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Zinc in PDB 6sqr: Crystal Structure of Cat MDM2-S429E Ring Domain Bound to UBCH5B-Ub

Enzymatic activity of Crystal Structure of Cat MDM2-S429E Ring Domain Bound to UBCH5B-Ub

All present enzymatic activity of Crystal Structure of Cat MDM2-S429E Ring Domain 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 Cat MDM2-S429E Ring Domain Bound to UBCH5B-Ub, PDB code: 6sqr 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) 70.00 / 2.18
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.510, 163.880, 70.600, 90.00, 96.03, 90.00
R / Rfree (%) 16.6 / 22.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Cat MDM2-S429E Ring Domain Bound to UBCH5B-Ub (pdb code 6sqr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Cat MDM2-S429E Ring Domain Bound to UBCH5B-Ub, PDB code: 6sqr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6sqr

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Zinc binding site 1 out of 8 in the Crystal Structure of Cat MDM2-S429E 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 MDM2-S429E 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
 SG A:CYS464 2.4 28.5 1.0
SG A:CYS441 2.4 26.0 1.0
SG A:CYS461 2.4 27.6 1.0
SG A:CYS438 2.4 27.0 1.0
CB A:CYS438 3.2 21.2 1.0
CB A:CYS464 3.2 24.5 1.0
CB A:CYS441 3.2 25.6 1.0
CB A:CYS461 3.5 25.8 1.0
N A:CYS441 3.6 24.6 1.0
NH2 A:ARG444 3.8 29.6 1.0
N A:CYS461 3.9 23.7 1.0
CA A:CYS441 4.0 24.7 1.0
NE A:ARG444 4.1 34.1 1.0
N A:CYS464 4.2 18.5 1.0
CA A:CYS461 4.3 26.6 1.0
CA A:CYS464 4.3 22.7 1.0
CZ A:ARG444 4.4 33.1 1.0
CB A:ILE440 4.6 19.0 1.0
CA A:CYS438 4.6 22.8 1.0
C A:ILE440 4.7 30.1 1.0
O A:CYS461 4.8 23.4 1.0
CB A:ARG444 4.8 27.1 1.0
C A:CYS441 4.9 28.9 1.0
C A:CYS461 4.9 28.1 1.0
N A:ILE440 5.0 29.2 1.0

Zinc binding site 2 out of 8 in 6sqr

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Zinc binding site 2 out of 8 in the Crystal Structure of Cat MDM2-S429E 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 MDM2-S429E Ring Domain Bound to UBCH5B-Ub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:24.2
occ:1.00
 ND1 A:HIS457 2.0 22.5 1.0
NE2 A:HIS452 2.1 26.5 1.0
SG A:CYS475 2.3 20.5 1.0
SG A:CYS478 2.3 25.2 1.0
CE1 A:HIS457 2.8 28.4 1.0
CD2 A:HIS452 3.0 23.8 1.0
CB A:CYS475 3.1 17.7 1.0
CE1 A:HIS452 3.1 31.8 1.0
CG A:HIS457 3.1 22.4 1.0
CB A:CYS478 3.5 22.5 1.0
CB A:HIS457 3.6 12.9 1.0
N A:CYS478 3.9 23.3 1.0
NE2 A:HIS457 4.0 26.7 1.0
CG2 A:VAL477 4.0 30.4 1.0
CD2 A:HIS457 4.2 24.4 1.0
CG A:HIS452 4.2 22.2 1.0
ND1 A:HIS452 4.2 27.4 1.0
CA A:CYS478 4.2 24.1 1.0
CA A:CYS475 4.6 23.3 1.0
NE2 A:GLN480 4.7 36.8 1.0
N A:HIS457 4.8 19.3 1.0
C A:VAL477 4.8 19.9 1.0
CA A:HIS457 4.9 17.8 1.0
C A:CYS478 4.9 23.0 1.0
CG2 A:ILE450 4.9 29.3 1.0
N A:VAL477 5.0 24.2 1.0

Zinc binding site 3 out of 8 in 6sqr

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Zinc binding site 3 out of 8 in the Crystal Structure of Cat MDM2-S429E 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 MDM2-S429E Ring Domain Bound to UBCH5B-Ub within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn504

b:30.6
occ:1.00
 SG D:CYS438 2.2 25.3 1.0
SG D:CYS464 2.4 33.2 1.0
SG D:CYS441 2.4 32.0 1.0
SG D:CYS461 2.4 24.5 1.0
CB D:CYS438 3.1 25.1 1.0
CB D:CYS441 3.2 28.8 1.0
CB D:CYS464 3.2 29.6 1.0
CB D:CYS461 3.4 22.7 1.0
N D:CYS441 3.6 34.6 1.0
N D:CYS461 3.8 26.1 1.0
CA D:CYS441 4.0 32.6 1.0
NH2 D:ARG444 4.1 37.2 1.0
CA D:CYS461 4.2 29.7 1.0
NE D:ARG444 4.3 36.6 1.0
N D:CYS464 4.3 21.1 1.0
CA D:CYS464 4.4 24.9 1.0
CB D:ILE440 4.6 26.0 1.0
CA D:CYS438 4.6 32.0 1.0
CZ D:ARG444 4.6 35.8 1.0
C D:ILE440 4.7 34.3 1.0
C D:CYS461 4.8 25.2 1.0
CB D:ARG444 4.8 24.5 1.0
O D:CYS461 4.8 25.1 1.0
C D:CYS441 4.8 32.9 1.0
C D:ALA460 4.9 28.6 1.0
N D:GLN442 5.0 35.9 1.0

Zinc binding site 4 out of 8 in 6sqr

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Zinc binding site 4 out of 8 in the Crystal Structure of Cat MDM2-S429E 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 MDM2-S429E Ring Domain Bound to UBCH5B-Ub within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn505

b:26.4
occ:1.00
 ND1 D:HIS457 2.0 22.5 1.0
NE2 D:HIS452 2.3 25.3 1.0
SG D:CYS475 2.3 24.6 1.0
SG D:CYS478 2.4 27.1 1.0
CE1 D:HIS457 2.8 19.9 1.0
CG D:HIS457 3.1 22.1 1.0
CD2 D:HIS452 3.1 24.1 1.0
CB D:CYS475 3.1 15.1 1.0
CE1 D:HIS452 3.3 30.4 1.0
CB D:CYS478 3.4 24.9 1.0
CB D:HIS457 3.6 18.1 1.0
NE2 D:HIS457 3.9 24.6 1.0
N D:CYS478 4.0 25.6 1.0
CD2 D:HIS457 4.1 22.0 1.0
CG2 D:VAL477 4.2 20.3 1.0
CA D:CYS478 4.3 19.0 1.0
CG D:HIS452 4.3 27.6 1.0
ND1 D:HIS452 4.4 26.4 1.0
CA D:CYS475 4.6 20.5 1.0
N D:HIS457 4.6 26.0 1.0
NE2 D:GLN480 4.7 33.2 1.0
CA D:HIS457 4.7 25.3 1.0
CG2 D:ILE450 4.9 20.4 1.0
C D:CYS478 4.9 21.2 1.0
N D:ARG479 5.0 18.2 1.0

Zinc binding site 5 out of 8 in 6sqr

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Zinc binding site 5 out of 8 in the Crystal Structure of Cat MDM2-S429E 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 5 of Crystal Structure of Cat MDM2-S429E Ring Domain Bound to UBCH5B-Ub within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn503

b:30.3
occ:1.00
 SG G:CYS461 2.3 25.5 1.0
SG G:CYS441 2.4 32.0 1.0
SG G:CYS464 2.4 30.6 1.0
SG G:CYS438 2.4 32.2 1.0
CB G:CYS441 3.1 28.1 1.0
CB G:CYS438 3.2 31.2 1.0
CB G:CYS464 3.2 25.9 1.0
CB G:CYS461 3.4 21.7 1.0
N G:CYS441 3.6 35.0 1.0
N G:CYS461 3.8 23.2 1.0
NH2 G:ARG444 3.8 48.5 1.0
CA G:CYS441 3.9 32.1 1.0
CA G:CYS461 4.2 24.0 1.0
N G:CYS464 4.2 31.3 1.0
NE G:ARG444 4.3 43.7 1.0
CA G:CYS464 4.3 24.4 1.0
CZ G:ARG444 4.4 50.3 1.0
CB G:ILE440 4.5 28.3 1.0
CA G:CYS438 4.6 26.8 1.0
C G:ILE440 4.7 32.9 1.0
C G:CYS461 4.8 20.6 1.0
C G:CYS441 4.8 40.2 1.0
O G:CYS461 4.8 25.2 1.0
CG2 G:ILE440 4.9 35.6 1.0
CB G:ARG444 4.9 27.1 1.0
C G:ALA460 4.9 28.1 1.0
N G:GLN442 5.0 33.5 1.0
CA G:ILE440 5.0 32.9 1.0
O G:HOH626 5.0 46.9 1.0

Zinc binding site 6 out of 8 in 6sqr

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Zinc binding site 6 out of 8 in the Crystal Structure of Cat MDM2-S429E 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 6 of Crystal Structure of Cat MDM2-S429E Ring Domain Bound to UBCH5B-Ub within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn504

b:22.5
occ:1.00
 ND1 G:HIS457 2.1 17.4 1.0
NE2 G:HIS452 2.2 25.7 1.0
SG G:CYS475 2.3 21.1 1.0
SG G:CYS478 2.3 22.6 1.0
CE1 G:HIS457 3.0 17.3 1.0
CE1 G:HIS452 3.0 29.2 1.0
CB G:CYS475 3.1 19.9 1.0
CG G:HIS457 3.2 20.6 1.0
CD2 G:HIS452 3.2 23.3 1.0
CB G:CYS478 3.4 14.3 1.0
CB G:HIS457 3.6 16.0 1.0
N G:CYS478 3.9 19.6 1.0
NE2 G:HIS457 4.1 20.9 1.0
ND1 G:HIS452 4.2 25.7 1.0
CA G:CYS478 4.2 20.3 1.0
CD2 G:HIS457 4.3 15.8 1.0
CG G:HIS452 4.3 23.9 1.0
N G:HIS457 4.6 22.9 1.0
CA G:CYS475 4.6 20.9 1.0
O I:HOH242 4.6 33.4 1.0
CA G:HIS457 4.7 21.5 1.0
C G:VAL477 4.9 18.5 1.0
C G:CYS478 4.9 23.5 1.0
CG2 G:ILE450 4.9 21.5 1.0
CB G:VAL477 4.9 25.8 1.0

Zinc binding site 7 out of 8 in 6sqr

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Zinc binding site 7 out of 8 in the Crystal Structure of Cat MDM2-S429E 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 7 of Crystal Structure of Cat MDM2-S429E Ring Domain Bound to UBCH5B-Ub within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn503

b:25.4
occ:1.00
 SG J:CYS464 2.3 24.3 1.0
SG J:CYS441 2.3 25.6 1.0
SG J:CYS438 2.4 20.8 1.0
SG J:CYS461 2.4 24.7 1.0
CB J:CYS438 3.1 23.2 1.0
CB J:CYS464 3.3 23.3 1.0
CB J:CYS441 3.3 23.6 1.0
CB J:CYS461 3.4 21.3 1.0
NH2 J:ARG444 3.6 19.0 1.0
N J:CYS441 3.6 27.6 1.0
N J:CYS461 3.8 23.2 1.0
CA J:CYS441 4.0 21.9 1.0
NE J:ARG444 4.2 19.6 1.0
CA J:CYS461 4.2 21.8 1.0
CZ J:ARG444 4.3 23.7 1.0
N J:CYS464 4.3 24.2 1.0
CA J:CYS464 4.4 28.0 1.0
CB J:ILE440 4.5 23.3 1.0
CA J:CYS438 4.6 27.4 1.0
C J:ILE440 4.7 27.4 1.0
CB J:ARG444 4.8 18.0 1.0
C J:CYS461 4.9 22.1 1.0
O J:CYS461 4.9 20.6 1.0
C J:CYS441 4.9 21.7 1.0
N J:ILE440 5.0 33.5 1.0
CA J:ILE440 5.0 23.1 1.0

Zinc binding site 8 out of 8 in 6sqr

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Zinc binding site 8 out of 8 in the Crystal Structure of Cat MDM2-S429E 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 8 of Crystal Structure of Cat MDM2-S429E Ring Domain Bound to UBCH5B-Ub within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn504

b:24.1
occ:1.00
 ND1 J:HIS457 1.9 27.7 1.0
NE2 J:HIS452 2.1 27.1 1.0
SG J:CYS475 2.3 23.8 1.0
SG J:CYS478 2.3 24.7 1.0
CE1 J:HIS457 2.8 29.7 1.0
CE1 J:HIS452 3.0 26.8 1.0
CG J:HIS457 3.1 25.2 1.0
CD2 J:HIS452 3.1 24.4 1.0
CB J:CYS475 3.1 23.3 1.0
CB J:CYS478 3.5 17.4 1.0
CB J:HIS457 3.6 25.4 1.0
CG2 J:VAL477 3.9 24.7 1.0
N J:CYS478 3.9 24.2 1.0
NE2 J:HIS457 3.9 26.1 1.0
CD2 J:HIS457 4.1 17.9 1.0
ND1 J:HIS452 4.2 23.4 1.0
CG J:HIS452 4.2 27.6 1.0
CA J:CYS478 4.2 24.7 1.0
CA J:CYS475 4.6 24.3 1.0
OE1 J:GLN480 4.7 44.1 1.0
N J:HIS457 4.7 19.1 1.0
CA J:HIS457 4.8 23.9 1.0
C J:CYS478 4.9 25.7 1.0
C J:VAL477 4.9 30.4 1.0
CG2 J:ILE450 4.9 17.7 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: Tue Oct 29 07:39:10 2024

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