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Chlorine in PDB 6sqo: Crystal Structure of Human MDM2 Ring Domain Homodimer Bound to UBCH5B- Ub

Enzymatic activity of Crystal Structure of Human MDM2 Ring Domain Homodimer Bound to UBCH5B- Ub

All present enzymatic activity of Crystal Structure of Human MDM2 Ring Domain Homodimer Bound to UBCH5B- Ub:
2.3.2.23; 2.3.2.24; 2.3.2.27;

Protein crystallography data

The structure of Crystal Structure of Human MDM2 Ring Domain Homodimer Bound to UBCH5B- Ub, PDB code: 6sqo was solved by H.M.Magnussen, S.F.Ahmed, D.T.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 112.00 / 1.41
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 129.709, 129.709, 70.537, 90.00, 90.00, 120.00
R / Rfree (%) 13.9 / 17.3

Other elements in 6sqo:

The structure of Crystal Structure of Human MDM2 Ring Domain Homodimer Bound to UBCH5B- Ub also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human MDM2 Ring Domain Homodimer Bound to UBCH5B- Ub (pdb code 6sqo). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Human MDM2 Ring Domain Homodimer Bound to UBCH5B- Ub, PDB code: 6sqo:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6sqo

Go back to Chlorine Binding Sites List in 6sqo
Chlorine binding site 1 out of 4 in the Crystal Structure of Human MDM2 Ring Domain Homodimer Bound to UBCH5B- Ub


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human MDM2 Ring Domain Homodimer Bound to UBCH5B- Ub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:55.1
occ:1.00
 N A:ILE485 3.2 24.1 1.0
O A:HOH630 3.5 55.3 1.0
CA A:MET484 3.7 26.6 1.0
NZ A:LYS466 3.9 37.9 1.0
C A:MET484 3.9 24.4 1.0
CB A:MET484 4.0 31.8 1.0
O A:ILE485 4.0 26.6 1.0
CB A:ILE485 4.1 23.0 1.0
CG A:LYS469 4.1 30.3 1.0
CA A:ILE485 4.1 21.9 1.0
CG1 A:ILE485 4.3 22.5 1.0
CE A:LYS469 4.3 35.6 1.0
CD A:LYS466 4.5 31.4 1.0
C A:ILE485 4.5 23.3 1.0
CD A:LYS469 4.5 31.7 1.0
CE A:LYS466 4.8 34.6 1.0
CB A:LYS469 4.9 25.9 1.0

Chlorine binding site 2 out of 4 in 6sqo

Go back to Chlorine Binding Sites List in 6sqo
Chlorine binding site 2 out of 4 in the Crystal Structure of Human MDM2 Ring Domain Homodimer Bound to UBCH5B- Ub


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human MDM2 Ring Domain Homodimer Bound to UBCH5B- Ub within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:65.4
occ:1.00
 O A:HOH622 2.8 51.0 1.0
N B:LYS4 3.3 27.4 1.0
O B:HOH388 3.3 34.8 1.0
N B:LEU3 3.4 28.1 1.0
N B:ALA2 3.5 29.7 1.0
O B:HOH355 3.9 39.4 1.0
CB B:LYS4 4.0 30.1 1.0
O B:HOH450 4.0 44.4 1.0
CA B:LEU3 4.1 28.0 1.0
C B:ALA2 4.1 26.9 1.0
CE B:LYS4 4.1 42.5 1.0
CB B:LEU3 4.1 31.4 1.0
C B:LEU3 4.2 26.8 1.0
CA B:LYS4 4.3 27.9 1.0
CA B:ALA2 4.4 28.5 1.0
CG B:LYS4 4.5 33.8 1.0
CD B:LYS4 5.0 37.2 1.0
O B:ALA2 5.0 24.2 1.0

Chlorine binding site 3 out of 4 in 6sqo

Go back to Chlorine Binding Sites List in 6sqo
Chlorine binding site 3 out of 4 in the Crystal Structure of Human MDM2 Ring Domain Homodimer Bound to UBCH5B- Ub


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human MDM2 Ring Domain Homodimer Bound to UBCH5B- Ub within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl503

b:52.2
occ:1.00
 O D:HOH620 3.2 60.1 1.0
N D:ILE485 3.3 24.9 1.0
NZ D:LYS466 3.7 39.5 1.0
CA D:MET484 3.9 27.6 1.0
CG D:LYS469 4.0 32.9 1.0
O D:ILE485 4.1 30.2 1.0
C D:MET484 4.1 25.4 1.0
CB D:ILE485 4.1 24.1 1.0
CB D:MET484 4.2 31.7 1.0
CA D:ILE485 4.2 24.0 1.0
CG1 D:ILE485 4.3 23.4 1.0
CD D:LYS466 4.4 35.0 1.0
CE D:LYS469 4.5 39.6 1.0
CD D:LYS469 4.6 36.0 1.0
C D:ILE485 4.6 25.9 1.0
CE D:LYS466 4.6 37.3 1.0
CB D:LYS469 4.9 28.7 1.0
O D:HOH627 4.9 47.6 1.0

Chlorine binding site 4 out of 4 in 6sqo

Go back to Chlorine Binding Sites List in 6sqo
Chlorine binding site 4 out of 4 in the Crystal Structure of Human MDM2 Ring Domain Homodimer Bound to UBCH5B- Ub


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human MDM2 Ring Domain Homodimer Bound to UBCH5B- Ub within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl201

b:71.0
occ:1.00
 O E:HOH422 3.0 29.1 1.0
N E:ALA2 3.4 27.0 1.0
N E:LYS4 3.4 27.8 1.0
N E:LEU3 3.5 25.2 1.0
O E:HOH459 3.7 46.2 1.0
CG E:LYS4 3.7 38.4 1.0
CB E:LYS4 3.8 31.6 1.0
O E:HOH348 3.9 40.4 1.0
C E:ALA2 4.0 24.9 1.0
CA E:LYS4 4.2 28.1 1.0
CA E:ALA2 4.2 25.8 1.0
CA E:LEU3 4.3 28.1 1.0
CD E:LYS4 4.3 43.5 1.0
C E:LEU3 4.3 26.6 1.0
CB E:LEU3 4.5 32.2 1.0
O E:ALA2 4.9 23.6 1.0
CE E:LYS4 4.9 49.7 1.0
O D:CYS441 5.0 31.7 1.0

Reference:

H.M.Magnussen, S.F.Ahmed, G.J.Sibbet, V.A.Hristova, K.Nomura, A.K.Hock, L.J.Archibald, A.G.Jamieson, D.Fushman, K.H.Vousden, A.M.Weissman, D.T.Huang. Structural Basis For Dna Damage-Induced Phosphoregulation of MDM2 Ring Domain Nat Commun 2020.
ISSN: ESSN 2041-1723
Page generated: Mon Jul 29 15:08:18 2024

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