.3 36.3 1.0
OG A:SER83 3.5 29.4 1.0
ND2 A:ASN79 3.8 22.1 1.0
O A:HOH2070 3.8 42.5 1.0
CB A:SER83 4.2 28.7 1.0
CG A:ASN81 4.3 41.5 1.0
CB A:ASN81 4.4 29.2 1.0
CG A:ASN79 4.8 26.6 1.0
OD1 A:ASN79 4.9 22.3 1.0

Chlorine binding site 4 out of 6 in 4v3k

Go back to Chlorine Binding Sites List in 4v3k
Chlorine binding site 4 out of 6 in the RNF38-UBCH5B-Ub Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of RNF38-UBCH5B-Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1148

b:55.3
occ:1.00
 O D:HOH2003 3.2 31.7 1.0
O D:HOH2002 3.7 26.9 1.0
N D:ALA2 3.7 29.3 1.0
N D:LYS4 3.9 20.4 1.0
N D:LEU3 4.0 23.0 1.0
CB D:LYS4 4.2 23.3 1.0
CB D:LEU3 4.6 25.3 1.0
CA D:LEU3 4.6 29.1 1.0
C D:ALA2 4.6 25.2 1.0
CA D:LYS4 4.7 22.0 1.0
C D:LEU3 4.7 24.1 1.0
CA D:ALA2 4.8 26.6 1.0

Chlorine binding site 5 out of 6 in 4v3k

Go back to Chlorine Binding Sites List in 4v3k
Chlorine binding site 5 out of 6 in the RNF38-UBCH5B-Ub Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of RNF38-UBCH5B-Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1149

b:47.8
occ:1.00
 OG D:SER83 3.1 23.9 1.0
ND2 D:ASN81 3.2 35.5 1.0
ND2 D:ASN79 3.4 21.5 1.0
CB D:SER83 3.9 21.5 1.0
CB D:ASN81 3.9 22.5 1.0
CG2 C:VAL460 3.9 26.4 1.0
CG D:ASN81 4.1 35.7 1.0
OD1 D:ASN79 4.2 20.9 1.0
CG D:ASN79 4.2 21.5 1.0
O D:HOH2056 4.8 32.2 1.0
CB C:VAL460 4.9 25.6 1.0

Chlorine binding site 6 out of 6 in 4v3k

Go back to Chlorine Binding Sites List in 4v3k
Chlorine binding site 6 out of 6 in the RNF38-UBCH5B-Ub Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of RNF38-UBCH5B-Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1150

b:42.5
occ:1.00
 O C:HOH2038 3.3 29.3 1.0
O D:HOH2027 3.4 33.0 1.0
OG D:SER91 3.6 19.8 1.0
O D:HOH2026 3.7 35.1 1.0
NE D:ARG90 3.7 26.5 1.0
CG D:ARG90 3.8 29.4 1.0
CB D:ASP87 4.2 21.0 1.0
N D:SER91 4.2 20.9 1.0
CB D:ARG90 4.3 22.3 1.0
CB D:SER91 4.3 20.0 1.0
CA D:ASP87 4.4 19.0 1.0
CD D:ARG90 4.4 23.6 1.0
CZ D:ARG90 4.7 29.4 1.0
NH2 D:ARG90 4.7 23.9 1.0
CA D:SER91 4.9 20.1 1.0
O D:ASP87 4.9 19.0 1.0
OE1 C:GLU459 4.9 27.9 0.6
O C:HOH2033 5.0 19.9 1.0
O E:HOH2047 5.0 35.2 1.0

Reference:

L.Buetow, M.Gabrielsen, N.G.Anthony, H.Dou, A.Patel, H.Aitkenhead, G.J.Sibbet, B.O.Smith, D.T.Huang. Activation of A Primed Ring E3-E2-Ubiquitin Complex By Non- Covalent Ubiquitin. Mol.Cell 2015.
ISSN: ESSN 1097-4164
PubMed: 25801170
DOI: 10.1016/J.MOLCEL.2015.02.017
Page generated: Fri Jul 11 22:21:01 2025

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