Zinc in PDB 6sqs: Crystal Structure of Cat Phospho-SER429 MDM2 Ring Domain Bound to UBCH5B-Ub

All present enzymatic activity of Crystal Structure of Cat Phospho-SER429 MDM2 Ring Domain Bound to UBCH5B-Ub:
2.3.2.23; 2.3.2.24; 2.3.2.27;

The structure of Crystal Structure of Cat Phospho-SER429 MDM2 Ring Domain Bound to UBCH5B-Ub, PDB code: 6sqs 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)	29.20 / 1.83
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	54.593, 56.438, 60.742, 66.44, 69.44, 89.10
R / Rfree (%)	21.1 / 24.2

The binding sites of Zinc atom in the Crystal Structure of Cat Phospho-SER429 MDM2 Ring Domain Bound to UBCH5B-Ub (pdb code 6sqs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Cat Phospho-SER429 MDM2 Ring Domain Bound to UBCH5B-Ub, PDB code: 6sqs:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Cat Phospho-SER429 MDM2 Ring Domain Bound to UBCH5B-Ub


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 Cat Phospho-SER429 MDM2 Ring Domain Bound to UBCH5B-Ub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:31.6 occ:1.00 SG A:CYS464 2.3 29.9 1.0 SG A:CYS461 2.3 30.8 1.0 SG A:CYS438 2.4 30.2 1.0 SG A:CYS441 2.4 33.6 1.0 CB A:CYS438 3.1 29.6 1.0 CB A:CYS464 3.2 30.1 1.0 CB A:CYS441 3.2 32.4 1.0 CB A:CYS461 3.5 30.3 1.0 N A:CYS441 3.8 30.9 1.0 NH2 A:ARG444 3.9 44.4 1.0 N A:CYS461 3.9 28.5 1.0 CA A:CYS441 4.1 31.3 1.0 NE A:ARG444 4.2 42.4 1.0 CA A:CYS461 4.2 29.3 1.0 N A:CYS464 4.3 30.9 1.0 CA A:CYS464 4.3 30.1 1.0 CZ A:ARG444 4.4 44.5 1.0 CA A:CYS438 4.6 30.3 1.0 CB A:ILE440 4.7 29.0 1.0 CB A:ARG444 4.7 35.4 1.0 O A:CYS461 4.8 30.9 1.0 C A:CYS461 4.9 29.1 1.0 C A:ILE440 4.9 28.3 1.0 C A:CYS441 5.0 31.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Cat Phospho-SER429 MDM2 Ring Domain Bound to UBCH5B-Ub


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 Cat Phospho-SER429 MDM2 Ring Domain Bound to UBCH5B-Ub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:26.1 occ:1.00 ND1 A:HIS457 2.0 22.9 1.0 NE2 A:HIS452 2.1 27.1 1.0 SG A:CYS475 2.2 24.2 1.0 SG A:CYS478 2.3 27.9 1.0 CE1 A:HIS457 2.9 22.8 1.0 CD2 A:HIS452 3.0 26.7 1.0 CB A:CYS475 3.0 25.4 1.0 CE1 A:HIS452 3.1 27.2 1.0 CG A:HIS457 3.1 23.7 1.0 CB A:CYS478 3.4 27.6 1.0 CB A:HIS457 3.6 24.4 1.0 N A:CYS478 3.9 26.0 1.0 NE2 A:HIS457 4.0 22.3 1.0 ND1 A:HIS452 4.1 26.0 1.0 CG A:HIS452 4.1 26.6 1.0 CD2 A:HIS457 4.2 23.9 1.0 CA A:CYS478 4.2 26.1 1.0 CA A:CYS475 4.5 25.7 1.0 N A:HIS457 4.6 27.1 1.0 OE1 A:GLN480 4.7 35.1 1.0 CA A:HIS457 4.8 25.8 1.0 CB A:VAL477 4.8 28.9 1.0 CG2 A:ILE450 4.8 29.6 1.0 C A:CYS478 4.8 26.6 1.0 C A:VAL477 4.8 25.5 1.0 N A:ARG479 5.0 26.3 1.0 C A:CYS475 5.0 24.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Cat Phospho-SER429 MDM2 Ring Domain Bound to UBCH5B-Ub


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 Cat Phospho-SER429 MDM2 Ring Domain Bound to UBCH5B-Ub within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:29.6 occ:1.00 SG D:CYS438 2.3 28.5 1.0 SG D:CYS464 2.4 32.8 1.0 SG D:CYS441 2.4 34.0 1.0 SG D:CYS461 2.4 30.7 1.0 CB D:CYS438 3.1 30.7 1.0 CB D:CYS441 3.2 33.6 1.0 CB D:CYS464 3.2 31.6 1.0 CB D:CYS461 3.5 28.8 1.0 N D:CYS441 3.7 31.6 1.0 N D:CYS461 3.9 28.1 1.0 NH2 D:ARG444 3.9 47.1 1.0 CA D:CYS441 4.0 34.1 1.0 CA D:CYS461 4.2 28.9 1.0 NE D:ARG444 4.3 45.3 1.0 N D:CYS464 4.3 30.4 1.0 CA D:CYS464 4.4 30.9 1.0 CZ D:ARG444 4.5 46.6 1.0 CA D:CYS438 4.5 31.3 1.0 CB D:ILE440 4.6 29.5 1.0 CB D:ARG444 4.8 39.9 1.0 C D:ILE440 4.8 31.4 1.0 O D:CYS461 4.8 29.2 1.0 C D:CYS461 4.9 29.4 1.0 C D:CYS441 4.9 35.0 1.0 CG2 D:ILE440 4.9 29.7 1.0 C D:CYS438 5.0 32.1 1.0 C D:ALA460 5.0 27.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Cat Phospho-SER429 MDM2 Ring Domain Bound to UBCH5B-Ub


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 Cat Phospho-SER429 MDM2 Ring Domain Bound to UBCH5B-Ub within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:28.0 occ:1.00 ND1 D:HIS457 2.0 27.2 1.0 NE2 D:HIS452 2.1 23.8 1.0 SG D:CYS475 2.2 27.2 1.0 SG D:CYS478 2.4 28.1 1.0 CE1 D:HIS457 2.8 28.1 1.0 CB D:CYS475 3.0 26.0 1.0 CD2 D:HIS452 3.0 24.9 1.0 CE1 D:HIS452 3.1 24.7 1.0 CG D:HIS457 3.1 26.1 1.0 CB D:CYS478 3.5 28.0 1.0 CB D:HIS457 3.6 27.1 1.0 NE2 D:HIS457 4.0 25.9 1.0 N D:CYS478 4.1 28.2 1.0 CD2 D:HIS457 4.1 26.8 1.0 ND1 D:HIS452 4.1 24.2 1.0 CG D:HIS452 4.2 25.3 1.0 CA D:CYS478 4.3 28.4 1.0 CA D:CYS475 4.5 26.3 1.0 N D:HIS457 4.6 27.0 1.0 CG2 D:ILE450 4.7 26.9 1.0 CA D:HIS457 4.7 26.3 1.0 NE2 D:GLN480 4.8 37.5 1.0 C D:CYS478 5.0 27.9 1.0 O D:ILE450 5.0 27.2 1.0

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