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Zinc in PDB 4aap: Crystal Structure of JMJD5 Domain of Human Lysine-Specific Demethylase 8 (KDM8) in Complex with N-Oxalylglycine (Nog)

Enzymatic activity of Crystal Structure of JMJD5 Domain of Human Lysine-Specific Demethylase 8 (KDM8) in Complex with N-Oxalylglycine (Nog)

All present enzymatic activity of Crystal Structure of JMJD5 Domain of Human Lysine-Specific Demethylase 8 (KDM8) in Complex with N-Oxalylglycine (Nog):
1.14.11.27;

Protein crystallography data

The structure of Crystal Structure of JMJD5 Domain of Human Lysine-Specific Demethylase 8 (KDM8) in Complex with N-Oxalylglycine (Nog), PDB code: 4aap was solved by M.Vollmar, C.Johansson, T.Krojer, P.Canning, C.Allerston, A.Gadhave, F.Vondelft, C.Bountra, C.H.Arrowsmith, J.Weigelt, A.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 89.67 / 2.60
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 68.575, 68.575, 269.003, 90.00, 90.00, 120.00
R / Rfree (%) 20.8 / 25.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of JMJD5 Domain of Human Lysine-Specific Demethylase 8 (KDM8) in Complex with N-Oxalylglycine (Nog) (pdb code 4aap). 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 JMJD5 Domain of Human Lysine-Specific Demethylase 8 (KDM8) in Complex with N-Oxalylglycine (Nog), PDB code: 4aap:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4aap

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Zinc binding site 1 out of 4 in the Crystal Structure of JMJD5 Domain of Human Lysine-Specific Demethylase 8 (KDM8) in Complex with N-Oxalylglycine (Nog)


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 JMJD5 Domain of Human Lysine-Specific Demethylase 8 (KDM8) in Complex with N-Oxalylglycine (Nog) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:76.7
occ:1.00
 O2' A:OGA501 1.9 54.0 1.0
NE2 A:HIS359 2.1 75.5 1.0
OD2 A:ASP361 2.1 67.3 1.0
O1 A:OGA501 2.1 73.8 1.0
NE2 A:HIS438 2.3 87.0 1.0
C2 A:OGA501 2.6 58.2 1.0
C1 A:OGA501 2.7 49.5 1.0
CG A:ASP361 2.9 67.2 1.0
OD1 A:ASP361 2.9 61.5 1.0
CD2 A:HIS359 2.9 73.6 1.0
CE1 A:HIS359 3.2 71.2 1.0
CD2 A:HIS438 3.2 85.5 1.0
CE1 A:HIS438 3.3 0.9 1.0
O2 A:OGA501 3.9 57.1 1.0
N1 A:OGA501 3.9 53.8 1.0
CG A:HIS359 4.2 77.5 1.0
ND1 A:HIS359 4.2 69.5 1.0
CB A:ASP361 4.4 65.3 1.0
CG A:HIS438 4.4 80.8 1.0
ND1 A:HIS438 4.4 78.8 1.0
CZ2 A:TRP452 4.4 69.2 1.0
C4 A:OGA501 4.7 52.8 1.0
ND2 A:ASN365 4.9 55.7 1.0
CH2 A:TRP348 5.0 73.3 1.0

Zinc binding site 2 out of 4 in 4aap

Go back to Zinc Binding Sites List in 4aap
Zinc binding site 2 out of 4 in the Crystal Structure of JMJD5 Domain of Human Lysine-Specific Demethylase 8 (KDM8) in Complex with N-Oxalylglycine (Nog)


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 JMJD5 Domain of Human Lysine-Specific Demethylase 8 (KDM8) in Complex with N-Oxalylglycine (Nog) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:91.0
occ:0.50
 NE2 A:HIS393 2.0 0.5 1.0
OD2 A:ASP283 2.5 0.0 1.0
CD2 A:HIS393 2.8 0.2 1.0
CG A:ASP283 3.0 0.9 1.0
CE1 A:HIS393 3.1 0.3 1.0
OD1 A:ASP283 3.4 0.2 1.0
CB A:ASP283 3.9 0.0 1.0
CG A:HIS393 4.1 0.9 1.0
ND1 A:HIS393 4.2 0.1 1.0

Zinc binding site 3 out of 4 in 4aap

Go back to Zinc Binding Sites List in 4aap
Zinc binding site 3 out of 4 in the Crystal Structure of JMJD5 Domain of Human Lysine-Specific Demethylase 8 (KDM8) in Complex with N-Oxalylglycine (Nog)


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 JMJD5 Domain of Human Lysine-Specific Demethylase 8 (KDM8) in Complex with N-Oxalylglycine (Nog) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:67.5
occ:1.00
 O2' B:OGA501 1.9 60.1 1.0
NE2 B:HIS359 2.0 64.1 1.0
OD2 B:ASP361 2.1 56.5 1.0
O1 B:OGA501 2.1 66.0 1.0
NE2 B:HIS438 2.2 68.2 1.0
C2 B:OGA501 2.7 66.4 1.0
C1 B:OGA501 2.7 58.8 1.0
CD2 B:HIS359 2.9 63.4 1.0
CG B:ASP361 2.9 63.6 1.0
OD1 B:ASP361 2.9 65.2 1.0
CD2 B:HIS438 3.1 67.2 1.0
CE1 B:HIS359 3.1 71.3 1.0
CE1 B:HIS438 3.2 71.1 1.0
O2 B:OGA501 4.0 61.0 1.0
N1 B:OGA501 4.0 61.4 1.0
CG B:HIS359 4.1 65.4 1.0
ND1 B:HIS359 4.2 76.5 1.0
CG B:HIS438 4.3 69.4 1.0
ND1 B:HIS438 4.3 66.6 1.0
CZ2 B:TRP452 4.4 57.6 1.0
CB B:ASP361 4.4 61.5 1.0
C4 B:OGA501 4.8 61.4 1.0

Zinc binding site 4 out of 4 in 4aap

Go back to Zinc Binding Sites List in 4aap
Zinc binding site 4 out of 4 in the Crystal Structure of JMJD5 Domain of Human Lysine-Specific Demethylase 8 (KDM8) in Complex with N-Oxalylglycine (Nog)


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 JMJD5 Domain of Human Lysine-Specific Demethylase 8 (KDM8) in Complex with N-Oxalylglycine (Nog) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:97.8
occ:0.50
 CD2 B:HIS393 2.7 0.6 1.0
NE2 B:HIS393 2.8 0.9 1.0
OD1 B:ASP283 3.4 0.3 1.0
OD2 B:ASP283 3.4 0.4 1.0
CG B:ASP283 3.5 0.8 1.0
CG B:HIS393 4.1 0.7 1.0
CE1 B:HIS393 4.2 0.8 1.0
CB B:ASP283 4.5 0.5 1.0
ND1 B:HIS393 4.8 0.2 1.0

Reference:

M.Vollmar, C.Johansson, T.Krojer, P.Canning, C.Allerston, A.Gadhave, F.Von Delft, C.Bountra, C.H.Arrowsmith, J.Weigelt, A.Edwards, U.Oppermann. Crystal Structure of JMJD5 Domain of Human Lysine- Specific Demethylase 8 (KDM8) in Complex with N- Oxalylglycine (Nog) To Be Published.
Page generated: Sat Oct 26 19:11:09 2024

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