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 26 02:41:13 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy