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Zinc in PDB 5fyv: Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Oxaloacetate

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Oxaloacetate, PDB code: 5fyv was solved by R.Nowak, J.Kopec, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, F.Von Delft, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.07 / 1.87
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 142.180, 142.180, 152.150, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 23

Other elements in 5fyv:

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Oxaloacetate also contains other interesting chemical elements:

Manganese (Mn) 1 atom
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Oxaloacetate (pdb code 5fyv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Oxaloacetate, PDB code: 5fyv:

Zinc binding site 1 out of 1 in 5fyv

Go back to Zinc Binding Sites List in 5fyv
Zinc binding site 1 out of 1 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Oxaloacetate


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 Catalytic Domain of Human JARID1B in Complex with Oxaloacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1754

b:33.6
occ:1.00
SG A:CYS692 2.1 32.5 1.0
ND1 A:HIS718 2.2 40.6 1.0
SG A:CYS715 2.3 34.5 1.0
SG A:CYS695 2.4 31.8 1.0
CE1 A:HIS718 3.0 39.0 1.0
CB A:CYS692 3.1 25.9 1.0
CG A:HIS718 3.3 41.6 1.0
CB A:CYS695 3.4 31.5 1.0
CB A:CYS715 3.5 34.9 1.0
CB A:HIS718 3.8 34.3 1.0
N A:CYS695 3.8 33.6 1.0
N A:CYS715 3.9 28.1 1.0
CA A:CYS695 4.1 31.0 1.0
NE2 A:HIS718 4.2 44.1 1.0
CA A:CYS715 4.2 32.6 1.0
CD2 A:HIS718 4.3 42.0 1.0
CG2 A:THR697 4.4 32.4 1.0
CA A:CYS692 4.6 32.0 1.0
N A:HIS718 4.6 33.3 1.0
CB A:LYS694 4.6 35.2 1.0
O A:CYS715 4.7 30.4 1.0
C A:CYS715 4.7 30.7 1.0
CD A:ARG619 4.7 38.9 0.7
CD A:ARG619 4.7 36.7 0.3
CB A:HIS717 4.8 33.4 1.0
C A:CYS695 4.8 33.6 1.0
CA A:HIS718 4.9 39.6 1.0
C A:LYS694 4.9 44.2 1.0
CG A:ARG619 5.0 36.0 0.3
N A:LYS696 5.0 33.2 1.0

Reference:

R.Nowak, J.Kopec, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, F.Von Delft, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, U.Oppermann. Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Oxaloacetate To Be Published.
Page generated: Wed Dec 16 06:17:15 2020

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