Atomistry » Zinc » PDB 4b3s-4bin » 4bbq
Atomistry »
  Zinc »
    PDB 4b3s-4bin »
      4bbq »

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

Go back to Zinc Binding Sites List in 4bbq
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

Go back to Zinc Binding Sites List in 4bbq
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

Go back to Zinc Binding Sites List in 4bbq
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

Go back to Zinc Binding Sites List in 4bbq
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

Go back to Zinc Binding Sites List in 4bbq
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

Go back to Zinc Binding Sites List in 4bbq
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

Go back to Zinc Binding Sites List in 4bbq
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

Go back to Zinc Binding Sites List in 4bbq
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

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