Zinc in PDB 4o64: Zinc Fingers of KDM2B

The structure of Zinc Fingers of KDM2B, PDB code: 4o64 was solved by K.Liu, C.Xu, W.Tempel, J.R.Walker, C.H.Arrowsmith, C.Bountra, A.M.Edwards, J.Min, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.13
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	107.322, 107.322, 34.130, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 22

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Zinc Fingers of KDM2B (pdb code 4o64). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Zinc Fingers of KDM2B, PDB code: 4o64:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Zinc Fingers of KDM2B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zinc Fingers of KDM2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:31.6 occ:1.00 SG A:CYS616 2.3 35.8 1.0 SG A:CYS651 2.3 27.9 1.0 SG A:CYS613 2.3 32.1 1.0 SG A:CYS619 2.4 32.3 1.0 CB A:CYS651 3.3 28.6 1.0 CB A:CYS619 3.4 34.9 1.0 CB A:CYS616 3.4 37.0 1.0 CB A:CYS613 3.5 31.3 1.0 N A:CYS613 3.6 32.5 1.0 CA A:CYS651 3.7 30.6 1.0 N A:ARG614 3.8 38.9 1.0 N A:CYS616 3.9 38.7 1.0 CA A:CYS613 4.0 32.1 1.0 N A:ILE652 4.0 37.9 1.0 CA A:CYS616 4.2 38.5 1.0 C A:CYS613 4.3 36.0 1.0 C A:CYS651 4.3 33.1 1.0 N A:CYS619 4.3 35.5 1.0 N A:LYS615 4.4 42.1 1.0 CA A:CYS619 4.4 35.6 1.0 C A:ARG612 4.6 32.0 1.0 N A:ALA653 4.6 35.2 1.0 CA A:ARG614 4.7 41.9 1.0 CB A:ARG612 4.8 31.6 1.0 CA A:ARG612 4.9 31.1 1.0 C A:CYS616 4.9 39.8 1.0 O A:ALA653 5.0 28.1 1.0 N A:CYS651 5.0 30.1 1.0 C A:LYS615 5.0 41.9 1.0

Zinc binding site 2 out of 12 in the Zinc Fingers of KDM2B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zinc Fingers of KDM2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2002 b:26.6 occ:1.00 SG A:CYS624 2.3 24.9 1.0 SG A:CYS646 2.3 26.1 1.0 SG A:CYS627 2.3 23.9 1.0 SG A:CYS630 2.4 23.8 1.0 CB A:CYS646 3.3 24.3 1.0 CB A:CYS630 3.3 22.7 1.0 CB A:CYS627 3.5 26.7 1.0 CB A:CYS624 3.5 28.1 1.0 N A:CYS624 3.6 28.4 1.0 CA A:CYS646 3.7 24.5 1.0 N A:CYS627 3.9 28.6 1.0 N A:GLY625 3.9 28.2 1.0 CA A:CYS624 3.9 28.7 1.0 N A:ILE647 4.0 27.3 1.0 CA A:CYS627 4.2 26.7 1.0 C A:CYS646 4.3 25.2 1.0 N A:CYS630 4.3 23.9 1.0 C A:CYS624 4.3 29.3 1.0 N A:GLU626 4.3 30.0 1.0 CA A:CYS630 4.4 23.3 1.0 C A:GLU623 4.6 29.8 1.0 CA A:GLY625 4.8 28.0 1.0 N A:MET648 4.9 33.6 1.0 CG1 A:ILE647 4.9 32.4 1.0 CG A:MET648 4.9 39.8 1.0 C A:CYS627 4.9 26.0 1.0 O A:CYS627 5.0 21.8 1.0 N A:CYS646 5.0 24.7 1.0 C A:GLU626 5.0 31.4 1.0 C A:GLY625 5.0 29.6 1.0 CA A:GLU623 5.0 30.5 1.0

Zinc binding site 3 out of 12 in the Zinc Fingers of KDM2B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zinc Fingers of KDM2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2003 b:27.9 occ:1.00 ND1 A:HIS696 2.1 25.8 1.0 SG A:CYS699 2.3 28.4 1.0 SG A:CYS662 2.3 25.8 1.0 SG A:CYS665 2.3 30.1 1.0 CE1 A:HIS696 3.0 26.6 1.0 CG A:HIS696 3.1 24.8 1.0 CB A:CYS662 3.1 26.2 1.0 CB A:CYS699 3.3 28.4 1.0 CB A:CYS665 3.3 32.0 1.0 CB A:HIS696 3.4 23.9 1.0 N A:CYS665 3.8 30.9 1.0 NE2 A:HIS696 4.1 26.1 1.0 CA A:CYS665 4.1 32.2 1.0 N A:HIS696 4.2 22.9 1.0 CD2 A:HIS696 4.2 25.0 1.0 CA A:HIS696 4.4 22.9 1.0 CB A:VAL664 4.5 34.8 1.0 CA A:CYS662 4.6 26.5 1.0 CA A:CYS699 4.7 30.1 1.0 C A:CYS665 4.9 31.2 1.0 C A:VAL664 4.9 33.1 1.0 O A:HIS696 4.9 24.7 1.0 N A:CYS699 5.0 27.6 1.0 CG1 A:VAL664 5.0 38.7 1.0

Zinc binding site 4 out of 12 in the Zinc Fingers of KDM2B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zinc Fingers of KDM2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2004 b:26.6 occ:1.00 SG A:CYS691 2.3 25.3 1.0 SG A:CYS722 2.3 27.8 1.0 SG A:CYS688 2.3 22.2 1.0 SG A:CYS719 2.3 25.4 1.0 CB A:CYS688 3.2 21.4 1.0 CB A:CYS691 3.3 27.7 1.0 CB A:CYS722 3.3 29.7 1.0 CB A:CYS719 3.5 24.6 1.0 N A:CYS691 3.7 27.2 1.0 N A:CYS719 4.0 26.6 1.0 CA A:CYS691 4.1 27.8 1.0 N A:CYS722 4.1 30.9 1.0 CA A:CYS719 4.3 26.4 1.0 O A:HOH2110 4.3 26.1 1.0 CA A:CYS722 4.4 31.8 1.0 CB A:LYS721 4.6 34.7 1.0 CA A:CYS688 4.6 20.9 1.0 CB A:ILE690 4.7 29.7 1.0 O A:CYS719 4.7 32.0 1.0 C A:CYS719 4.7 29.1 1.0 C A:ILE690 4.8 29.2 1.0 C A:CYS691 4.9 28.2 1.0 C A:LYS721 4.9 34.0 1.0 O A:HOH2109 4.9 19.5 1.0 N A:ASN692 5.0 26.7 1.0

Zinc binding site 5 out of 12 in the Zinc Fingers of KDM2B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Zinc Fingers of KDM2B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2001 b:25.2 occ:1.00 SG B:CYS613 2.3 23.6 1.0 SG B:CYS651 2.3 24.4 1.0 SG B:CYS616 2.3 26.1 1.0 SG B:CYS619 2.3 27.2 1.0 CB B:CYS651 3.3 27.0 1.0 CB B:CYS616 3.3 25.8 1.0 CB B:CYS619 3.4 26.6 1.0 CB B:CYS613 3.4 24.6 1.0 N B:CYS613 3.5 27.1 1.0 CA B:CYS651 3.7 28.6 1.0 N B:ARG614 3.8 28.3 1.0 N B:CYS616 3.8 26.8 1.0 CA B:CYS613 3.9 25.5 1.0 CA B:CYS616 4.1 27.4 1.0 N B:ILE652 4.1 31.5 1.0 C B:CYS613 4.2 26.2 1.0 N B:CYS619 4.3 26.9 1.0 N B:LYS615 4.4 30.1 1.0 C B:CYS651 4.4 29.1 1.0 CA B:CYS619 4.4 26.4 1.0 C B:ARG612 4.6 27.5 1.0 CA B:ARG614 4.7 29.5 1.0 N B:ALA653 4.8 31.4 1.0 C B:CYS616 4.8 26.8 1.0 CB B:ARG612 4.9 27.5 0.5 O B:HOH2129 4.9 31.8 1.0 CA B:ARG612 4.9 28.5 0.5 CA B:ARG612 4.9 29.0 0.5 C B:LYS615 4.9 30.3 1.0 N B:CYS651 5.0 29.5 1.0

Zinc binding site 6 out of 12 in the Zinc Fingers of KDM2B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Zinc Fingers of KDM2B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2002 b:33.5 occ:1.00 SG B:CYS627 2.3 29.3 1.0 SG B:CYS646 2.3 30.2 1.0 SG B:CYS630 2.4 30.6 1.0 SG B:CYS624 2.4 30.9 1.0 CB B:CYS646 3.3 29.6 1.0 CB B:CYS630 3.3 30.1 1.0 CB B:CYS627 3.4 29.7 1.0 CB B:CYS624 3.4 32.3 1.0 N B:CYS624 3.6 33.9 1.0 CA B:CYS646 3.7 29.9 1.0 N B:CYS627 3.8 30.0 1.0 N B:GLY625 3.9 34.0 1.0 CA B:CYS624 3.9 33.4 1.0 N B:ILE647 4.1 29.0 1.0 CA B:CYS627 4.2 29.4 1.0 C B:CYS624 4.3 34.6 1.0 C B:CYS646 4.3 30.2 1.0 N B:CYS630 4.3 29.9 1.0 CA B:CYS630 4.4 30.1 1.0 N B:GLU626 4.4 33.5 1.0 C B:GLU623 4.6 34.1 1.0 CG1 B:ILE647 4.8 31.3 1.0 N B:MET648 4.8 30.2 1.0 C B:CYS627 4.9 28.8 1.0 O B:CYS627 4.9 27.0 1.0 CA B:GLY625 4.9 35.7 1.0 CA B:GLU623 4.9 35.3 1.0 N B:CYS646 5.0 30.6 1.0 C B:GLU626 5.0 31.6 1.0 CG B:MET648 5.0 35.5 1.0

Zinc binding site 7 out of 12 in the Zinc Fingers of KDM2B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Zinc Fingers of KDM2B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2003 b:35.9 occ:1.00 ND1 B:HIS696 2.1 31.9 1.0 SG B:CYS665 2.3 40.2 1.0 SG B:CYS699 2.3 36.0 1.0 SG B:CYS662 2.3 29.5 1.0 CG B:HIS696 3.1 29.5 1.0 CE1 B:HIS696 3.1 32.1 1.0 CB B:CYS662 3.1 30.2 1.0 CB B:CYS699 3.3 33.2 1.0 CB B:HIS696 3.3 29.6 1.0 CB B:CYS665 3.4 44.3 1.0 N B:CYS665 3.8 41.0 1.0 N B:HIS696 4.1 27.0 1.0 CA B:CYS665 4.2 44.3 1.0 NE2 B:HIS696 4.2 31.9 1.0 CD2 B:HIS696 4.2 29.7 1.0 CA B:HIS696 4.3 27.5 1.0 CA B:CYS662 4.6 30.0 1.0 CA B:CYS699 4.6 35.9 1.0 CB B:VAL664 4.7 42.8 1.0 C B:VAL664 4.9 44.5 1.0 C B:CYS665 4.9 43.7 1.0 O B:HIS696 5.0 30.0 1.0 N B:CYS699 5.0 34.6 1.0

Zinc binding site 8 out of 12 in the Zinc Fingers of KDM2B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Zinc Fingers of KDM2B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2004 b:29.3 occ:1.00 SG B:CYS688 2.3 24.9 1.0 SG B:CYS722 2.3 32.2 1.0 SG B:CYS719 2.3 28.7 1.0 SG B:CYS691 2.3 25.7 1.0 CB B:CYS688 3.1 23.2 1.0 CB B:CYS691 3.3 27.9 1.0 CB B:CYS722 3.3 35.1 1.0 CB B:CYS719 3.4 29.1 1.0 N B:CYS691 3.7 25.7 1.0 N B:CYS719 4.0 29.2 1.0 CA B:CYS691 4.1 26.4 1.0 N B:CYS722 4.1 35.3 1.0 CA B:CYS719 4.2 29.4 1.0 CA B:CYS722 4.3 39.1 1.0 O B:HOH2126 4.4 22.4 1.0 CB B:ILE690 4.5 29.0 0.6 CA B:CYS688 4.6 23.5 1.0 CB B:ILE690 4.6 28.9 0.4 CB B:LYS721 4.6 35.8 1.0 O B:CYS719 4.6 30.0 1.0 C B:CYS719 4.6 30.3 1.0 C B:ILE690 4.8 26.7 1.0 C B:CYS691 4.8 26.2 1.0 C B:LYS721 4.9 37.0 1.0 N B:ASN692 4.9 25.8 1.0 O B:HOH2125 5.0 25.0 1.0

Zinc binding site 9 out of 12 in the Zinc Fingers of KDM2B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Zinc Fingers of KDM2B within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2001 b:22.8 occ:1.00 SG C:CYS616 2.3 23.6 1.0 SG C:CYS613 2.3 23.4 1.0 SG C:CYS619 2.3 23.2 1.0 SG C:CYS651 2.3 22.3 1.0 CB C:CYS651 3.4 23.9 1.0 CB C:CYS619 3.4 20.9 1.0 CB C:CYS616 3.4 25.6 1.0 CB C:CYS613 3.4 25.0 1.0 N C:CYS613 3.6 25.3 1.0 CA C:CYS651 3.7 24.9 1.0 N C:CYS616 3.8 25.3 1.0 N C:ARG614 3.9 28.9 1.0 CA C:CYS613 4.0 25.2 1.0 N C:ILE652 4.1 32.0 1.0 CA C:CYS616 4.2 25.9 1.0 N C:CYS619 4.2 23.0 1.0 C C:CYS613 4.3 27.2 1.0 CA C:CYS619 4.4 20.6 1.0 C C:CYS651 4.4 29.4 1.0 N C:LYS615 4.4 27.6 1.0 C C:ARG612 4.7 26.0 1.0 CB C:ARG612 4.7 23.8 0.5 CA C:ARG614 4.8 29.9 1.0 N C:ALA653 4.8 31.1 1.0 O C:CYS616 4.8 26.6 1.0 C C:CYS616 4.8 25.7 1.0 CG1 C:ILE652 4.8 43.6 1.0 UNK C:UNX2007 4.9 33.3 1.0 CA C:ARG612 4.9 26.0 0.5 CA C:ARG612 4.9 26.9 0.5 N C:CYS651 5.0 26.3 1.0 C C:LYS615 5.0 29.1 1.0

Zinc binding site 10 out of 12 in the Zinc Fingers of KDM2B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Zinc Fingers of KDM2B within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2002 b:30.8 occ:1.00 SG C:CYS624 2.3 30.5 1.0 SG C:CYS630 2.3 23.4 1.0 SG C:CYS646 2.3 25.4 1.0 SG C:CYS627 2.4 28.3 1.0 CB C:CYS646 3.3 24.4 1.0 CB C:CYS630 3.3 25.4 1.0 CB C:CYS624 3.4 30.1 1.0 CB C:CYS627 3.4 32.5 1.0 N C:CYS624 3.6 27.6 1.0 CA C:CYS646 3.7 25.2 1.0 N C:GLY625 3.7 31.8 1.0 N C:CYS627 3.8 35.5 1.0 CA C:CYS624 3.9 29.1 1.0 N C:ILE647 4.1 28.2 1.0 CA C:CYS627 4.2 34.5 1.0 C C:CYS624 4.2 32.5 1.0 N C:GLU626 4.3 36.1 1.0 C C:CYS646 4.3 27.4 1.0 N C:CYS630 4.3 25.0 1.0 CA C:CYS630 4.4 25.0 1.0 C C:GLU623 4.7 27.2 1.0 CA C:GLY625 4.7 31.4 1.0 N C:MET648 4.7 29.2 1.0 O C:HOH2156 4.7 39.7 1.0 CG C:MET648 4.7 35.4 1.0 C C:CYS627 4.9 34.1 1.0 C C:GLU626 4.9 38.0 1.0 C C:GLY625 4.9 34.9 1.0 O C:CYS627 4.9 30.6 1.0 N C:CYS646 5.0 25.2 1.0 CA C:GLU623 5.0 25.5 1.0 CG1 C:ILE647 5.0 32.9 1.0

K.Liu, C.Xu, W.Tempel, J.R.Walker, C.H.Arrowsmith, C.Bountra, A.M.Edwards, J.Min, Structural Genomics Consortium (Sgc). Zinc Fingers of KDM2B To Be Published.