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Nickel 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:

Manganese (Mn) 8 atoms
Zinc (Zn) 8 atoms

Nickel Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Nickel 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 Nickel atom.
In total 15 binding sites of Nickel where determined in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A, PDB code: 5fpv:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 15 in 5fpv

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Nickel binding site 1 out of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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:Ni1360

b:65.2
occ:1.00
 NZ H:LYS106 2.5 47.8 1.0
N A:GLY230 3.5 42.9 1.0
CA A:GLY230 3.7 43.4 1.0
CE H:LYS106 3.8 44.8 1.0
N A:SER231 3.9 44.1 1.0
CA A:PHE228 4.0 40.7 1.0
C A:PHE228 4.0 43.3 1.0
OG A:SER231 4.2 45.2 1.0
CD A:PRO229 4.2 44.2 1.0
N A:PRO229 4.2 43.7 1.0
C A:GLY230 4.3 44.7 1.0
CB A:PHE228 4.4 37.7 1.0
O A:PHE228 4.5 45.2 1.0
CD1 A:PHE228 4.5 37.9 1.0
CD H:LYS106 4.6 42.5 1.0
C A:PRO229 4.6 43.0 1.0
CG A:PRO229 4.8 44.9 1.0
CG A:PHE228 4.9 37.0 1.0
CB A:SER231 5.0 45.1 1.0
CA A:SER231 5.0 44.1 1.0

Nickel binding site 2 out of 15 in 5fpv

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Nickel binding site 2 out of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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
A:Ni1361

b:87.5
occ:1.00
 N A:LYS91 3.6 38.4 1.0
NZ A:LYS90 3.8 45.0 1.0
CE A:LYS90 4.0 43.2 1.0
CB A:LYS91 4.0 43.7 1.0
CG A:LYS91 4.0 48.6 1.0
CD A:LYS90 4.1 41.5 1.0
CA A:LYS90 4.3 38.9 1.0
CB A:LYS90 4.3 39.8 1.0
CA A:LYS91 4.4 38.7 1.0
C A:LYS90 4.5 38.7 1.0
CD A:LYS91 4.7 54.7 1.0
CG A:LYS90 4.9 40.2 1.0

Nickel binding site 3 out of 15 in 5fpv

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Nickel binding site 3 out of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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
A:Ni1362

b:85.3
occ:1.00
 O A:TYR60 3.7 44.0 1.0
CE1 A:PHE203 4.2 24.4 1.0
CZ A:PHE203 4.3 23.8 1.0
CE2 A:PHE284 4.6 27.4 1.0
CB A:TYR60 4.6 35.9 1.0
C A:TYR60 4.6 42.8 1.0
CD1 A:PHE203 4.6 24.4 1.0
NE A:ARG99 4.7 39.4 1.0
CE2 A:PHE203 4.8 22.7 1.0
OD1 A:ASP64 4.8 42.8 1.0
NH2 A:ARG99 4.9 40.0 1.0

Nickel binding site 4 out of 15 in 5fpv

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Nickel binding site 4 out of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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
B:Ni1360

b:73.4
occ:1.00
 N B:GLY230 3.6 49.6 1.0
CA B:GLY230 3.7 49.5 1.0
N B:SER231 3.7 50.5 1.0
OG B:SER231 3.8 54.6 1.0
CA B:PHE228 4.1 43.7 1.0
C B:PHE228 4.1 45.5 1.0
C B:GLY230 4.2 49.9 1.0
CB B:PHE228 4.3 40.3 1.0
N B:PRO229 4.3 46.0 1.0
O B:PHE228 4.4 45.9 1.0
CD1 B:PHE228 4.4 37.5 1.0
CD B:PRO229 4.5 45.7 1.0
NZ G:LYS106 4.7 54.5 1.0
CB B:SER231 4.7 52.8 1.0
C B:PRO229 4.7 48.6 1.0
CA B:SER231 4.8 50.6 1.0
CG B:PHE228 4.9 37.9 1.0

Nickel binding site 5 out of 15 in 5fpv

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Nickel binding site 5 out of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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
B:Ni1361

b:69.4
occ:1.00
 O B:HOH2128 3.5 30.1 1.0
O B:TYR60 3.9 36.8 1.0
NE B:ARG99 4.1 33.2 1.0
CE1 B:PHE203 4.2 26.4 1.0
NH2 B:ARG99 4.2 33.7 1.0
CZ B:PHE203 4.3 26.4 1.0
O B:HOH2029 4.3 44.4 1.0
CE2 B:PHE284 4.3 22.9 1.0
CZ B:ARG99 4.6 35.5 1.0
CD1 B:PHE203 4.7 25.9 1.0
OD1 B:ASP64 4.8 39.7 1.0
CZ B:PHE284 4.8 22.6 1.0
CE2 B:PHE203 4.9 25.3 1.0
C B:TYR60 4.9 35.6 1.0

Nickel binding site 6 out of 15 in 5fpv

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Nickel binding site 6 out of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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
C:Ni1360

b:90.4
occ:1.00
 CB C:ARG96 3.5 27.1 1.0
OD1 C:ASP65 3.7 37.8 1.0
O C:HOH2049 4.0 36.0 1.0
CB C:ASP64 4.1 36.9 1.0
O C:ASP64 4.1 34.9 1.0
C C:ASP64 4.5 35.9 1.0
CG C:ASP65 4.8 37.8 1.0
OD2 C:ASP64 4.9 38.7 1.0
CA C:ASP64 4.9 36.3 1.0
CA C:ARG96 5.0 29.1 1.0

Nickel binding site 7 out of 15 in 5fpv

Go back to Nickel Binding Sites List in 5fpv
Nickel binding site 7 out of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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
C:Ni1361

b:63.0
occ:1.00
 O C:TYR60 3.8 37.4 1.0
O C:HOH2022 4.1 30.1 1.0
CE1 C:PHE203 4.1 26.5 1.0
CZ C:PHE203 4.2 27.5 1.0
NH2 C:ARG99 4.4 31.6 1.0
CE2 C:PHE284 4.4 25.2 1.0
NE C:ARG99 4.4 31.4 1.0
OD1 C:ASP64 4.5 40.2 1.0
CD1 C:PHE203 4.7 25.7 1.0
C C:TYR60 4.8 35.6 1.0
CE2 C:PHE203 4.8 26.5 1.0
CZ C:PHE284 4.8 26.1 1.0
CB C:TYR60 4.9 30.5 1.0
CZ C:ARG99 4.9 32.6 1.0

Nickel binding site 8 out of 15 in 5fpv

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Nickel binding site 8 out of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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
D:Ni1360

b:64.3
occ:1.00
 N D:GLY230 3.6 39.0 1.0
CE E:LYS106 3.6 46.9 1.0
CA D:GLY230 3.7 39.9 1.0
N D:SER231 3.8 40.6 1.0
OG D:SER231 3.9 40.7 1.0
CA D:PHE228 4.0 37.2 1.0
C D:PHE228 4.0 38.8 1.0
NZ E:LYS106 4.2 48.5 1.0
C D:GLY230 4.2 40.9 1.0
CB D:PHE228 4.3 35.9 1.0
N D:PRO229 4.3 39.7 1.0
CD1 D:PHE228 4.3 31.7 1.0
CD D:PRO229 4.4 39.9 1.0
O D:PHE228 4.4 38.2 1.0
C D:PRO229 4.7 37.0 1.0
CD E:LYS106 4.7 45.6 1.0
CB D:SER231 4.8 40.2 1.0
CG D:PHE228 4.8 32.7 1.0
CA D:SER231 4.9 41.1 1.0

Nickel binding site 9 out of 15 in 5fpv

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Nickel binding site 9 out of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni1361

b:80.2
occ:1.00
 O D:TYR60 4.0 40.4 1.0
CE1 D:PHE203 4.0 21.3 1.0
CZ D:PHE203 4.2 22.0 1.0
CD1 D:PHE203 4.5 19.9 1.0
CE2 D:PHE284 4.5 25.4 1.0
CB D:TYR60 4.7 30.5 1.0
CE2 D:PHE203 4.8 20.9 1.0
NE D:ARG99 4.8 41.2 1.0
C D:TYR60 4.8 38.3 1.0
OD1 D:ASP64 5.0 39.3 1.0
CZ D:PHE284 5.0 25.8 1.0

Nickel binding site 10 out of 15 in 5fpv

Go back to Nickel Binding Sites List in 5fpv
Nickel binding site 10 out of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni1362

b:0.4
occ:1.00
 O D:HOH2039 3.3 27.0 1.0
O D:HOH2030 3.5 29.6 1.0
O D:HOH2068 4.0 48.7 1.0
O D:SER185 4.1 19.7 1.0
NE2 D:GLN74 4.3 20.4 1.0
CE2 D:TYR133 4.3 28.9 1.0
CD2 D:TYR133 4.4 27.4 1.0
CB D:ALA135 4.5 29.7 1.0
CD1 D:ILE72 4.6 62.3 1.0
CA D:PHE186 4.8 24.3 1.0
CB D:PHE186 4.8 18.9 1.0
OD2 D:ASP136 4.9 37.1 1.0
NE2 D:GLN85 5.0 24.9 1.0
OAU D:MMK1358 5.0 31.0 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: Thu Oct 10 06:23:11 2024

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