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Zinc in PDB 5fy8: Crystal Structure of Human JMJD2A in Complex with D-Threo-Isocitrate

Protein crystallography data

The structure of Crystal Structure of Human JMJD2A in Complex with D-Threo-Isocitrate, PDB code: 5fy8 was solved by R.Nowak, J.Kopec, C.Johansson, A.Szykowska, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.98 / 2.34
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.930, 148.910, 57.050, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.9

Other elements in 5fy8:

The structure of Crystal Structure of Human JMJD2A in Complex with D-Threo-Isocitrate also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human JMJD2A in Complex with D-Threo-Isocitrate (pdb code 5fy8). 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 Human JMJD2A in Complex with D-Threo-Isocitrate, PDB code: 5fy8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5fy8

Go back to Zinc Binding Sites List in 5fy8
Zinc binding site 1 out of 2 in the Crystal Structure of Human JMJD2A in Complex with D-Threo-Isocitrate


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 Human JMJD2A in Complex with D-Threo-Isocitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:40.6
occ:1.00
NE2 A:HIS240 2.1 41.7 1.0
SG A:CYS306 2.1 43.9 1.0
SG A:CYS234 2.3 41.8 1.0
SG A:CYS308 2.4 44.9 1.0
CE1 A:HIS240 3.0 34.1 1.0
CD2 A:HIS240 3.1 39.7 1.0
CB A:CYS234 3.2 44.6 1.0
CB A:CYS306 3.4 38.5 1.0
CB A:CYS308 3.5 49.3 1.0
N A:CYS308 3.6 44.8 1.0
CA A:CYS306 3.9 45.5 1.0
N A:SER307 3.9 45.1 1.0
CA A:CYS308 4.0 48.0 1.0
ND1 A:HIS240 4.1 35.1 1.0
C A:CYS306 4.2 47.5 1.0
CG A:HIS240 4.2 38.2 1.0
CB A:LYS310 4.4 47.2 1.0
C A:CYS308 4.4 44.0 1.0
CA A:CYS234 4.5 44.6 1.0
N A:LYS310 4.5 46.9 1.0
N A:ARG309 4.5 44.0 1.0
O A:HOH2096 4.5 51.9 1.0
C A:SER307 4.7 54.1 1.0
O A:ALA236 4.8 36.9 1.0
CA A:PHE237 4.8 38.6 1.0
CG A:LYS310 4.9 50.8 1.0
N A:ASP311 4.9 56.7 1.0
CA A:SER307 4.9 43.9 1.0
CA A:LYS310 5.0 44.6 1.0
C A:ALA236 5.0 41.6 1.0

Zinc binding site 2 out of 2 in 5fy8

Go back to Zinc Binding Sites List in 5fy8
Zinc binding site 2 out of 2 in the Crystal Structure of Human JMJD2A in Complex with D-Threo-Isocitrate


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 Human JMJD2A in Complex with D-Threo-Isocitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:45.2
occ:1.00
NE2 B:HIS240 2.1 47.9 1.0
SG B:CYS306 2.2 44.6 1.0
SG B:CYS234 2.2 47.5 1.0
SG B:CYS308 2.3 53.8 1.0
CE1 B:HIS240 3.1 39.6 1.0
CD2 B:HIS240 3.1 41.5 1.0
CB B:CYS234 3.3 53.4 1.0
CB B:CYS306 3.4 42.3 1.0
CB B:CYS308 3.5 58.1 1.0
N B:CYS308 3.6 57.9 1.0
CA B:CYS306 3.9 52.8 1.0
N B:SER307 3.9 52.5 1.0
CA B:CYS308 4.0 57.2 1.0
ND1 B:HIS240 4.2 43.4 1.0
C B:CYS306 4.2 57.1 1.0
CG B:HIS240 4.2 36.6 1.0
C B:CYS308 4.5 59.3 1.0
N B:ARG309 4.5 59.1 1.0
CA B:CYS234 4.6 55.9 1.0
CG B:ARG309 4.6 61.1 1.0
C B:SER307 4.7 67.0 1.0
CD B:ARG309 4.7 57.3 1.0
CA B:PHE237 4.8 46.5 1.0
O B:ALA236 4.8 41.1 1.0
NE B:ARG309 4.8 63.8 1.0
CA B:SER307 4.9 59.0 1.0

Reference:

R.Nowak, J.Kopec, C.Johansson, A.Szykowska, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, U.Oppermann. Crystal Structure of Human JMJD2A in Complex with D-Threo-Isocitrate To Be Published.
Page generated: Wed Dec 16 06:17:08 2020

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