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Zinc in PDB 5ij8: Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor

Enzymatic activity of Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor

All present enzymatic activity of Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor:
2.1.1.43;

Protein crystallography data

The structure of Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor, PDB code: 5ij8 was solved by K.S.Gajiwala, A.Brooun, Y.-L.Deng, W.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.28 / 2.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.331, 115.133, 153.939, 90.00, 103.35, 90.00
R / Rfree (%) 18.8 / 24

Other elements in 5ij8:

The structure of Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor (pdb code 5ij8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor, PDB code: 5ij8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 5ij8

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Zinc binding site 1 out of 14 in the Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn9002

b:59.8
occ:0.74
 NE2 A:HIS525 1.9 85.8 1.0
SG A:CYS534 2.1 69.0 1.0
SG A:CYS523 2.2 65.6 1.0
SG A:CYS530 2.3 73.6 1.0
CE1 A:HIS525 2.7 85.5 1.0
CD2 A:HIS525 3.1 86.1 1.0
CB A:CYS523 3.2 61.6 1.0
CB A:CYS534 3.4 65.5 1.0
CB A:CYS530 3.5 70.1 1.0
ZN A:ZN9003 3.7 45.5 0.8
ND1 A:HIS525 3.9 86.0 1.0
ZN A:ZN9004 3.9 45.7 0.8
CA A:CYS530 3.9 71.0 1.0
SG A:CYS543 4.0 54.8 1.0
CG A:HIS525 4.1 84.0 1.0
SG A:CYS536 4.4 60.3 1.0
CA A:CYS534 4.5 66.0 1.0
CB A:CYS536 4.6 56.9 1.0
CA A:CYS523 4.6 61.2 1.0
CD A:PRO535 4.7 65.7 1.0
CB A:CYS549 4.7 58.7 1.0
N A:CYS530 4.8 72.4 1.0
C A:CYS523 5.0 69.8 1.0

Zinc binding site 2 out of 14 in 5ij8

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Zinc binding site 2 out of 14 in the Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn9003

b:45.5
occ:0.75
 SG A:CYS547 2.2 52.0 1.0
SG A:CYS536 2.3 60.3 1.0
SG A:CYS543 2.5 54.8 1.0
SG A:CYS523 2.5 65.6 1.0
CB A:CYS547 3.1 48.7 1.0
CB A:CYS543 3.3 51.0 1.0
CB A:CYS523 3.4 61.6 1.0
CB A:CYS536 3.5 56.9 1.0
CA A:CYS543 3.6 50.5 1.0
N A:CYS523 3.7 59.3 1.0
ZN A:ZN9002 3.7 59.8 0.7
ZN A:ZN9004 4.0 45.7 0.8
CA A:CYS523 4.1 61.2 1.0
CA A:CYS547 4.4 49.3 1.0
SG A:CYS530 4.5 73.6 1.0
SG A:CYS549 4.5 62.0 1.0
N A:CYS543 4.6 50.7 1.0
SG A:CYS534 4.6 69.0 1.0
C A:CYS543 4.7 53.8 1.0
N A:GLU544 4.8 52.1 1.0
CE1 A:TYR520 4.8 52.9 1.0
C A:PRO522 4.8 57.9 1.0
O A:CYS523 4.8 69.3 1.0
CA A:CYS536 4.9 57.2 1.0
C A:CYS523 4.9 69.8 1.0
OH A:TYR520 5.0 56.2 1.0

Zinc binding site 3 out of 14 in 5ij8

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Zinc binding site 3 out of 14 in the Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn9004

b:45.7
occ:0.81
 SG A:CYS530 2.2 73.6 1.0
SG A:CYS549 2.3 62.0 1.0
SG A:CYS553 2.3 67.5 1.0
SG A:CYS543 2.5 54.8 1.0
CB A:CYS549 3.1 58.7 1.0
CB A:CYS553 3.3 63.3 1.0
CB A:CYS530 3.3 70.1 1.0
CB A:CYS543 3.4 51.0 1.0
ZN A:ZN9002 3.9 59.8 0.7
ZN A:ZN9003 4.0 45.5 0.8
SG A:CYS523 4.3 65.6 1.0
CG A:ARG556 4.5 54.8 1.0
CA A:CYS549 4.5 59.6 1.0
CA A:CYS530 4.7 71.0 1.0
CA A:CYS553 4.7 62.9 1.0
NE A:ARG556 4.8 62.0 1.0
CA A:CYS543 4.8 50.5 1.0
CB A:ASN555 4.8 51.9 1.0
CB A:CYS547 4.9 48.7 1.0
CE1 A:HIS525 4.9 85.5 1.0

Zinc binding site 4 out of 14 in 5ij8

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Zinc binding site 4 out of 14 in the Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn9005

b:0.0
occ:0.80
 SG A:CYS566 2.2 59.7 1.0
CB A:CYS566 2.6 56.9 1.0
O A:ALA564 2.8 71.5 1.0
N A:CYS566 2.9 60.7 1.0
CB A:CYS588 3.0 59.1 1.0
C A:ALA564 3.0 71.4 1.0
ZN A:ZN9006 3.0 37.2 0.8
CA A:CYS566 3.2 58.1 1.0
C A:GLN565 3.3 67.0 1.0
N A:GLN565 3.5 67.6 1.0
CA A:ALA564 3.7 65.9 1.0
SG A:CYS588 3.8 63.0 1.0
O A:GLN565 3.8 66.8 1.0
CB A:CYS562 3.8 57.0 1.0
CA A:GLN565 3.9 66.5 1.0
SG A:CYS601 4.0 60.0 1.0
N A:ALA564 4.1 66.1 1.0
CA A:CYS601 4.1 58.1 1.0
CA A:CYS588 4.2 58.8 1.0
CB A:CYS601 4.2 56.9 1.0
SG A:CYS562 4.2 60.5 1.0
O A:CYS588 4.5 60.1 1.0
C A:CYS566 4.7 60.7 1.0
C A:CYS588 4.7 61.1 1.0
O A:SER600 4.9 66.8 1.0
SG A:CYS560 4.9 60.6 1.0
N A:LYS602 4.9 56.6 1.0
C A:CYS562 4.9 64.5 1.0
CA A:CYS562 5.0 57.4 1.0
CB A:GLN565 5.0 67.9 1.0
N A:CYS601 5.0 60.3 1.0

Zinc binding site 5 out of 14 in 5ij8

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Zinc binding site 5 out of 14 in the Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn9006

b:37.2
occ:0.75
 SG A:CYS601 2.2 60.0 1.0
SG A:CYS588 2.4 63.0 1.0
SG A:CYS580 2.4 48.9 1.0
SG A:CYS566 2.6 59.7 1.0
CB A:CYS566 3.0 56.9 1.0
ZN A:ZN9005 3.0 0.0 0.8
CB A:CYS588 3.3 59.1 1.0
CB A:CYS601 3.3 56.9 1.0
CB A:CYS580 3.4 45.7 1.0
ZN A:ZN9007 3.9 39.8 0.7
SG A:CYS560 4.0 60.6 1.0
CA A:CYS601 4.2 58.1 1.0
CB A:ASN603 4.4 40.8 1.0
CB A:ALA590 4.5 57.9 1.0
CA A:CYS566 4.5 58.1 1.0
CA A:CYS588 4.7 58.8 1.0
CB A:CYS585 4.8 50.5 1.0
CA A:CYS580 4.8 45.8 1.0
N A:ASN603 4.9 48.6 1.0
C A:CYS588 4.9 61.1 1.0

Zinc binding site 6 out of 14 in 5ij8

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Zinc binding site 6 out of 14 in the Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn9007

b:39.8
occ:0.71
 SG A:CYS580 2.1 48.9 1.0
SG A:CYS585 2.2 53.5 1.0
SG A:CYS573 2.3 45.3 1.0
SG A:CYS560 2.4 60.6 1.0
CB A:CYS580 3.1 45.7 1.0
CB A:CYS585 3.2 50.5 1.0
CB A:CYS560 3.3 57.4 1.0
CB A:CYS573 3.4 42.0 1.0
N A:CYS560 3.6 60.3 1.0
CA A:CYS580 3.6 45.8 1.0
ZN A:ZN9006 3.9 37.2 0.8
CA A:CYS560 3.9 58.5 1.0
SG A:CYS566 4.3 59.7 1.0
SG A:CYS588 4.3 63.0 1.0
SG A:CYS571 4.4 52.9 1.0
N A:ASP581 4.4 51.7 1.0
CA A:CYS585 4.5 51.4 1.0
O A:CYS560 4.5 64.2 1.0
C A:GLY559 4.5 65.6 1.0
C A:CYS580 4.6 53.3 1.0
N A:CYS580 4.6 45.2 1.0
C A:CYS560 4.7 64.0 1.0
CA A:CYS573 4.8 43.0 1.0
CA A:GLY559 4.8 58.6 1.0

Zinc binding site 7 out of 14 in 5ij8

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Zinc binding site 7 out of 14 in the Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn9008

b:35.4
occ:0.70
 ND1 A:HIS297 1.9 53.5 1.0
SG A:CYS289 2.2 53.8 1.0
SG A:CYS286 2.2 54.1 1.0
SG A:CYS294 2.2 57.3 1.0
CE1 A:HIS297 2.9 52.4 1.0
CG A:HIS297 3.0 52.5 1.0
CB A:CYS286 3.2 50.2 1.0
CB A:CYS294 3.3 53.7 1.0
CB A:HIS297 3.3 51.4 1.0
CB A:CYS289 3.7 50.0 1.0
N A:HIS297 3.9 51.8 1.0
N A:CYS289 4.0 48.5 1.0
NE2 A:HIS297 4.0 52.5 1.0
CD2 A:HIS297 4.1 52.8 1.0
CA A:HIS297 4.2 53.1 1.0
CA A:CYS289 4.4 49.2 1.0
CB A:ARG288 4.4 41.6 1.0
CB A:LEU296 4.5 48.1 1.0
CA A:CYS286 4.6 50.1 1.0
CA A:CYS294 4.7 53.3 1.0
C A:LEU296 4.8 53.1 1.0
C A:ARG288 4.8 51.5 1.0
N A:LEU296 4.8 48.7 1.0
CA A:LEU296 5.0 48.2 1.0
O A:HIS297 5.0 69.6 1.0

Zinc binding site 8 out of 14 in 5ij8

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Zinc binding site 8 out of 14 in the Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn9002

b:53.3
occ:0.65
 SG B:CYS553 2.2 73.3 1.0
SG B:CYS549 2.2 78.7 1.0
SG B:CYS530 2.3 98.5 1.0
SG B:CYS543 2.6 68.4 1.0
CB B:CYS549 3.1 75.3 1.0
CB B:CYS553 3.1 70.4 1.0
CB B:CYS543 3.3 64.2 1.0
CB B:CYS530 3.4 95.3 1.0
ZN B:ZN9003 3.9 61.1 0.8
ZN B:ZN9004 3.9 59.6 0.6
SG B:CYS523 4.4 75.0 1.0
CG B:ARG556 4.4 59.4 1.0
CA B:CYS549 4.5 76.2 1.0
CA B:CYS553 4.6 71.2 1.0
NE B:ARG556 4.7 51.5 1.0
CB B:ASN555 4.8 71.0 1.0
CA B:CYS530 4.8 95.9 1.0
CA B:CYS543 4.8 63.1 1.0
CB B:CYS547 4.9 63.8 1.0
N B:ARG556 5.0 68.5 1.0

Zinc binding site 9 out of 14 in 5ij8

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Zinc binding site 9 out of 14 in the Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn9003

b:61.1
occ:0.81
 SG B:CYS536 2.3 63.3 1.0
SG B:CYS547 2.5 67.2 1.0
SG B:CYS523 2.5 75.0 1.0
SG B:CYS543 2.7 68.4 1.0
CB B:CYS543 3.1 64.2 1.0
CB B:CYS536 3.3 60.7 1.0
CB B:CYS547 3.4 63.8 1.0
CB B:CYS523 3.4 71.8 1.0
CA B:CYS543 3.5 63.1 1.0
ZN B:ZN9004 3.6 59.6 0.6
ZN B:ZN9002 3.9 53.3 0.7
N B:CYS523 3.9 70.7 1.0
CA B:CYS523 4.2 72.1 1.0
SG B:CYS530 4.3 98.5 1.0
SG B:CYS534 4.4 87.0 1.0
SG B:CYS549 4.5 78.7 1.0
N B:CYS543 4.5 62.3 1.0
CA B:CYS547 4.7 64.0 1.0
C B:CYS543 4.7 66.2 1.0
CA B:CYS536 4.8 62.8 1.0
N B:GLU544 4.9 60.9 1.0
CE1 B:TYR520 5.0 56.7 1.0

Zinc binding site 10 out of 14 in 5ij8

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Zinc binding site 10 out of 14 in the Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of the Primary Oncogenic Mutant Y641N Hs/ACPRC2 in Complex with A Pyridone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn9004

b:59.6
occ:0.59
 NE2 B:HIS525 1.9 0.8 1.0
SG B:CYS534 2.2 87.0 1.0
SG B:CYS530 2.2 98.5 1.0
SG B:CYS523 2.4 75.0 1.0
CE1 B:HIS525 2.6 0.5 1.0
CD2 B:HIS525 3.1 1.0 1.0
CB B:CYS530 3.3 95.3 1.0
CB B:CYS534 3.4 83.9 1.0
CB B:CYS523 3.4 71.8 1.0
ZN B:ZN9003 3.6 61.1 0.8
CA B:CYS530 3.7 95.9 1.0
ND1 B:HIS525 3.9 0.2 1.0
ZN B:ZN9002 3.9 53.3 0.7
CG B:HIS525 4.1 0.2 1.0
SG B:CYS543 4.2 68.4 1.0
CA B:CYS534 4.5 84.8 1.0
SG B:CYS536 4.5 63.3 1.0
N B:CYS530 4.6 96.3 1.0
CB B:CYS536 4.6 60.7 1.0
CB B:CYS549 4.7 75.3 1.0
CD B:PRO535 4.8 76.2 1.0
CA B:CYS523 4.8 72.1 1.0
C B:CYS530 4.9 0.2 1.0
O B:PRO529 4.9 99.6 1.0
SG B:CYS549 5.0 78.7 1.0

Reference:

A.Brooun, K.S.Gajiwala, Y.L.Deng, W.Liu, B.Bolanos, P.Bingham, Y.A.He, W.Diehl, N.Grable, P.P.Kung, S.Sutton, K.A.Maegley, X.Yu, A.E.Stewart. Polycomb Repressive Complex 2 Structure with Inhibitor Reveals A Mechanism of Activation and Drug Resistance. Nat Commun V. 7 11384 2016.
ISSN: ESSN 2041-1723
PubMed: 27122193
DOI: 10.1038/NCOMMS11384
Page generated: Sun Oct 27 18:07:23 2024

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