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Zinc in PDB 3o37: Crystal Structure of TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide

Protein crystallography data

The structure of Crystal Structure of TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide, PDB code: 3o37 was solved by Z.Wang, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.67 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 35.667, 63.848, 79.299, 89.92, 89.99, 89.80
R / Rfree (%) 22.7 / 25.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide (pdb code 3o37). 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 TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide, PDB code: 3o37:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3o37

Go back to Zinc Binding Sites List in 3o37
Zinc binding site 1 out of 8 in the Crystal Structure of TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide


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 TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:46.5
occ:1.00
 SG A:CYS870 2.3 42.1 1.0
SG A:CYS841 2.5 48.2 1.0
SG A:CYS867 2.5 35.8 1.0
SG A:CYS844 2.6 50.7 1.0
CB A:CYS844 3.2 53.9 1.0
CB A:CYS870 3.3 37.6 1.0
CB A:CYS841 3.5 51.2 1.0
N A:CYS844 3.7 55.5 1.0
CB A:CYS867 3.7 34.6 1.0
CA A:CYS844 4.0 53.6 1.0
N A:CYS870 4.0 33.4 1.0
N A:CYS867 4.1 36.8 1.0
CA A:CYS870 4.3 35.1 1.0
CA A:CYS867 4.3 35.4 1.0
C A:LYS843 4.4 57.9 1.0
CB A:LYS843 4.5 60.3 1.0
C A:CYS844 4.6 51.9 1.0
O A:CYS844 4.6 52.5 1.0
CB A:PHE869 4.7 32.2 1.0
O A:CYS867 4.7 31.6 1.0
C A:CYS867 4.7 33.4 1.0
N A:LYS843 4.8 57.6 1.0
CA A:LYS843 4.8 58.1 1.0
C A:PHE869 4.9 31.9 1.0
CA A:CYS841 4.9 53.8 1.0

Zinc binding site 2 out of 8 in 3o37

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Zinc binding site 2 out of 8 in the Crystal Structure of TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide


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 TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:47.0
occ:1.00
 ND1 A:HIS849 2.2 45.8 1.0
SG A:CYS829 2.3 41.1 1.0
SG A:CYS852 2.4 40.9 1.0
SG A:CYS832 2.5 41.3 1.0
CE1 A:HIS849 3.1 48.3 1.0
CB A:CYS829 3.1 47.9 1.0
CB A:CYS852 3.2 37.9 1.0
CG A:HIS849 3.2 47.3 1.0
CB A:CYS832 3.4 42.2 1.0
CB A:HIS849 3.6 44.1 1.0
N A:CYS832 3.6 41.2 1.0
CA A:CYS832 4.1 42.8 1.0
N A:HIS849 4.1 42.5 1.0
NE2 A:HIS849 4.2 50.8 1.0
CD2 A:HIS849 4.3 49.3 1.0
CA A:HIS849 4.5 43.2 1.0
CB A:VAL831 4.5 37.7 1.0
CA A:CYS829 4.6 47.2 1.0
CA A:CYS852 4.7 36.0 1.0
C A:VAL831 4.8 39.6 1.0
C A:CYS832 4.8 45.4 1.0
N A:GLN833 4.9 48.8 1.0

Zinc binding site 3 out of 8 in 3o37

Go back to Zinc Binding Sites List in 3o37
Zinc binding site 3 out of 8 in the Crystal Structure of TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide


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 TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:45.4
occ:1.00
 SG B:CYS829 2.2 42.2 1.0
ND1 B:HIS849 2.3 41.4 1.0
SG B:CYS852 2.4 42.3 1.0
SG B:CYS832 2.5 43.6 1.0
CB B:CYS829 3.0 46.8 1.0
CE1 B:HIS849 3.1 42.6 1.0
CB B:CYS852 3.1 37.5 1.0
CG B:HIS849 3.2 42.6 1.0
CB B:CYS832 3.5 43.2 1.0
CB B:HIS849 3.7 40.1 1.0
N B:CYS832 3.7 40.9 1.0
N B:HIS849 4.1 40.2 1.0
CA B:CYS832 4.1 43.3 1.0
NE2 B:HIS849 4.1 44.9 1.0
CD2 B:HIS849 4.2 43.6 1.0
CA B:CYS829 4.5 46.3 1.0
CB B:VAL831 4.5 35.8 1.0
CA B:HIS849 4.5 40.4 1.0
CA B:CYS852 4.6 33.7 1.0
C B:VAL831 4.8 38.8 1.0
C B:CYS832 4.9 45.8 1.0
C B:CYS829 4.9 43.5 1.0
N B:VAL831 4.9 37.1 1.0
N B:GLN833 4.9 48.8 1.0
CA B:VAL831 5.0 37.3 1.0

Zinc binding site 4 out of 8 in 3o37

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Zinc binding site 4 out of 8 in the Crystal Structure of TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide


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 TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:49.6
occ:1.00
 SG B:CYS870 2.2 39.1 1.0
SG B:CYS841 2.5 43.4 1.0
SG B:CYS867 2.5 33.1 1.0
SG B:CYS844 2.6 47.5 1.0
CB B:CYS844 3.1 48.6 1.0
CB B:CYS870 3.3 35.6 1.0
CB B:CYS841 3.5 47.4 1.0
CB B:CYS867 3.7 33.2 1.0
N B:CYS844 3.9 50.8 1.0
N B:CYS870 4.0 32.1 1.0
N B:CYS867 4.0 35.2 1.0
CA B:CYS844 4.1 49.2 1.0
CA B:CYS870 4.3 33.8 1.0
CA B:CYS867 4.3 33.4 1.0
C B:LYS843 4.5 53.8 1.0
O B:CYS867 4.6 31.4 1.0
O B:HOH149 4.6 37.1 1.0
C B:CYS844 4.6 47.0 1.0
CB B:PHE869 4.6 30.6 1.0
C B:CYS867 4.7 31.6 1.0
O B:CYS844 4.7 47.4 1.0
N B:LYS843 4.8 55.4 1.0
CA B:CYS841 4.9 51.4 1.0
CG B:LYS846 4.9 53.7 1.0
C B:PHE869 4.9 30.8 1.0
O B:LYS843 4.9 53.6 1.0

Zinc binding site 5 out of 8 in 3o37

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Zinc binding site 5 out of 8 in the Crystal Structure of TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide


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 TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1

b:45.7
occ:1.00
 ND1 C:HIS849 2.2 52.5 1.0
SG C:CYS829 2.4 43.1 1.0
SG C:CYS852 2.4 38.5 1.0
SG C:CYS832 2.5 42.4 1.0
CE1 C:HIS849 3.0 53.8 1.0
CB C:CYS829 3.1 47.3 1.0
CB C:CYS852 3.2 36.1 1.0
CG C:HIS849 3.3 51.6 1.0
CB C:CYS832 3.3 42.6 1.0
N C:CYS832 3.7 39.8 1.0
CB C:HIS849 3.7 47.9 1.0
CA C:CYS832 4.1 41.4 1.0
NE2 C:HIS849 4.2 55.7 1.0
N C:HIS849 4.3 44.2 1.0
CD2 C:HIS849 4.3 53.6 1.0
CA C:CYS829 4.6 45.9 1.0
CB C:VAL831 4.6 36.2 1.0
CA C:HIS849 4.6 45.0 1.0
CA C:CYS852 4.7 35.4 1.0
C C:VAL831 4.8 39.2 1.0
C C:CYS832 4.8 43.6 1.0
N C:GLN833 4.9 46.6 1.0

Zinc binding site 6 out of 8 in 3o37

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Zinc binding site 6 out of 8 in the Crystal Structure of TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide


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 TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2

b:51.5
occ:1.00
 SG C:CYS870 2.3 37.8 1.0
SG C:CYS867 2.5 34.6 1.0
SG C:CYS841 2.5 43.9 1.0
SG C:CYS844 2.5 48.7 1.0
CB C:CYS844 3.2 49.8 1.0
CB C:CYS870 3.4 35.0 1.0
CB C:CYS841 3.4 45.6 1.0
CB C:CYS867 3.5 34.8 1.0
N C:CYS844 3.8 51.0 1.0
CA C:CYS844 4.0 50.0 1.0
N C:CYS870 4.0 31.3 1.0
N C:CYS867 4.0 37.1 1.0
CA C:CYS867 4.3 34.5 1.0
CA C:CYS870 4.4 32.5 1.0
C C:LYS843 4.5 53.8 1.0
CB C:PHE869 4.6 30.4 1.0
C C:CYS844 4.6 48.6 1.0
O C:CYS867 4.7 31.3 1.0
C C:CYS867 4.7 32.3 1.0
CB C:LYS843 4.7 57.9 1.0
O C:CYS844 4.7 49.2 1.0
CA C:CYS841 4.8 49.0 1.0
CG2 C:ILE866 4.8 44.5 1.0
N C:LYS843 4.9 54.1 1.0
C C:PHE869 4.9 28.6 1.0
CA C:LYS843 5.0 54.2 1.0

Zinc binding site 7 out of 8 in 3o37

Go back to Zinc Binding Sites List in 3o37
Zinc binding site 7 out of 8 in the Crystal Structure of TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide


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 TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1

b:45.6
occ:1.00
 ND1 D:HIS849 2.2 49.8 1.0
SG D:CYS829 2.3 43.2 1.0
SG D:CYS852 2.4 41.8 1.0
SG D:CYS832 2.5 44.9 1.0
CE1 D:HIS849 3.0 50.2 1.0
CB D:CYS829 3.1 49.3 1.0
CB D:CYS852 3.2 39.2 1.0
CG D:HIS849 3.2 49.4 1.0
CB D:CYS832 3.4 44.5 1.0
CB D:HIS849 3.6 46.2 1.0
N D:CYS832 3.7 42.3 1.0
N D:HIS849 4.1 43.3 1.0
CA D:CYS832 4.1 44.2 1.0
NE2 D:HIS849 4.1 52.1 1.0
CD2 D:HIS849 4.2 50.6 1.0
CA D:HIS849 4.5 44.2 1.0
CA D:CYS829 4.5 48.2 1.0
CB D:VAL831 4.6 39.6 1.0
CA D:CYS852 4.7 36.1 1.0
C D:VAL831 4.8 41.5 1.0
C D:CYS832 4.8 46.4 1.0
N D:GLN833 5.0 48.5 1.0

Zinc binding site 8 out of 8 in 3o37

Go back to Zinc Binding Sites List in 3o37
Zinc binding site 8 out of 8 in the Crystal Structure of TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide


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 TRIM24 Phd-Bromo Complexed with H3(1-10)K4 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2

b:47.0
occ:1.00
 SG D:CYS870 2.3 43.2 1.0
SG D:CYS841 2.4 47.8 1.0
SG D:CYS867 2.5 36.4 1.0
SG D:CYS844 2.6 48.4 1.0
CB D:CYS844 3.1 49.6 1.0
CB D:CYS870 3.2 37.4 1.0
CB D:CYS841 3.4 51.5 1.0
CB D:CYS867 3.6 36.8 1.0
N D:CYS844 3.7 52.1 1.0
N D:CYS870 3.9 33.1 1.0
CA D:CYS844 4.0 49.4 1.0
N D:CYS867 4.0 37.4 1.0
CA D:CYS870 4.2 34.6 1.0
CA D:CYS867 4.3 35.0 1.0
C D:LYS843 4.4 55.4 1.0
CB D:LYS843 4.5 60.2 1.0
O D:CYS867 4.6 31.9 1.0
C D:CYS867 4.7 33.4 1.0
C D:CYS844 4.7 46.9 1.0
CB D:PHE869 4.7 30.9 1.0
CA D:LYS843 4.8 56.5 1.0
N D:LYS843 4.8 57.6 1.0
CA D:CYS841 4.8 55.1 1.0
CG2 D:ILE866 4.8 46.6 1.0
O D:CYS844 4.8 46.8 1.0
C D:PHE869 4.9 30.5 1.0

Reference:

W.W.Tsai, Z.Wang, T.T.Yiu, K.C.Akdemir, W.Xia, S.Winter, C.Y.Tsai, X.Shi, D.Schwarzer, W.Plunkett, B.Aronow, O.Gozani, W.Fischle, M.C.Hung, D.J.Patel, M.C.Barton. TRIM24 Links A Non-Canonical Histone Signature to Breast Cancer. Nature V. 468 927 2010.
ISSN: ISSN 0028-0836
PubMed: 21164480
DOI: 10.1038/NATURE09542
Page generated: Sat Oct 26 10:42:15 2024

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