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Zinc 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:

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human MDM2 Ring Domain Homodimer Bound to UBCH5B- Ub, PDB code: 6sqo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6sqo

Go back to Zinc Binding Sites List in 6sqo
Zinc 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 Zinc with other atoms in the Zn 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:Zn501

b:25.0
occ:1.00
 SG A:CYS461 2.3 24.7 1.0
SG A:CYS441 2.3 26.4 1.0
SG A:CYS464 2.4 24.4 1.0
SG A:CYS438 2.4 22.1 1.0
CB A:CYS438 3.2 22.6 1.0
CB A:CYS464 3.2 23.2 1.0
CB A:CYS441 3.2 26.0 1.0
CB A:CYS461 3.5 23.9 1.0
N A:CYS441 3.7 24.0 1.0
N A:CYS461 3.9 22.9 1.0
NH1 A:ARG444 3.9 41.2 1.0
CA A:CYS441 4.0 26.0 1.0
CA A:CYS461 4.2 23.4 1.0
N A:CYS464 4.3 23.5 1.0
CA A:CYS464 4.3 24.3 1.0
CB A:ILE440 4.5 22.3 1.0
CA A:CYS438 4.6 22.4 1.0
C A:ILE440 4.7 23.3 1.0
CB A:ARG444 4.8 30.8 1.0
C A:CYS441 4.8 27.8 1.0
C A:CYS461 4.9 22.7 1.0
O A:CYS461 4.9 22.3 1.0
N A:GLN442 4.9 26.5 1.0
CD A:ARG444 4.9 36.8 1.0
O A:HOH628 4.9 38.0 1.0
CA A:ILE440 5.0 21.6 1.0
CG2 A:ILE440 5.0 24.3 1.0

Zinc binding site 2 out of 4 in 6sqo

Go back to Zinc Binding Sites List in 6sqo
Zinc 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 Zinc with other atoms in the Zn 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
A:Zn502

b:21.1
occ:1.00
 ND1 A:HIS457 2.0 21.7 1.0
NE2 A:HIS452 2.1 20.8 1.0
SG A:CYS475 2.3 20.5 1.0
SG A:CYS478 2.3 21.3 1.0
CE1 A:HIS457 2.9 21.6 1.0
CD2 A:HIS452 3.0 21.1 1.0
CE1 A:HIS452 3.0 22.5 1.0
CB A:CYS475 3.1 19.2 1.0
CG A:HIS457 3.1 20.9 1.0
CB A:CYS478 3.5 20.6 1.0
CB A:HIS457 3.6 20.3 1.0
N A:CYS478 3.9 20.4 1.0
CG2 A:VAL477 4.0 29.8 1.0
NE2 A:HIS457 4.1 21.5 1.0
ND1 A:HIS452 4.1 22.4 1.0
CG A:HIS452 4.1 21.4 1.0
CD2 A:HIS457 4.2 20.9 1.0
CA A:CYS478 4.2 20.2 1.0
CA A:CYS475 4.5 18.2 1.0
OE1 A:GLN480 4.5 24.7 0.5
N A:HIS457 4.6 21.7 1.0
CA A:HIS457 4.7 20.9 1.0
C A:CYS478 4.9 20.9 1.0
CG2 A:ILE450 4.9 22.3 1.0
C A:VAL477 4.9 18.1 1.0
N A:VAL477 5.0 17.9 1.0
CB A:GLN480 5.0 24.2 0.5
C A:CYS475 5.0 19.3 1.0

Zinc binding site 3 out of 4 in 6sqo

Go back to Zinc Binding Sites List in 6sqo
Zinc 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 Zinc with other atoms in the Zn 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:Zn501

b:26.1
occ:1.00
 SG D:CYS464 2.3 25.3 1.0
SG D:CYS461 2.3 25.9 1.0
SG D:CYS441 2.3 27.7 1.0
SG D:CYS438 2.3 24.4 1.0
CB D:CYS438 3.2 25.4 1.0
CB D:CYS441 3.2 28.0 1.0
CB D:CYS464 3.3 24.7 1.0
CB D:CYS461 3.5 27.3 1.0
N D:CYS441 3.7 26.7 1.0
N D:CYS461 3.9 24.4 1.0
NH2 D:ARG444 4.0 42.1 1.0
CA D:CYS441 4.0 27.7 1.0
N D:CYS464 4.2 24.8 1.0
NE D:ARG444 4.2 41.4 1.0
CA D:CYS461 4.3 25.9 1.0
CA D:CYS464 4.3 24.2 1.0
CZ D:ARG444 4.6 42.1 1.0
CB D:ILE440 4.6 24.8 1.0
CA D:CYS438 4.6 24.8 1.0
C D:ILE440 4.8 27.4 1.0
CB D:ARG444 4.8 31.6 1.0
O D:CYS461 4.8 23.4 1.0
C D:CYS441 4.8 29.7 1.0
C D:CYS461 4.9 24.1 1.0
O D:HOH618 4.9 42.6 1.0
N D:GLN442 4.9 29.5 1.0
C D:ALA460 5.0 24.1 1.0

Zinc binding site 4 out of 4 in 6sqo

Go back to Zinc Binding Sites List in 6sqo
Zinc 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 Zinc with other atoms in the Zn 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
D:Zn502

b:21.4
occ:1.00
 ND1 D:HIS457 2.0 21.5 1.0
NE2 D:HIS452 2.1 19.7 1.0
SG D:CYS475 2.3 20.4 1.0
SG D:CYS478 2.3 22.2 1.0
CE1 D:HIS457 2.9 21.4 1.0
CE1 D:HIS452 3.0 21.8 1.0
CD2 D:HIS452 3.1 21.1 1.0
CB D:CYS475 3.1 18.9 1.0
CG D:HIS457 3.1 19.9 1.0
CB D:CYS478 3.4 21.0 1.0
CB D:HIS457 3.6 20.6 1.0
CG2 D:VAL477 3.9 28.8 1.0
N D:CYS478 4.0 19.8 1.0
NE2 D:HIS457 4.0 22.3 1.0
ND1 D:HIS452 4.1 22.9 1.0
CG D:HIS452 4.2 22.1 1.0
CD2 D:HIS457 4.2 21.8 1.0
CA D:CYS478 4.2 19.8 1.0
CA D:CYS475 4.5 19.4 1.0
OE1 D:GLN480 4.6 27.0 0.5
N D:HIS457 4.7 20.5 1.0
CA D:HIS457 4.8 18.6 1.0
C D:CYS478 4.9 21.5 1.0
CG2 D:ILE450 4.9 21.1 1.0
C D:VAL477 4.9 19.1 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: Tue Oct 29 07:38:15 2024

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