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Zinc in PDB 4bbq: Crystal Structure of the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11)

Enzymatic activity of Crystal Structure of the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11)

All present enzymatic activity of Crystal Structure of the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11):
1.14.11.27;

Protein crystallography data

The structure of Crystal Structure of the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11), PDB code: 4bbq was solved by C.K.Allerston, A.A.Watson, C.Edlich, B.Li, Y.Chen, L.Ball, T.Krojer, C.H.Arrowsmith, A.Edwards, C.Bountra, F.Von Delft, E.D.Laue, O.Gileadi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 90.79 / 2.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.024, 30.053, 90.824, 90.00, 91.66, 90.00
R / Rfree (%) 19.7 / 22.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11) (pdb code 4bbq). 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 the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11), PDB code: 4bbq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4bbq

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Zinc binding site 1 out of 8 in the Crystal Structure of the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11)


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 the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1678

b:28.8
occ:1.00
 SG A:CYS604 2.3 28.7 1.0
SG A:CYS588 2.3 26.4 1.0
SG A:CYS582 2.4 32.4 1.0
SG A:CYS585 2.5 28.0 1.0
CB A:CYS604 3.1 24.7 1.0
CB A:CYS588 3.3 21.8 1.0
CB A:CYS585 3.5 25.1 1.0
N A:CYS582 3.6 30.3 1.0
CB A:CYS582 3.6 30.0 1.0
CA A:CYS604 3.6 25.2 1.0
N A:GLY583 3.9 27.3 1.0
CA A:CYS582 4.0 30.1 1.0
N A:CYS585 4.0 24.1 1.0
N A:VAL605 4.1 30.1 1.0
C A:CYS604 4.2 31.1 1.0
N A:CYS588 4.3 21.0 1.0
CA A:CYS585 4.3 24.6 1.0
C A:CYS582 4.3 31.8 1.0
CA A:CYS588 4.3 21.3 1.0
N A:VAL584 4.5 23.8 1.0
C A:GLU581 4.6 33.4 1.0
CA A:GLY583 4.8 25.1 1.0
CA A:GLU581 4.9 28.3 1.0
CG2 A:VAL605 4.9 36.7 1.0
N A:CYS604 4.9 26.1 1.0
C A:CYS585 4.9 29.5 1.0
O A:CYS585 5.0 27.3 1.0
N A:LEU606 5.0 33.1 1.0

Zinc binding site 2 out of 8 in 4bbq

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Zinc binding site 2 out of 8 in the Crystal Structure of the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11)


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 the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1679

b:30.6
occ:0.82
 SG A:CYS609 2.2 36.6 1.0
SG A:CYS574 2.2 35.5 1.0
SG A:CYS577 2.3 39.6 1.0
SG A:CYS571 2.5 46.4 1.0
CB A:CYS609 3.2 31.9 1.0
CB A:CYS574 3.4 34.8 1.0
CB A:CYS577 3.5 37.4 1.0
CB A:CYS571 3.6 41.4 1.0
CA A:CYS609 3.6 32.7 1.0
N A:CYS571 3.7 41.8 1.0
N A:CYS574 3.8 38.0 1.0
N A:ARG572 3.9 37.6 1.0
N A:LEU610 4.0 37.7 1.0
CA A:CYS571 4.0 41.0 1.0
CA A:CYS574 4.2 37.0 1.0
C A:CYS609 4.2 37.4 1.0
N A:CYS577 4.3 36.9 1.0
C A:CYS571 4.3 43.2 1.0
N A:LYS573 4.4 40.6 1.0
N A:ALA611 4.4 41.9 1.0
CA A:CYS577 4.5 36.9 1.0
C A:ARG570 4.8 46.3 1.0
O A:ALA611 4.8 43.7 1.0
N A:CYS609 4.9 32.1 1.0
CA A:ARG572 4.9 37.8 1.0
C A:CYS574 4.9 42.6 1.0
CG A:ARG570 4.9 48.0 1.0
C A:ALA611 5.0 42.9 1.0
C A:LYS573 5.0 45.6 1.0
O A:CYS574 5.0 41.1 1.0

Zinc binding site 3 out of 8 in 4bbq

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Zinc binding site 3 out of 8 in the Crystal Structure of the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11)


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 the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1680

b:36.3
occ:0.86
 SG A:CYS642 2.3 38.4 1.0
SG A:CYS675 2.3 47.3 1.0
SG A:CYS672 2.4 37.9 1.0
SG A:CYS645 2.4 45.6 1.0
CB A:CYS642 3.2 33.9 1.0
CB A:CYS675 3.2 44.4 1.0
CB A:CYS672 3.4 33.5 1.0
CB A:CYS645 3.5 42.5 1.0
N A:CYS645 3.8 43.1 1.0
N A:CYS672 4.0 33.2 1.0
N A:CYS675 4.1 43.7 1.0
CA A:CYS672 4.2 33.5 1.0
CA A:CYS645 4.2 42.7 1.0
CA A:CYS675 4.3 44.9 1.0
O A:HOH2044 4.4 35.4 1.0
CA A:CYS642 4.6 34.4 1.0
CB A:ILE644 4.7 48.4 1.0
O A:CYS672 4.7 39.6 1.0
C A:CYS672 4.8 39.3 1.0
C A:ILE644 4.9 47.1 1.0
CB A:LYS674 4.9 41.4 1.0

Zinc binding site 4 out of 8 in 4bbq

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Zinc binding site 4 out of 8 in the Crystal Structure of the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11)


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 the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1681

b:47.3
occ:0.94
 ND1 A:HIS650 2.2 46.6 1.0
SG A:CYS653 2.3 49.1 1.0
SG A:CYS620 2.3 47.0 1.0
SG A:CYS623 2.4 58.4 1.0
CB A:CYS620 3.0 44.1 1.0
CG A:HIS650 3.2 44.4 1.0
CE1 A:HIS650 3.2 47.0 1.0
CB A:CYS653 3.4 43.6 1.0
CB A:HIS650 3.4 39.7 1.0
CB A:CYS623 3.5 55.0 1.0
N A:CYS623 3.9 53.0 1.0
N A:HIS650 4.0 36.5 1.0
CA A:CYS623 4.3 54.4 1.0
NE2 A:HIS650 4.3 47.6 1.0
CD2 A:HIS650 4.3 47.0 1.0
CA A:HIS650 4.3 37.4 1.0
CA A:CYS620 4.5 43.9 1.0
CA A:CYS653 4.8 43.2 1.0
CB A:LEU622 4.8 49.9 1.0
C A:LEU622 4.9 56.5 1.0
O A:HIS650 5.0 39.2 1.0

Zinc binding site 5 out of 8 in 4bbq

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Zinc binding site 5 out of 8 in the Crystal Structure of the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11)


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 the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1677

b:26.2
occ:1.00
 SG B:CYS604 2.3 25.6 1.0
SG B:CYS582 2.3 26.6 1.0
SG B:CYS588 2.3 28.0 1.0
SG B:CYS585 2.5 24.4 1.0
CB B:CYS604 3.2 21.4 1.0
CB B:CYS588 3.3 23.3 1.0
CB B:CYS585 3.5 22.0 1.0
CB B:CYS582 3.5 25.6 1.0
N B:CYS582 3.6 26.5 1.0
CA B:CYS604 3.6 22.3 1.0
N B:GLY583 3.8 25.4 1.0
N B:CYS585 3.9 23.8 1.0
CA B:CYS582 4.0 26.0 1.0
N B:VAL605 4.0 25.3 1.0
CA B:CYS585 4.2 22.7 1.0
C B:CYS604 4.2 27.7 1.0
N B:CYS588 4.3 22.2 1.0
C B:CYS582 4.3 30.4 1.0
CA B:CYS588 4.3 22.3 1.0
N B:VAL584 4.5 23.7 1.0
C B:GLU581 4.6 32.0 1.0
N B:LEU606 4.8 29.5 1.0
CA B:GLY583 4.8 23.9 1.0
C B:CYS585 4.9 27.6 1.0
CA B:GLU581 4.9 28.8 1.0
O B:CYS585 4.9 27.5 1.0
N B:CYS604 5.0 24.2 1.0

Zinc binding site 6 out of 8 in 4bbq

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Zinc binding site 6 out of 8 in the Crystal Structure of the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11)


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 the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1678

b:37.4
occ:0.86
 SG B:CYS609 2.2 38.5 1.0
SG B:CYS577 2.3 39.6 1.0
SG B:CYS574 2.3 45.5 1.0
SG B:CYS571 2.5 45.6 1.0
CB B:CYS609 3.2 33.9 1.0
CB B:CYS577 3.4 37.7 1.0
CB B:CYS571 3.5 41.5 1.0
CB B:CYS574 3.5 43.8 1.0
CA B:CYS609 3.6 34.1 1.0
N B:CYS571 3.6 41.0 1.0
N B:ARG572 3.8 43.4 1.0
N B:CYS574 3.9 45.9 1.0
CA B:CYS571 3.9 41.5 1.0
N B:LEU610 4.1 42.5 1.0
CA B:CYS574 4.2 45.3 1.0
C B:CYS571 4.3 46.5 1.0
C B:CYS609 4.3 40.6 1.0
N B:CYS577 4.4 37.5 1.0
N B:LYS573 4.4 46.2 1.0
CA B:CYS577 4.5 37.3 1.0
N B:ALA611 4.5 45.5 1.0
O B:ALA611 4.6 47.1 1.0
C B:ARG570 4.7 46.6 1.0
CA B:ARG572 4.8 44.4 1.0
N B:CYS609 4.8 33.7 1.0
CG B:ARG570 4.8 43.6 1.0
C B:ALA611 4.8 46.3 1.0
C B:CYS574 4.9 49.3 1.0
C B:LYS573 5.0 52.7 1.0
CA B:ARG570 5.0 43.6 1.0

Zinc binding site 7 out of 8 in 4bbq

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Zinc binding site 7 out of 8 in the Crystal Structure of the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11)


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 the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1679

b:39.6
occ:0.68
 SG B:CYS642 2.2 48.5 1.0
SG B:CYS675 2.2 59.8 1.0
SG B:CYS645 2.4 65.6 1.0
SG B:CYS672 2.5 55.5 1.0
CB B:CYS642 3.1 44.1 1.0
CB B:CYS675 3.2 56.5 1.0
CB B:CYS645 3.4 62.4 1.0
CB B:CYS672 3.5 50.3 1.0
N B:CYS645 3.7 59.7 1.0
N B:CYS672 4.0 49.4 1.0
CA B:CYS645 4.1 60.9 1.0
N B:CYS675 4.1 57.3 1.0
CA B:CYS672 4.3 49.8 1.0
CA B:CYS675 4.3 57.6 1.0
CA B:CYS642 4.5 43.5 1.0
CB B:ILE644 4.5 62.6 1.0
O B:HOH2047 4.7 55.1 1.0
O B:HOH2037 4.7 43.2 1.0
C B:ILE644 4.8 63.4 1.0
O B:CYS672 4.8 54.7 1.0
C B:CYS672 4.8 54.6 1.0
C B:CYS645 4.9 63.5 1.0
CA B:ILE644 5.0 58.7 1.0

Zinc binding site 8 out of 8 in 4bbq

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Zinc binding site 8 out of 8 in the Crystal Structure of the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11)


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 the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1680

b:57.5
occ:0.66
 SG B:CYS620 2.2 68.9 1.0
SG B:CYS653 2.3 72.3 1.0
ND1 B:HIS650 2.3 63.6 1.0
SG B:CYS623 2.4 74.6 1.0
CB B:CYS620 3.0 65.1 1.0
CE1 B:HIS650 3.2 64.2 1.0
CG B:HIS650 3.3 60.9 1.0
CB B:CYS653 3.3 66.5 1.0
CB B:CYS623 3.4 72.5 1.0
CB B:HIS650 3.7 56.8 1.0
N B:CYS623 3.8 71.2 1.0
N B:HIS650 4.1 54.0 1.0
CA B:CYS623 4.2 72.7 1.0
NE2 B:HIS650 4.3 64.0 1.0
CD2 B:HIS650 4.4 63.1 1.0
CA B:CYS620 4.4 63.8 1.0
CA B:HIS650 4.5 54.4 1.0
CB B:LEU622 4.7 68.9 1.0
CA B:CYS653 4.7 66.0 1.0
C B:LEU622 4.8 75.3 1.0
N B:LEU622 5.0 68.7 1.0
C B:CYS620 5.0 69.3 1.0
C B:CYS623 5.0 76.5 1.0
O B:HIS650 5.0 57.1 1.0

Reference:

C.K.Allerston, A.A.Watson, C.Edlich, B.Li, Y.Chen, L.Ball, T.Krojer, C.H.Arrowsmith, A.Edwards, C.Bountra, F.Von Delft, E.D.Laue, O.Gileadi. Crystal Structure of the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (KDM2A)(FBXL11) To Be Published.
Page generated: Sat Oct 26 19:38:15 2024

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