Atomistry » Zinc » PDB 5evk-5f8g » 5f39
Atomistry »
  Zinc »
    PDB 5evk-5f8g »
      5f39 »

Zinc in PDB 5f39: Crystal Structure of Human KDM4A in Complex with Compound 37

Protein crystallography data

The structure of Crystal Structure of Human KDM4A in Complex with Compound 37, PDB code: 5f39 was solved by Y.-V.Le Bihan, S.Dempster, I.M.Westwood, R.L.M.Van Montfort, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.63 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.409, 102.061, 143.474, 90.00, 99.82, 90.00
R / Rfree (%) 16.9 / 21

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human KDM4A in Complex with Compound 37 (pdb code 5f39). 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 KDM4A in Complex with Compound 37, PDB code: 5f39:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5f39

Go back to Zinc Binding Sites List in 5f39
Zinc binding site 1 out of 8 in the Crystal Structure of Human KDM4A in Complex with Compound 37


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 KDM4A in Complex with Compound 37 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:64.8
occ:1.00
N3 A:5UB403 2.0 72.8 0.9
OE2 A:GLU190 2.1 43.7 1.0
NE2 A:HIS276 2.2 58.1 1.0
NE2 A:HIS188 2.2 54.0 1.0
O A:HOH512 2.2 45.5 1.0
N2 A:5UB403 2.3 59.0 0.9
C7 A:5UB403 2.8 69.6 0.9
C6 A:5UB403 3.0 61.7 0.9
C9 A:5UB403 3.0 75.0 0.9
CE1 A:HIS276 3.0 59.0 1.0
CD2 A:HIS188 3.1 55.2 1.0
CE1 A:HIS188 3.2 53.4 1.0
CD A:GLU190 3.2 64.3 1.0
CD2 A:HIS276 3.3 57.5 1.0
C5 A:5UB403 3.3 58.6 0.9
OE1 A:GLU190 3.6 79.6 1.0
C8 A:5UB403 4.0 72.0 0.9
O A:HOH501 4.1 61.0 1.0
ND1 A:HIS276 4.2 59.7 1.0
ND1 A:HIS188 4.3 54.5 1.0
CG A:HIS188 4.3 54.2 1.0
CG A:HIS276 4.3 56.6 1.0
C2 A:5UB403 4.3 57.9 0.9
S A:5UB403 4.4 76.3 0.9
CG A:GLU190 4.5 62.5 1.0
C4 A:5UB403 4.6 55.7 0.9
OG A:SER196 4.6 64.4 1.0

Zinc binding site 2 out of 8 in 5f39

Go back to Zinc Binding Sites List in 5f39
Zinc binding site 2 out of 8 in the Crystal Structure of Human KDM4A in Complex with Compound 37


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 KDM4A in Complex with Compound 37 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:66.8
occ:0.72
SG A:CYS234 2.1 82.8 1.0
NE2 A:HIS240 2.2 70.2 1.0
SG A:CYS306 2.3 81.6 1.0
SG A:CYS308 2.4 99.3 1.0
CB A:CYS234 3.0 80.0 1.0
CE1 A:HIS240 3.1 69.9 1.0
CD2 A:HIS240 3.3 69.0 1.0
CB A:CYS308 3.4 96.7 1.0
N A:SER307 3.4 87.2 1.0
CB A:CYS306 3.4 77.7 1.0
N A:CYS308 3.8 90.9 1.0
CA A:CYS306 3.8 79.7 1.0
C A:SER307 3.9 96.1 1.0
C A:CYS306 4.0 88.3 1.0
CA A:CYS308 4.2 98.4 1.0
ND1 A:HIS240 4.3 69.2 1.0
CA A:SER307 4.3 90.3 1.0
CG A:HIS240 4.3 66.6 1.0
O A:ALA236 4.4 76.3 1.0
O A:SER307 4.4 97.6 1.0
CA A:CYS234 4.4 82.3 1.0
C A:ALA236 4.7 76.7 1.0
CA A:PHE237 4.7 64.8 1.0
N A:PHE237 4.9 68.7 1.0
OG A:SER307 5.0 99.3 1.0

Zinc binding site 3 out of 8 in 5f39

Go back to Zinc Binding Sites List in 5f39
Zinc binding site 3 out of 8 in the Crystal Structure of Human KDM4A in Complex with Compound 37


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 KDM4A in Complex with Compound 37 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:62.6
occ:1.00
O B:HOH516 2.0 52.2 1.0
NE2 B:HIS276 2.1 55.9 1.0
N3 B:5UB403 2.1 66.0 0.8
OE2 B:GLU190 2.1 59.3 1.0
N2 B:5UB403 2.2 43.0 0.8
NE2 B:HIS188 2.3 53.2 1.0
C7 B:5UB403 2.9 61.4 0.8
C6 B:5UB403 3.0 50.9 0.8
CE1 B:HIS276 3.0 56.3 1.0
C9 B:5UB403 3.1 67.6 0.8
CD2 B:HIS276 3.2 55.9 1.0
CD B:GLU190 3.2 59.6 1.0
CE1 B:HIS188 3.2 52.7 1.0
C5 B:5UB403 3.2 40.8 0.8
CD2 B:HIS188 3.3 54.9 1.0
OE1 B:GLU190 3.7 67.7 1.0
O B:HOH503 4.0 56.9 1.0
C8 B:5UB403 4.1 64.1 0.8
ND1 B:HIS276 4.2 57.0 1.0
CG B:HIS276 4.2 54.5 1.0
C2 B:5UB403 4.3 45.9 0.8
ND1 B:HIS188 4.3 54.1 1.0
CG B:HIS188 4.4 53.7 1.0
CG B:GLU190 4.4 62.1 1.0
C4 B:5UB403 4.5 42.8 0.8
S B:5UB403 4.5 67.6 0.8
OG B:SER196 4.6 66.1 1.0
C3 B:5UB403 5.0 45.3 0.8

Zinc binding site 4 out of 8 in 5f39

Go back to Zinc Binding Sites List in 5f39
Zinc binding site 4 out of 8 in the Crystal Structure of Human KDM4A in Complex with Compound 37


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 KDM4A in Complex with Compound 37 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:68.5
occ:0.85
SG B:CYS234 2.2 83.1 1.0
NE2 B:HIS240 2.2 73.2 1.0
SG B:CYS306 2.3 87.4 1.0
SG B:CYS308 2.5 99.4 1.0
CE1 B:HIS240 3.1 73.5 1.0
CB B:CYS234 3.2 81.1 1.0
CD2 B:HIS240 3.2 71.5 1.0
CB B:CYS306 3.4 81.4 1.0
CA B:CYS306 3.8 81.0 1.0
CB B:CYS308 3.9 98.3 1.0
N B:SER307 3.9 89.1 1.0
N B:CYS308 4.0 95.2 1.0
C B:CYS306 4.2 89.4 1.0
ND1 B:HIS240 4.3 73.0 1.0
CG B:HIS240 4.3 69.3 1.0
CA B:CYS308 4.4 98.4 1.0
O B:ALA236 4.5 76.6 1.0
N B:ARG309 4.5 0.4 1.0
CA B:CYS234 4.6 83.5 1.0
C B:SER307 4.7 96.6 1.0
C B:ALA236 4.7 77.6 1.0
CA B:PHE237 4.8 71.0 1.0
CG B:ARG309 4.8 98.1 1.0
CD B:ARG309 4.8 89.5 1.0
CA B:SER307 4.8 91.2 1.0
OG B:SER307 4.9 94.6 1.0
N B:PHE237 4.9 72.4 1.0
C B:CYS308 5.0 0.4 1.0

Zinc binding site 5 out of 8 in 5f39

Go back to Zinc Binding Sites List in 5f39
Zinc binding site 5 out of 8 in the Crystal Structure of Human KDM4A in Complex with Compound 37


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 KDM4A in Complex with Compound 37 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:63.2
occ:1.00
N3 C:5UB403 2.0 63.5 0.7
OE2 C:GLU190 2.1 67.5 1.0
NE2 C:HIS276 2.2 61.4 1.0
O C:HOH520 2.2 52.3 1.0
NE2 C:HIS188 2.2 58.6 1.0
N2 C:5UB403 2.3 41.8 0.7
C7 C:5UB403 2.8 57.4 0.7
C6 C:5UB403 3.0 44.3 0.7
C9 C:5UB403 3.0 63.7 0.7
CE1 C:HIS276 3.0 61.6 1.0
CD2 C:HIS188 3.1 59.2 1.0
CE1 C:HIS188 3.2 57.7 1.0
CD C:GLU190 3.2 75.6 1.0
CD2 C:HIS276 3.3 61.6 1.0
C5 C:5UB403 3.4 41.9 0.7
OE1 C:GLU190 3.6 56.0 1.0
C8 C:5UB403 4.0 59.9 0.7
ND1 C:HIS276 4.2 62.3 1.0
ND1 C:HIS188 4.3 58.0 1.0
CG C:HIS188 4.3 56.8 1.0
CG C:HIS276 4.3 60.0 1.0
C2 C:5UB403 4.3 39.5 0.7
S C:5UB403 4.4 60.0 0.7
CG C:GLU190 4.4 69.6 1.0
C4 C:5UB403 4.6 39.1 0.7
OG C:SER196 4.7 56.6 1.0
O C:HOH501 4.7 58.7 1.0
C2 C:DMS405 4.8 88.0 0.9

Zinc binding site 6 out of 8 in 5f39

Go back to Zinc Binding Sites List in 5f39
Zinc binding site 6 out of 8 in the Crystal Structure of Human KDM4A in Complex with Compound 37


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 KDM4A in Complex with Compound 37 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:75.5
occ:0.95
SG C:CYS306 2.2 87.7 1.0
NE2 C:HIS240 2.3 74.1 1.0
SG C:CYS234 2.3 88.3 1.0
SG C:CYS308 2.4 96.0 1.0
CB C:CYS234 3.2 85.7 1.0
CE1 C:HIS240 3.3 74.0 1.0
CD2 C:HIS240 3.3 72.2 1.0
CB C:CYS306 3.4 82.9 1.0
N C:CYS308 3.7 94.0 1.0
N C:SER307 3.7 93.8 1.0
CB C:CYS308 3.7 93.3 1.0
CA C:CYS306 3.8 82.8 1.0
C C:CYS306 4.0 93.4 1.0
CA C:CYS308 4.2 94.0 1.0
N C:ARG309 4.2 98.2 1.0
C C:SER307 4.4 98.6 1.0
ND1 C:HIS240 4.4 73.0 1.0
CG C:HIS240 4.5 70.2 1.0
CA C:CYS234 4.6 88.4 1.0
CA C:SER307 4.6 94.5 1.0
CG C:ARG309 4.6 93.1 1.0
O C:ALA236 4.6 72.7 1.0
CD C:ARG309 4.7 94.4 1.0
C C:CYS308 4.7 0.2 1.0
OG C:SER307 4.8 0.3 1.0
CB C:ARG309 4.9 94.8 1.0
O C:CYS306 5.0 93.5 1.0
C C:ALA236 5.0 75.4 1.0

Zinc binding site 7 out of 8 in 5f39

Go back to Zinc Binding Sites List in 5f39
Zinc binding site 7 out of 8 in the Crystal Structure of Human KDM4A in Complex with Compound 37


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 KDM4A in Complex with Compound 37 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:64.1
occ:0.90
SG D:CYS308 2.2 97.2 1.0
SG D:CYS306 2.2 78.4 1.0
NE2 D:HIS240 2.2 61.0 1.0
SG D:CYS234 2.3 70.0 1.0
CE1 D:HIS240 3.1 61.3 1.0
CB D:CYS234 3.1 67.5 1.0
CD2 D:HIS240 3.3 61.0 1.0
CB D:CYS306 3.5 71.3 1.0
CB D:CYS308 3.6 97.6 1.0
N D:CYS308 3.8 94.4 1.0
N D:SER307 3.9 83.7 1.0
CA D:CYS306 4.0 71.7 1.0
CA D:CYS308 4.2 98.0 1.0
C D:CYS306 4.2 82.6 1.0
N D:ARG309 4.2 0.1 1.0
ND1 D:HIS240 4.3 62.1 1.0
CG D:HIS240 4.4 60.1 1.0
C D:SER307 4.5 95.9 1.0
CA D:CYS234 4.5 69.2 1.0
CG D:ARG309 4.5 0.7 1.0
CD D:ARG309 4.6 0.3 1.0
C D:CYS308 4.7 0.9 1.0
O D:ALA236 4.7 68.0 1.0
CA D:SER307 4.7 87.3 1.0
OG D:SER307 4.8 97.1 1.0
CB D:ARG309 4.9 0.8 1.0

Zinc binding site 8 out of 8 in 5f39

Go back to Zinc Binding Sites List in 5f39
Zinc binding site 8 out of 8 in the Crystal Structure of Human KDM4A in Complex with Compound 37


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 KDM4A in Complex with Compound 37 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:67.7
occ:1.00
N3 D:5UB403 2.1 67.6 0.8
OE2 D:GLU190 2.1 63.1 1.0
NE2 D:HIS276 2.1 53.8 1.0
NE2 D:HIS188 2.1 58.3 1.0
O D:HOH504 2.2 72.1 1.0
N2 D:5UB403 2.3 44.7 0.8
C7 D:5UB403 2.9 59.9 0.8
CE1 D:HIS276 3.0 53.1 1.0
C6 D:5UB403 3.0 47.9 0.8
C9 D:5UB403 3.1 70.7 0.8
CD2 D:HIS188 3.1 58.6 1.0
CE1 D:HIS188 3.1 58.2 1.0
CD D:GLU190 3.2 67.9 1.0
CD2 D:HIS276 3.2 54.3 1.0
C5 D:5UB403 3.4 42.6 0.8
OE1 D:GLU190 3.7 60.9 1.0
C8 D:5UB403 4.1 64.6 0.8
ND1 D:HIS276 4.1 54.2 1.0
ND1 D:HIS188 4.2 58.8 1.0
CG D:HIS188 4.2 56.8 1.0
CG D:HIS276 4.2 52.9 1.0
C2 D:5UB403 4.4 42.1 0.8
CG D:GLU190 4.4 61.3 1.0
S D:5UB403 4.5 68.9 0.8
C4 D:5UB403 4.6 41.7 0.8
OG D:SER196 4.7 53.6 1.0

Reference:

V.Bavetsias, R.M.Lanigan, G.F.Ruda, B.Atrash, M.G.Mclaughlin, A.Tumber, N.Y.Mok, Y.V.Le Bihan, S.Dempster, K.J.Boxall, F.Jeganathan, S.B.Hatch, P.Savitsky, S.Velupillai, T.Krojer, K.S.England, J.Sejberg, C.Thai, A.Donovan, A.Pal, G.Scozzafava, J.M.Bennett, A.Kawamura, C.Johansson, A.Szykowska, C.Gileadi, N.A.Burgess-Brown, F.Von Delft, U.Oppermann, Z.Walters, J.Shipley, F.I.Raynaud, S.M.Westaway, R.K.Prinjha, O.Fedorov, R.Burke, C.J.Schofield, I.M.Westwood, C.Bountra, S.Muller, R.L.Van Montfort, P.E.Brennan, J.Blagg. 8-Substituted Pyrido[3,4-D]Pyrimidin-4(3H)-One Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors. J.Med.Chem. V. 59 1388 2016.
ISSN: ISSN 0022-2623
PubMed: 26741168
DOI: 10.1021/ACS.JMEDCHEM.5B01635
Page generated: Sun Oct 27 15:40:11 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy