Atomistry » Zinc » PDB 6siz-6sqr » 6sqr
Atomistry »
  Zinc »
    PDB 6siz-6sqr »
      6sqr »

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

Go back to Zinc Binding Sites List in 6sqr
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

Go back to Zinc Binding Sites List in 6sqr
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

Go back to Zinc Binding Sites List in 6sqr
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

Go back to Zinc Binding Sites List in 6sqr
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

Go back to Zinc Binding Sites List in 6sqr
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

Go back to Zinc Binding Sites List in 6sqr
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

Go back to Zinc Binding Sites List in 6sqr
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

Go back to Zinc Binding Sites List in 6sqr
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy