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Zinc in PDB 6sqp: Crystal Structure of Cat MDM2-S429E Ring Domain Homodimer

Enzymatic activity of Crystal Structure of Cat MDM2-S429E Ring Domain Homodimer

All present enzymatic activity of Crystal Structure of Cat MDM2-S429E Ring Domain Homodimer:
2.3.2.27;

Protein crystallography data

The structure of Crystal Structure of Cat MDM2-S429E Ring Domain Homodimer, PDB code: 6sqp 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) 23.53 / 1.21
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 29.240, 39.760, 104.380, 90.00, 93.40, 90.00
R / Rfree (%) 17.1 / 21.2

Other elements in 6sqp:

The structure of Crystal Structure of Cat MDM2-S429E Ring Domain Homodimer also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Cat MDM2-S429E Ring Domain Homodimer (pdb code 6sqp). 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 Homodimer, PDB code: 6sqp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6sqp

Go back to Zinc Binding Sites List in 6sqp
Zinc binding site 1 out of 8 in the Crystal Structure of Cat MDM2-S429E Ring Domain Homodimer


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 Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:13.2
occ:1.00
 SG A:CYS464 2.3 13.1 1.0
SG A:CYS461 2.3 11.8 1.0
SG A:CYS441 2.4 14.4 1.0
SG A:CYS438 2.4 12.1 1.0
CB A:CYS438 3.2 12.2 1.0
CB A:CYS441 3.2 14.9 1.0
CB A:CYS464 3.2 12.9 1.0
CB A:CYS461 3.5 11.4 1.0
N A:CYS441 3.7 12.0 1.0
N A:CYS461 3.9 12.0 1.0
CA A:CYS441 4.1 13.5 1.0
O A:HOH655 4.2 31.6 1.0
CA A:CYS461 4.2 12.3 1.0
N A:CYS464 4.3 13.2 1.0
CA A:CYS464 4.4 11.0 1.0
CB A:ARG444 4.5 14.1 1.0
CB A:ILE440 4.6 12.6 1.0
CA A:CYS438 4.7 12.6 1.0
CG A:ARG444 4.7 19.8 1.0
C A:ILE440 4.7 13.1 1.0
O A:CYS461 4.8 11.8 1.0
C A:CYS461 4.8 11.2 1.0
C A:CYS441 4.9 16.7 1.0

Zinc binding site 2 out of 8 in 6sqp

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Zinc binding site 2 out of 8 in the Crystal Structure of Cat MDM2-S429E Ring Domain Homodimer


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 Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:11.9
occ:1.00
 ND1 A:HIS457 2.0 13.6 1.0
NE2 A:HIS452 2.1 12.0 1.0
SG A:CYS475 2.3 11.0 1.0
SG A:CYS478 2.4 12.1 1.0
CE1 A:HIS457 2.9 13.5 1.0
CD2 A:HIS452 3.0 13.0 1.0
CE1 A:HIS452 3.1 12.6 1.0
CB A:CYS475 3.1 12.7 1.0
CG A:HIS457 3.1 14.6 1.0
CB A:CYS478 3.5 11.7 1.0
CB A:HIS457 3.6 13.7 1.0
N A:CYS478 3.8 12.2 1.0
NE2 A:HIS457 4.1 16.5 1.0
ND1 A:HIS452 4.1 10.4 1.0
CG A:HIS452 4.1 12.2 1.0
CA A:CYS478 4.2 11.0 1.0
CD2 A:HIS457 4.2 16.4 1.0
O A:HOH654 4.3 22.1 1.0
CA A:CYS475 4.6 12.5 1.0
CB A:VAL477 4.6 14.4 1.0
CA A:HIS457 4.8 12.3 1.0
N A:HIS457 4.8 12.4 1.0
C A:VAL477 4.8 11.7 1.0
CG2 A:ILE450 4.9 13.4 1.0
C A:CYS478 4.9 10.9 1.0
N A:VAL477 4.9 12.5 1.0
N A:ARG479 5.0 11.9 1.0
O A:HOH605 5.0 26.8 1.0

Zinc binding site 3 out of 8 in 6sqp

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Zinc binding site 3 out of 8 in the Crystal Structure of Cat MDM2-S429E Ring Domain Homodimer


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 Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:20.4
occ:1.00
 SG B:CYS441 2.3 22.2 1.0
SG B:CYS464 2.3 20.1 1.0
SG B:CYS461 2.3 20.6 1.0
SG B:CYS438 2.4 17.7 1.0
CB B:CYS464 3.1 17.9 1.0
CB B:CYS438 3.1 16.6 1.0
CB B:CYS441 3.2 21.9 1.0
CB B:CYS461 3.5 19.1 1.0
NH2 B:ARG444 3.6 35.8 1.0
N B:CYS441 3.6 19.8 1.0
N B:CYS461 3.9 17.2 1.0
CA B:CYS441 4.0 21.1 1.0
NE B:ARG444 4.1 29.9 1.0
CZ B:ARG444 4.2 33.4 1.0
N B:CYS464 4.2 19.0 1.0
CA B:CYS461 4.2 16.6 1.0
CA B:CYS464 4.3 17.7 1.0
CB B:ARG444 4.6 22.4 1.0
CA B:CYS438 4.6 15.9 1.0
CB B:ILE440 4.7 18.8 1.0
C B:ILE440 4.7 20.9 1.0
C B:CYS461 4.8 17.2 1.0
O B:CYS461 4.8 17.1 1.0
C B:CYS441 4.9 24.3 1.0
N B:GLN442 5.0 23.8 1.0

Zinc binding site 4 out of 8 in 6sqp

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Zinc binding site 4 out of 8 in the Crystal Structure of Cat MDM2-S429E Ring Domain Homodimer


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 Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:13.5
occ:1.00
 ND1 B:HIS457 2.1 13.2 1.0
NE2 B:HIS452 2.1 12.2 1.0
SG B:CYS475 2.3 13.5 1.0
SG B:CYS478 2.3 15.3 1.0
CE1 B:HIS457 2.9 14.9 1.0
CE1 B:HIS452 3.0 13.4 1.0
CD2 B:HIS452 3.1 13.0 1.0
CB B:CYS475 3.1 13.6 1.0
CG B:HIS457 3.2 12.2 1.0
CB B:CYS478 3.4 14.9 1.0
CB B:HIS457 3.7 12.0 1.0
N B:CYS478 3.9 14.6 1.0
NE2 B:HIS457 4.0 16.0 1.0
ND1 B:HIS452 4.1 12.2 1.0
CG B:HIS452 4.2 12.4 1.0
CA B:CYS478 4.2 13.6 1.0
CD2 B:HIS457 4.2 13.8 1.0
CA B:CYS475 4.6 14.2 1.0
N B:HIS457 4.6 11.4 1.0
CB B:VAL477 4.7 15.0 1.0
CG2 B:ILE450 4.8 12.6 1.0
CA B:HIS457 4.8 11.3 1.0
OE1 B:GLN480 4.8 27.1 1.0
C B:CYS478 4.9 16.5 1.0
C B:VAL477 4.9 14.4 1.0
N B:ARG479 5.0 15.7 1.0
C B:CYS475 5.0 13.9 1.0

Zinc binding site 5 out of 8 in 6sqp

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Zinc binding site 5 out of 8 in the Crystal Structure of Cat MDM2-S429E Ring Domain Homodimer


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 Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:9.9
occ:1.00
 SG C:CYS441 2.3 12.3 1.0
SG C:CYS464 2.3 11.2 1.0
SG C:CYS461 2.3 9.6 1.0
SG C:CYS438 2.4 8.6 1.0
CB C:CYS438 3.1 8.2 1.0
CB C:CYS441 3.2 13.1 1.0
CB C:CYS464 3.2 10.6 1.0
CB C:CYS461 3.6 8.4 1.0
N C:CYS441 3.7 10.5 1.0
N C:CYS461 3.9 8.4 1.0
CA C:CYS441 4.0 11.2 1.0
O C:HOH651 4.1 30.2 1.0
N C:CYS464 4.3 9.0 1.0
CA C:CYS461 4.3 8.0 1.0
O C:HOH652 4.3 27.5 1.0
CA C:CYS464 4.4 8.9 1.0
CB C:ARG444 4.4 11.2 1.0
CB C:ILE440 4.5 10.0 0.5
CB C:ILE440 4.6 10.6 0.5
CG C:ARG444 4.6 14.8 1.0
CA C:CYS438 4.6 8.6 1.0
C C:ILE440 4.7 10.3 1.0
C C:CYS441 4.9 12.1 1.0
C C:CYS461 4.9 8.6 1.0
O C:CYS461 4.9 8.6 1.0
CG2 C:ILE440 5.0 10.6 0.5
N C:GLN442 5.0 11.4 1.0
CA C:ILE440 5.0 9.2 0.5

Zinc binding site 6 out of 8 in 6sqp

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Zinc binding site 6 out of 8 in the Crystal Structure of Cat MDM2-S429E Ring Domain Homodimer


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 Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:8.9
occ:1.00
 ND1 C:HIS457 2.0 11.0 1.0
NE2 C:HIS452 2.0 9.6 1.0
SG C:CYS475 2.3 8.6 1.0
SG C:CYS478 2.4 10.3 1.0
CE1 C:HIS457 2.9 12.7 1.0
CD2 C:HIS452 3.0 8.9 1.0
CE1 C:HIS452 3.0 10.1 1.0
CG C:HIS457 3.1 10.9 1.0
CB C:CYS475 3.1 9.0 1.0
CB C:CYS478 3.5 9.4 1.0
CB C:HIS457 3.5 10.6 1.0
N C:CYS478 3.8 9.0 1.0
NE2 C:HIS457 4.1 14.3 1.0
ND1 C:HIS452 4.1 9.2 1.0
CG C:HIS452 4.1 9.4 1.0
CD2 C:HIS457 4.2 14.4 1.0
CA C:CYS478 4.2 9.7 1.0
O C:HOH649 4.3 18.1 1.0
CA C:CYS475 4.6 8.2 1.0
CB C:VAL477 4.6 11.2 1.0
CA C:HIS457 4.8 9.3 1.0
N C:HIS457 4.8 9.3 1.0
C C:VAL477 4.9 10.5 1.0
C C:CYS478 4.9 8.7 1.0
N C:ARG479 4.9 8.9 1.0
CG2 C:ILE450 5.0 9.9 1.0
N C:VAL477 5.0 9.7 1.0
CG1 C:VAL477 5.0 12.2 1.0

Zinc binding site 7 out of 8 in 6sqp

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Zinc binding site 7 out of 8 in the Crystal Structure of Cat MDM2-S429E Ring Domain Homodimer


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 Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:13.8
occ:1.00
 SG D:CYS464 2.3 15.5 1.0
SG D:CYS461 2.3 14.3 1.0
SG D:CYS441 2.3 15.3 1.0
SG D:CYS438 2.4 12.1 1.0
CB D:CYS438 3.2 13.2 1.0
CB D:CYS464 3.2 13.2 1.0
CB D:CYS441 3.3 14.5 1.0
CB D:CYS461 3.5 14.4 1.0
N D:CYS441 3.7 13.9 1.0
N D:CYS461 3.9 11.2 1.0
NE D:ARG444 3.9 27.5 0.0
NH1 D:ARG444 3.9 32.8 1.0
CA D:CYS441 4.1 13.7 1.0
N D:CYS464 4.2 14.6 1.0
CA D:CYS461 4.3 11.7 1.0
CZ D:ARG444 4.3 30.6 1.0
CA D:CYS464 4.3 14.4 1.0
CB D:ARG444 4.6 18.0 1.0
CB D:ILE440 4.6 16.6 1.0
CA D:CYS438 4.6 11.8 1.0
C D:ILE440 4.7 16.3 1.0
C D:CYS461 4.9 13.4 1.0
C D:CYS441 4.9 15.5 1.0
O D:CYS461 4.9 12.5 1.0
N D:GLN442 4.9 15.2 1.0
CD D:ARG444 4.9 25.1 1.0

Zinc binding site 8 out of 8 in 6sqp

Go back to Zinc Binding Sites List in 6sqp
Zinc binding site 8 out of 8 in the Crystal Structure of Cat MDM2-S429E Ring Domain Homodimer


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 Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:11.6
occ:1.00
 ND1 D:HIS457 2.0 10.2 1.0
NE2 D:HIS452 2.1 11.4 1.0
SG D:CYS475 2.3 12.0 1.0
SG D:CYS478 2.3 13.5 1.0
CE1 D:HIS457 2.9 12.3 1.0
CE1 D:HIS452 3.0 11.7 1.0
CD2 D:HIS452 3.0 10.3 1.0
CB D:CYS475 3.1 13.5 1.0
CG D:HIS457 3.2 9.4 1.0
CB D:CYS478 3.5 14.9 1.0
CB D:HIS457 3.6 10.2 1.0
N D:CYS478 3.8 16.4 1.0
NE2 D:HIS457 4.0 11.1 1.0
ND1 D:HIS452 4.1 9.7 1.0
CG D:HIS452 4.2 9.8 1.0
CD2 D:HIS457 4.2 12.0 1.0
CA D:CYS478 4.2 16.5 1.0
CA D:CYS475 4.5 14.4 1.0
CB D:VAL477 4.6 15.7 1.0
N D:HIS457 4.6 7.8 1.0
NE2 D:GLN480 4.7 20.8 1.0
CA D:HIS457 4.7 9.4 1.0
CG2 D:ILE450 4.8 11.6 1.0
C D:VAL477 4.8 14.7 1.0
C D:CYS478 4.9 16.4 1.0
N D:VAL477 5.0 15.2 1.0
C D:CYS475 5.0 14.4 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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