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Zinc in PDB 5fpv: Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A

Enzymatic activity of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A

All present enzymatic activity of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A:
1.14.11.27;

Protein crystallography data

The structure of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A, PDB code: 5fpv was solved by V.Srikannathasan, C.Gileadi, 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) 85.327 / 2.44
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 111.346, 103.509, 157.103, 90.00, 106.37, 90.00
R / Rfree (%) 19.55 / 22.89

Other elements in 5fpv:

The structure of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A also contains other interesting chemical elements:

Nickel (Ni) 15 atoms
Manganese (Mn) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A (pdb code 5fpv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A, PDB code: 5fpv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5fpv

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Zinc binding site 1 out of 8 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A


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 Compound KDOAM20A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1359

b:38.1
occ:1.00
 NE2 A:HIS241 2.1 32.3 1.0
SG A:CYS235 2.2 37.5 1.0
SG A:CYS307 2.3 37.5 1.0
SG A:CYS309 2.4 42.4 1.0
CE1 A:HIS241 3.0 31.4 1.0
CD2 A:HIS241 3.2 31.3 1.0
CB A:CYS235 3.2 49.5 1.0
CB A:CYS307 3.3 49.1 1.0
CB A:CYS309 3.5 65.8 1.0
N A:CYS309 3.7 62.3 1.0
CA A:CYS307 3.9 49.4 1.0
N A:SER308 3.9 55.0 1.0
CA A:CYS309 4.1 65.9 1.0
ND1 A:HIS241 4.1 31.9 1.0
C A:CYS307 4.2 51.8 1.0
CG A:HIS241 4.3 31.9 1.0
CG A:ARG310 4.3 70.2 1.0
CD A:ARG310 4.3 68.5 1.0
N A:ARG310 4.3 72.8 1.0
C A:CYS309 4.5 70.2 1.0
CA A:CYS235 4.6 49.7 1.0
NE A:ARG310 4.6 67.6 1.0
O A:ALA237 4.7 40.8 1.0
CA A:PHE238 4.7 32.7 1.0
C A:SER308 4.8 61.2 1.0
C A:ALA237 4.9 41.1 1.0
CA A:SER308 4.9 58.4 1.0

Zinc binding site 2 out of 8 in 5fpv

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Zinc binding site 2 out of 8 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A


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 Compound KDOAM20A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1359

b:82.3
occ:1.00
 NE2 B:HIS241 2.0 41.3 1.0
SG B:CYS235 2.1 55.8 1.0
SG B:CYS309 2.2 51.6 1.0
CE1 B:HIS241 2.8 40.1 1.0
CD2 B:HIS241 3.0 39.9 1.0
SG B:CYS307 3.0 50.8 1.0
CB B:CYS235 3.1 74.3 1.0
CB B:CYS309 3.4 78.2 1.0
CB B:CYS307 3.6 63.5 1.0
O B:ALA237 3.7 56.6 1.0
CA B:CYS307 3.8 60.6 1.0
ND1 B:HIS241 3.8 39.3 1.0
CA B:PHE238 3.9 40.7 1.0
CG B:HIS241 4.0 38.0 1.0
N B:CYS309 4.0 74.6 1.0
C B:ALA237 4.0 56.4 1.0
N B:SER308 4.2 62.5 1.0
N B:PHE238 4.2 48.6 1.0
CA B:CYS309 4.3 79.1 1.0
C B:CYS307 4.4 63.2 1.0
CA B:CYS235 4.5 70.0 1.0
CB B:PHE238 4.7 37.6 1.0
N B:ALA237 4.7 67.1 1.0
C B:PHE238 4.9 34.9 1.0
CA B:ALA237 4.9 63.3 1.0
C B:CYS235 4.9 70.8 1.0

Zinc binding site 3 out of 8 in 5fpv

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Zinc binding site 3 out of 8 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1359

b:46.1
occ:1.00
 NE2 C:HIS241 2.0 36.7 1.0
SG C:CYS307 2.2 60.2 1.0
SG C:CYS235 2.4 43.8 1.0
SG C:CYS309 2.4 47.3 1.0
CE1 C:HIS241 2.9 36.2 1.0
CD2 C:HIS241 3.1 35.2 1.0
CB C:CYS235 3.3 45.8 1.0
CB C:CYS307 3.5 51.9 1.0
CB C:CYS309 3.5 70.1 1.0
N C:CYS309 3.7 65.4 1.0
N C:SER308 4.0 57.6 1.0
CA C:CYS307 4.0 52.4 1.0
ND1 C:HIS241 4.0 36.4 1.0
CA C:CYS309 4.1 69.6 1.0
CG C:HIS241 4.2 34.6 1.0
C C:CYS307 4.3 55.0 1.0
N C:ARG310 4.5 76.7 1.0
C C:CYS309 4.6 72.0 1.0
CA C:CYS235 4.7 47.3 1.0
O C:ALA237 4.7 39.4 1.0
CG C:ARG310 4.8 81.4 1.0
C C:SER308 4.8 61.9 1.0
CA C:PHE238 4.8 33.6 1.0
CA C:SER308 4.9 59.5 1.0

Zinc binding site 4 out of 8 in 5fpv

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Zinc binding site 4 out of 8 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1359

b:39.5
occ:1.00
 NE2 D:HIS241 2.1 32.4 1.0
SG D:CYS307 2.3 39.7 1.0
SG D:CYS235 2.3 33.9 1.0
SG D:CYS309 2.4 45.4 1.0
CE1 D:HIS241 2.9 32.0 1.0
CD2 D:HIS241 3.2 31.7 1.0
CB D:CYS235 3.3 38.3 1.0
CB D:CYS307 3.5 47.9 1.0
CB D:CYS309 3.5 70.2 1.0
N D:CYS309 3.6 65.1 1.0
CA D:CYS307 4.0 49.1 1.0
N D:SER308 4.0 55.4 1.0
CA D:CYS309 4.0 69.5 1.0
ND1 D:HIS241 4.1 32.9 1.0
N D:ARG310 4.2 79.0 1.0
CG D:HIS241 4.2 32.1 1.0
C D:CYS307 4.2 52.4 1.0
C D:CYS309 4.5 73.1 1.0
CD D:ARG310 4.5 70.1 1.0
CA D:CYS235 4.7 38.4 1.0
O D:ALA237 4.7 33.5 1.0
C D:SER308 4.7 61.9 1.0
CB D:ARG310 4.8 80.0 1.0
CA D:PHE238 4.9 28.9 1.0
CG D:ARG310 4.9 74.8 1.0
NE D:ARG310 4.9 66.7 1.0
CA D:SER308 5.0 58.0 1.0

Zinc binding site 5 out of 8 in 5fpv

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Zinc binding site 5 out of 8 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1359

b:38.8
occ:1.00
 NE2 E:HIS241 2.1 34.6 1.0
SG E:CYS307 2.2 32.4 1.0
SG E:CYS235 2.3 36.1 1.0
SG E:CYS309 2.4 50.4 1.0
CE1 E:HIS241 2.9 34.1 1.0
CD2 E:HIS241 3.2 33.0 1.0
CB E:CYS235 3.2 52.2 1.0
CB E:CYS307 3.5 36.9 1.0
CB E:CYS309 3.5 68.6 1.0
N E:CYS309 3.7 63.2 1.0
CA E:CYS307 4.0 40.1 1.0
ND1 E:HIS241 4.1 34.2 1.0
N E:SER308 4.1 47.9 1.0
CA E:CYS309 4.1 68.2 1.0
CG E:ARG310 4.1 81.0 1.0
CG E:HIS241 4.2 32.4 1.0
N E:ARG310 4.3 80.4 1.0
C E:CYS307 4.3 43.9 1.0
C E:CYS309 4.5 73.4 1.0
CA E:CYS235 4.6 52.3 1.0
O E:ALA237 4.6 44.2 1.0
CA E:PHE238 4.8 33.6 1.0
C E:SER308 4.8 59.5 1.0
CB E:ARG310 4.8 84.4 1.0
C E:ALA237 5.0 43.7 1.0

Zinc binding site 6 out of 8 in 5fpv

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Zinc binding site 6 out of 8 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1359

b:38.2
occ:1.00
 NE2 F:HIS241 2.1 34.1 1.0
SG F:CYS307 2.1 34.8 1.0
SG F:CYS235 2.3 37.9 1.0
SG F:CYS309 2.4 47.7 1.0
CE1 F:HIS241 2.9 33.3 1.0
CB F:CYS235 3.1 47.8 1.0
CD2 F:HIS241 3.2 32.8 1.0
CB F:CYS307 3.4 42.2 1.0
CB F:CYS309 3.4 57.4 1.0
N F:CYS309 3.7 54.5 1.0
ND1 F:HIS241 4.0 33.3 1.0
CA F:CYS309 4.0 58.1 1.0
CA F:CYS307 4.1 43.0 1.0
N F:SER308 4.1 46.3 1.0
CG F:HIS241 4.2 32.3 1.0
C F:CYS307 4.4 43.4 1.0
N F:ARG310 4.4 67.4 1.0
CA F:CYS235 4.5 46.3 1.0
C F:CYS309 4.5 62.7 1.0
O F:ALA237 4.6 41.0 1.0
CA F:PHE238 4.7 33.4 1.0
C F:SER308 4.8 52.5 1.0
CG F:ARG310 4.9 66.3 1.0
CD F:ARG310 4.9 63.8 1.0
CE F:MET313 4.9 44.0 1.0
C F:ALA237 5.0 39.0 1.0
NE F:ARG310 5.0 61.2 1.0

Zinc binding site 7 out of 8 in 5fpv

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Zinc binding site 7 out of 8 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1359

b:41.9
occ:1.00
 NE2 G:HIS241 2.1 33.9 1.0
SG G:CYS307 2.2 40.1 1.0
SG G:CYS309 2.3 46.2 1.0
SG G:CYS235 2.3 46.2 1.0
CE1 G:HIS241 2.9 34.4 1.0
CD2 G:HIS241 3.2 33.4 1.0
CB G:CYS235 3.3 61.0 1.0
CB G:CYS307 3.5 44.5 1.0
CB G:CYS309 3.5 57.6 1.0
N G:CYS309 3.6 56.4 1.0
CA G:CYS307 3.9 43.9 1.0
N G:SER308 4.0 47.0 1.0
CA G:CYS309 4.0 58.6 1.0
ND1 G:HIS241 4.1 34.9 1.0
C G:CYS307 4.2 44.4 1.0
CG G:HIS241 4.3 34.1 1.0
N G:ARG310 4.3 64.8 1.0
CD G:ARG310 4.4 65.3 1.0
NE G:ARG310 4.4 66.4 1.0
C G:CYS309 4.5 62.1 1.0
CG G:ARG310 4.5 64.7 1.0
CA G:CYS235 4.6 60.7 1.0
C G:SER308 4.7 53.3 1.0
O G:ALA237 4.8 44.6 1.0
CA G:PHE238 4.9 34.7 1.0
CA G:SER308 4.9 50.6 1.0

Zinc binding site 8 out of 8 in 5fpv

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Zinc binding site 8 out of 8 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1359

b:35.2
occ:1.00
 NE2 H:HIS241 2.1 27.5 1.0
SG H:CYS307 2.3 46.9 1.0
SG H:CYS309 2.3 35.0 1.0
SG H:CYS235 2.4 48.3 1.0
CE1 H:HIS241 2.9 27.7 1.0
CD2 H:HIS241 3.1 27.4 1.0
CB H:CYS235 3.3 43.5 1.0
CB H:CYS307 3.5 39.1 1.0
CB H:CYS309 3.5 58.0 1.0
N H:CYS309 3.7 56.5 1.0
CA H:CYS307 4.0 40.0 1.0
N H:SER308 4.0 46.0 1.0
CA H:CYS309 4.0 59.7 1.0
ND1 H:HIS241 4.1 27.1 1.0
CG H:HIS241 4.2 27.8 1.0
C H:CYS307 4.3 43.5 1.0
N H:ARG310 4.3 70.9 1.0
CD H:ARG310 4.5 68.1 1.0
CG H:ARG310 4.5 70.1 1.0
C H:CYS309 4.5 65.2 1.0
CA H:CYS235 4.6 43.5 1.0
NE H:ARG310 4.8 66.5 1.0
C H:SER308 4.8 53.5 1.0
O H:ALA237 4.8 34.7 1.0
CA H:PHE238 4.8 29.4 1.0
CB H:ARG310 4.9 72.9 1.0

Reference:

C.Johansson, S.Velupillai, A.Tumber, A.Szykowska, E.S.Hookway, R.P.Nowak, C.Strain-Damerell, C.Gileadi, M.Philpott, N.Burgess-Brown, N.Wu, J.Kopec, A.Nuzzi, H.Steuber, U.Egner, V.Badock, S.Munro, N.B.Lathangue, S.Westaway, J.Brown, N.Athanasou, R.Prinjha, P.E.Brennan, U.Oppermann. Structural Analysis of Human KDM5B Guides Histone Demethylase Inhibitor Development. Nat.Chem.Biol. V. 12 539 2016.
ISSN: ISSN 1552-4450
PubMed: 27214403
DOI: 10.1038/NCHEMBIO.2087
Page generated: Wed Dec 16 06:16:02 2020

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