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Zinc in PDB 6rbi: Crystal Structure of KDM5B in Complex with 5-(1H-Tetrazol-5-Yl) Quinolin-8-Ol

Protein crystallography data

The structure of Crystal Structure of KDM5B in Complex with 5-(1H-Tetrazol-5-Yl) Quinolin-8-Ol, PDB code: 6rbi was solved by C.Johansson, J.A.Newman, A.Kawamura, C.J.Schofield, C.H.Arrowsmith, C.Bountra, A.Edwards, U.C.T.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.73 / 2.21
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 142.150, 142.150, 151.540, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 20.1

Other elements in 6rbi:

The structure of Crystal Structure of KDM5B in Complex with 5-(1H-Tetrazol-5-Yl) Quinolin-8-Ol also contains other interesting chemical elements:

Manganese (Mn) 1 atom
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of KDM5B in Complex with 5-(1H-Tetrazol-5-Yl) Quinolin-8-Ol (pdb code 6rbi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of KDM5B in Complex with 5-(1H-Tetrazol-5-Yl) Quinolin-8-Ol, PDB code: 6rbi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6rbi

Go back to Zinc Binding Sites List in 6rbi
Zinc binding site 1 out of 2 in the Crystal Structure of KDM5B in Complex with 5-(1H-Tetrazol-5-Yl) Quinolin-8-Ol


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 KDM5B in Complex with 5-(1H-Tetrazol-5-Yl) Quinolin-8-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:40.6
occ:1.00
ND1 A:HIS718 2.1 47.2 1.0
SG A:CYS692 2.2 35.3 1.0
SG A:CYS715 2.3 38.9 1.0
SG A:CYS695 2.4 42.6 1.0
CE1 A:HIS718 2.9 44.9 1.0
CB A:CYS692 3.2 35.4 1.0
CG A:HIS718 3.2 47.7 1.0
CB A:CYS695 3.4 37.8 1.0
CB A:CYS715 3.5 38.8 1.0
CB A:HIS718 3.8 41.2 1.0
N A:CYS695 3.8 41.2 1.0
N A:CYS715 4.0 39.5 1.0
NE2 A:HIS718 4.1 51.1 1.0
CA A:CYS695 4.2 45.1 1.0
CD2 A:HIS718 4.3 46.0 1.0
CA A:CYS715 4.3 39.8 1.0
CG2 A:THR697 4.3 35.9 1.0
CD A:ARG619 4.6 42.4 0.8
CA A:CYS692 4.6 34.5 1.0
CB A:LYS694 4.6 43.9 1.0
N A:HIS718 4.6 46.5 1.0
C A:CYS715 4.7 37.5 1.0
O A:CYS715 4.7 37.9 1.0
CG A:ARG619 4.8 44.8 0.2
CA A:HIS718 4.8 40.4 1.0
C A:CYS695 4.9 46.8 1.0
CB A:HIS717 4.9 40.9 1.0
C A:LYS694 4.9 42.1 1.0
CD A:ARG619 4.9 43.5 0.2
CG A:ARG619 5.0 45.4 0.8

Zinc binding site 2 out of 2 in 6rbi

Go back to Zinc Binding Sites List in 6rbi
Zinc binding site 2 out of 2 in the Crystal Structure of KDM5B in Complex with 5-(1H-Tetrazol-5-Yl) Quinolin-8-Ol


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 KDM5B in Complex with 5-(1H-Tetrazol-5-Yl) Quinolin-8-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn809

b:55.0
occ:1.00
SG A:CYS708 2.3 53.6 1.0
SG A:CYS723 2.3 48.0 1.0
SG A:CYS706 2.4 48.3 1.0
SG A:CYS725 2.5 54.6 1.0
CB A:CYS725 3.2 49.0 1.0
CB A:CYS708 3.2 48.7 1.0
CB A:CYS706 3.3 38.5 1.0
CB A:CYS723 3.3 42.0 1.0
N A:CYS725 4.2 56.0 1.0
CA A:CYS708 4.3 49.0 1.0
CE1 A:TYR730 4.3 47.4 1.0
N A:CYS708 4.3 46.8 1.0
CA A:CYS725 4.3 51.7 1.0
CA A:CYS706 4.7 40.7 1.0
CA A:CYS723 4.7 46.4 1.0
C A:CYS708 4.8 50.2 1.0
C A:CYS706 4.9 43.8 1.0
N A:LYS709 4.9 50.2 1.0
CD1 A:TYR730 5.0 46.4 1.0

Reference:

C.Johansson, J.A.Newman, A.Kawamura, C.J.Schofield, C.H.Arrowsmith, C.Bountra, A.Edwards, U.C.T.Oppermann. Crystal Structure of KDM5B in Complex with 5-(1H-Tetrazol-5-Yl)Quinolin-8-Ol To Be Published.
Page generated: Wed Dec 16 12:36:58 2020

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