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Zinc in PDB 5a1l: Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty with S21056A

Protein crystallography data

The structure of Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty with S21056A, PDB code: 5a1l was solved by V.Srikannathasan, C.Gileadi, C.Johansson, T.Krojer, A.Tumber, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, P.Brennan, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.12 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.711, 110.500, 119.460, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22.5

Other elements in 5a1l:

The structure of Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty with S21056A also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty with S21056A (pdb code 5a1l). 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 Jmjc Domain of Human Histone Demethylase Uty with S21056A, PDB code: 5a1l:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5a1l

Go back to Zinc Binding Sites List in 5a1l
Zinc binding site 1 out of 2 in the Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty with S21056A


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 Jmjc Domain of Human Histone Demethylase Uty with S21056A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4002

b:25.9
occ:1.00
SG A:CYS1199 2.2 21.6 1.0
SG A:CYS1226 2.2 25.4 1.0
SG A:CYS1202 2.3 29.0 1.0
SG A:CYS1229 2.4 28.1 1.0
CB A:CYS1199 3.1 24.2 1.0
CB A:CYS1229 3.1 26.1 1.0
CB A:CYS1202 3.3 29.7 1.0
CB A:CYS1226 3.4 23.2 1.0
N A:CYS1202 3.8 30.4 1.0
N A:CYS1226 4.0 22.1 1.0
CA A:CYS1202 4.1 29.8 1.0
CG1 A:VAL1204 4.2 26.3 1.0
N A:CYS1229 4.2 26.8 1.0
CA A:CYS1226 4.3 22.1 1.0
O A:HOH3323 4.3 46.3 1.0
CA A:CYS1229 4.3 26.3 1.0
CA A:CYS1199 4.5 25.3 1.0
O A:HOH3317 4.6 43.3 1.0
CB A:ILE1201 4.7 34.9 1.0
C A:CYS1202 4.8 30.9 1.0
C A:ILE1201 4.9 32.7 1.0
C A:CYS1226 4.9 22.1 1.0
O A:CYS1226 4.9 19.6 1.0
N A:GLU1203 4.9 30.2 1.0

Zinc binding site 2 out of 2 in 5a1l

Go back to Zinc Binding Sites List in 5a1l
Zinc binding site 2 out of 2 in the Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty with S21056A


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 Jmjc Domain of Human Histone Demethylase Uty with S21056A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4002

b:27.0
occ:1.00
SG B:CYS1226 2.2 23.9 1.0
SG B:CYS1199 2.3 24.6 1.0
SG B:CYS1202 2.3 28.1 1.0
SG B:CYS1229 2.4 28.9 1.0
CB B:CYS1199 3.1 23.7 1.0
CB B:CYS1229 3.2 25.9 1.0
CB B:CYS1202 3.3 29.4 1.0
CB B:CYS1226 3.5 24.2 1.0
N B:CYS1202 3.7 30.4 1.0
CA B:CYS1202 4.1 30.3 1.0
N B:CYS1226 4.1 22.0 1.0
N B:CYS1229 4.2 25.4 1.0
CA B:CYS1229 4.3 25.9 1.0
CG1 B:VAL1204 4.3 27.7 1.0
CA B:CYS1226 4.3 22.7 1.0
O B:HOH3283 4.4 43.2 1.0
O B:HOH3305 4.5 35.6 1.0
CB B:ILE1201 4.6 31.9 1.0
CA B:CYS1199 4.6 24.1 1.0
C B:CYS1202 4.8 30.8 1.0
O B:CYS1226 4.8 21.0 1.0
C B:ILE1201 4.8 32.1 1.0
C B:CYS1226 4.9 23.3 1.0
N B:GLU1203 5.0 32.0 1.0

Reference:

V.Srikannathasan, C.Gileadi, C.Johansson, T.Krojer, A.Tumber, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, P.Brennan, U.Oppermann. Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty with S21056A To Be Published.
Page generated: Wed Dec 16 06:01:17 2020

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