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Zinc in PDB 3u5m: Crystal Structure of TRIM33 Phd-Bromo in the Free State

Protein crystallography data

The structure of Crystal Structure of TRIM33 Phd-Bromo in the Free State, PDB code: 3u5m 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) 27.36 / 3.08
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 79.527, 79.781, 134.160, 89.90, 89.96, 59.97
R / Rfree (%) 20.7 / 29.3

Other elements in 3u5m:

The structure of Crystal Structure of TRIM33 Phd-Bromo in the Free State also contains other interesting chemical elements:

Calcium (Ca) 12 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of TRIM33 Phd-Bromo in the Free State (pdb code 3u5m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Crystal Structure of TRIM33 Phd-Bromo in the Free State, PDB code: 3u5m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in 3u5m

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Zinc binding site 1 out of 24 in the Crystal Structure of TRIM33 Phd-Bromo in the Free State


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 TRIM33 Phd-Bromo in the Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:0.1
occ:1.00
ND1 A:HIS910 2.3 0.3 1.0
SG A:CYS890 2.5 0.7 1.0
SG A:CYS893 2.5 0.2 1.0
SG A:CYS913 2.6 0.6 1.0
CB A:CYS913 3.0 0.1 1.0
CG A:HIS910 3.2 0.1 1.0
CB A:CYS890 3.3 0.9 1.0
CE1 A:HIS910 3.3 0.9 1.0
CB A:HIS910 3.3 0.1 1.0
CB A:CYS893 3.6 0.6 1.0
N A:CYS893 3.9 0.8 1.0
N A:HIS910 3.9 0.3 1.0
CA A:HIS910 4.2 0.6 1.0
CA A:CYS893 4.3 0.5 1.0
CD2 A:HIS910 4.4 0.4 1.0
NE2 A:HIS910 4.4 0.7 1.0
CA A:CYS913 4.5 0.9 1.0
CB A:VAL892 4.5 0.1 1.0
CA A:CYS890 4.8 0.6 1.0
N A:CYS913 4.9 0.1 1.0
C A:VAL892 5.0 0.4 1.0
N A:VAL892 5.0 0.6 1.0

Zinc binding site 2 out of 24 in 3u5m

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Zinc binding site 2 out of 24 in the Crystal Structure of TRIM33 Phd-Bromo in the Free State


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 TRIM33 Phd-Bromo in the Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:0.6
occ:1.00
SG A:CYS931 2.4 0.3 1.0
SG A:CYS902 2.5 0.5 1.0
SG A:CYS928 2.7 0.3 1.0
CB A:CYS905 2.9 0.8 1.0
SG A:CYS905 2.9 0.2 1.0
CB A:CYS902 3.2 0.9 1.0
CB A:CYS931 3.5 0.2 1.0
CA A:CYS905 4.0 0.9 1.0
N A:CYS905 4.0 0.9 1.0
CB A:CYS928 4.1 0.9 1.0
C A:LYS904 4.3 0.8 1.0
N A:CYS931 4.4 0.4 1.0
N A:CYS928 4.6 0.9 1.0
CA A:CYS931 4.6 1.0 1.0
O A:LYS904 4.6 0.8 1.0
CA A:CYS902 4.7 0.3 1.0
C A:CYS905 4.7 0.9 1.0
CB A:LYS907 4.8 0.6 1.0
CB A:LYS904 4.9 0.6 1.0
CA A:CYS928 4.9 0.9 1.0
CA A:LYS904 5.0 0.5 1.0

Zinc binding site 3 out of 24 in 3u5m

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Zinc binding site 3 out of 24 in the Crystal Structure of TRIM33 Phd-Bromo in the Free State


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 TRIM33 Phd-Bromo in the Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:0.4
occ:1.00
SG B:CYS893 2.3 0.4 1.0
ND1 B:HIS910 2.3 0.3 1.0
SG B:CYS913 2.4 0.6 1.0
SG B:CYS890 2.6 0.3 1.0
CG B:HIS910 3.2 0.2 1.0
CB B:CYS890 3.2 0.9 1.0
CB B:HIS910 3.3 0.6 1.0
CB B:CYS913 3.4 0.4 1.0
CE1 B:HIS910 3.4 0.6 1.0
CB B:CYS893 3.5 0.2 1.0
N B:CYS893 4.0 0.8 1.0
N B:HIS910 4.1 0.2 1.0
CA B:HIS910 4.3 0.4 1.0
CA B:CYS893 4.3 0.5 1.0
CD2 B:HIS910 4.4 0.3 1.0
NE2 B:HIS910 4.5 0.2 1.0
CA B:CYS890 4.7 0.1 1.0
CA B:CYS913 4.8 0.5 1.0
CB B:VAL892 4.9 0.5 1.0

Zinc binding site 4 out of 24 in 3u5m

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Zinc binding site 4 out of 24 in the Crystal Structure of TRIM33 Phd-Bromo in the Free State


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 TRIM33 Phd-Bromo in the Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:0.4
occ:1.00
SG B:CYS902 2.4 0.6 1.0
SG B:CYS931 2.5 0.2 1.0
SG B:CYS928 2.7 0.0 1.0
SG B:CYS905 3.0 0.2 1.0
CB B:CYS905 3.1 0.4 1.0
CB B:CYS902 3.2 0.5 1.0
CB B:CYS931 3.6 0.6 1.0
CB B:CYS928 4.0 0.5 1.0
N B:CYS931 4.1 0.0 1.0
N B:CYS905 4.2 0.6 1.0
CA B:CYS905 4.2 0.6 1.0
C B:LYS904 4.4 0.7 1.0
N B:CYS928 4.5 0.1 1.0
CA B:CYS931 4.5 0.2 1.0
CB B:LYS904 4.6 0.1 1.0
O B:LYS904 4.7 0.5 1.0
CB B:PHE930 4.7 0.4 1.0
CA B:CYS902 4.7 1.0 1.0
CA B:CYS928 4.8 0.7 1.0
C B:CYS905 4.9 0.1 1.0
CB B:LYS907 5.0 0.1 1.0
CA B:LYS904 5.0 0.3 1.0
C B:PHE930 5.0 0.6 1.0

Zinc binding site 5 out of 24 in 3u5m

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Zinc binding site 5 out of 24 in the Crystal Structure of TRIM33 Phd-Bromo in the Free State


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 TRIM33 Phd-Bromo in the Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1

b:0.1
occ:1.00
ND1 C:HIS910 2.3 0.4 1.0
SG C:CYS893 2.4 0.4 1.0
SG C:CYS890 2.4 0.6 1.0
SG C:CYS913 2.6 0.2 1.0
CB C:CYS890 3.1 0.2 1.0
CG C:HIS910 3.1 0.4 1.0
CB C:HIS910 3.2 0.6 1.0
CB C:CYS913 3.2 0.4 1.0
CE1 C:HIS910 3.4 0.9 1.0
CB C:CYS893 3.4 0.1 1.0
N C:HIS910 3.9 0.9 1.0
N C:CYS893 3.9 0.5 1.0
CA C:HIS910 4.1 0.7 1.0
CA C:CYS893 4.3 0.2 1.0
CD2 C:HIS910 4.3 0.6 1.0
NE2 C:HIS910 4.4 0.8 1.0
CA C:CYS890 4.6 0.3 1.0
CA C:CYS913 4.6 0.9 1.0
CB C:VAL892 4.7 0.4 1.0
N C:CYS913 4.9 0.9 1.0

Zinc binding site 6 out of 24 in 3u5m

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Zinc binding site 6 out of 24 in the Crystal Structure of TRIM33 Phd-Bromo in the Free State


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 TRIM33 Phd-Bromo in the Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2

b:0.4
occ:1.00
SG C:CYS931 2.4 0.5 1.0
SG C:CYS902 2.5 0.7 1.0
SG C:CYS928 2.5 0.8 1.0
SG C:CYS905 2.7 0.0 1.0
CB C:CYS931 3.2 0.7 1.0
CB C:CYS902 3.5 0.7 1.0
CB C:CYS905 3.5 0.8 1.0
N C:CYS905 3.8 0.9 1.0
CB C:CYS928 3.9 0.9 1.0
N C:CYS931 3.9 0.9 1.0
CA C:CYS931 4.2 0.4 1.0
CA C:CYS905 4.2 0.9 1.0
N C:CYS928 4.2 0.8 1.0
CB C:LYS904 4.3 0.6 1.0
CA C:CYS928 4.6 0.7 1.0
CB C:PHE930 4.8 0.6 1.0
C C:LYS904 4.9 0.3 1.0
C C:CYS928 4.9 0.5 1.0
C C:PHE930 4.9 0.8 1.0
C C:CYS905 4.9 0.7 1.0
CB C:LYS907 4.9 0.3 1.0
CA C:CYS902 4.9 0.7 1.0

Zinc binding site 7 out of 24 in 3u5m

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Zinc binding site 7 out of 24 in the Crystal Structure of TRIM33 Phd-Bromo in the Free State


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 TRIM33 Phd-Bromo in the Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1

b:0.9
occ:1.00
SG D:CYS893 2.3 0.4 1.0
SG D:CYS913 2.3 0.2 1.0
ND1 D:HIS910 2.3 0.5 1.0
SG D:CYS890 2.5 1.0 1.0
CB D:CYS890 3.2 0.5 1.0
CB D:CYS913 3.3 0.1 1.0
CG D:HIS910 3.3 0.0 1.0
CE1 D:HIS910 3.3 0.9 1.0
CB D:HIS910 3.5 1.0 1.0
CB D:CYS893 3.6 0.8 1.0
N D:HIS910 4.0 0.6 1.0
N D:CYS893 4.0 0.1 1.0
CA D:CYS893 4.4 0.8 1.0
CA D:HIS910 4.4 0.4 1.0
NE2 D:HIS910 4.4 0.3 1.0
CD2 D:HIS910 4.5 0.9 1.0
CB D:VAL892 4.7 0.2 1.0
CA D:CYS913 4.7 0.1 1.0
CA D:CYS890 4.7 0.2 1.0

Zinc binding site 8 out of 24 in 3u5m

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Zinc binding site 8 out of 24 in the Crystal Structure of TRIM33 Phd-Bromo in the Free State


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 TRIM33 Phd-Bromo in the Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2

b:0.6
occ:1.00
SG D:CYS902 2.4 0.6 1.0
SG D:CYS931 2.4 0.5 1.0
SG D:CYS928 2.6 0.2 1.0
SG D:CYS905 2.9 0.4 1.0
CB D:CYS902 3.0 0.5 1.0
CB D:CYS905 3.3 0.3 1.0
CB D:CYS931 3.6 0.6 1.0
N D:CYS905 3.8 0.4 1.0
CB D:CYS928 3.8 0.8 1.0
CA D:CYS905 4.1 0.7 1.0
N D:CYS931 4.2 0.6 1.0
N D:CYS928 4.4 0.8 1.0
CA D:CYS902 4.5 0.2 1.0
CA D:CYS931 4.5 0.7 1.0
CB D:LYS904 4.6 0.3 1.0
CA D:CYS928 4.6 0.8 1.0
C D:CYS905 4.7 0.2 1.0
C D:LYS904 4.8 0.4 1.0
CB D:PHE930 4.9 0.1 1.0
CB D:LYS907 4.9 0.0 1.0
O D:CYS905 5.0 0.1 1.0

Zinc binding site 9 out of 24 in 3u5m

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Zinc binding site 9 out of 24 in the Crystal Structure of TRIM33 Phd-Bromo in the Free State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of TRIM33 Phd-Bromo in the Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1

b:0.6
occ:1.00
SG E:CYS893 2.3 0.2 1.0
ND1 E:HIS910 2.3 0.9 1.0
SG E:CYS913 2.3 0.1 1.0
SG E:CYS890 2.4 0.8 1.0
CG E:HIS910 3.1 0.2 1.0
CB E:CYS890 3.1 0.4 1.0
CB E:HIS910 3.2 0.5 1.0
CB E:CYS893 3.4 0.4 1.0
CB E:CYS913 3.4 0.9 1.0
CE1 E:HIS910 3.4 0.6 1.0
N E:CYS893 3.9 0.7 1.0
N E:HIS910 4.1 0.5 1.0
CA E:CYS893 4.2 0.4 1.0
CA E:HIS910 4.2 0.4 1.0
CD2 E:HIS910 4.3 0.1 1.0
NE2 E:HIS910 4.5 0.8 1.0
CA E:CYS890 4.6 0.3 1.0
CA E:CYS913 4.7 0.5 1.0
CB E:VAL892 4.8 0.8 1.0

Zinc binding site 10 out of 24 in 3u5m

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Zinc binding site 10 out of 24 in the Crystal Structure of TRIM33 Phd-Bromo in the Free State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of TRIM33 Phd-Bromo in the Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn2

b:0.3
occ:1.00
SG E:CYS931 2.4 0.7 1.0
SG E:CYS902 2.5 0.5 1.0
SG E:CYS928 2.6 0.8 1.0
SG E:CYS905 2.8 0.4 1.0
CB E:CYS931 3.1 0.2 1.0
CB E:CYS905 3.3 0.5 1.0
CB E:CYS902 3.4 0.8 1.0
N E:CYS905 3.6 0.3 1.0
CB E:CYS928 3.8 0.7 1.0
N E:CYS931 3.9 0.4 1.0
CA E:CYS905 4.0 0.0 1.0
CA E:CYS931 4.2 0.5 1.0
N E:CYS928 4.5 0.9 1.0
CB E:LYS904 4.5 0.1 1.0
C E:LYS904 4.6 0.6 1.0
CA E:CYS928 4.6 0.9 1.0
C E:CYS905 4.8 0.3 1.0
CB E:PHE930 4.8 0.9 1.0
CA E:CYS902 4.8 0.6 1.0
C E:PHE930 4.8 0.8 1.0
C E:CYS928 4.9 0.4 1.0
CA E:LYS904 4.9 0.8 1.0
O E:CYS928 5.0 0.4 1.0

Reference:

Q.Xi, Z.Wang, A.I.Zaromytidou, X.H.Zhang, L.F.Chow-Tsang, J.X.Liu, H.Kim, A.Barlas, K.Manova-Todorova, V.Kaartinen, L.Studer, W.Mark, D.J.Patel, J.Massague. A Poised Chromatin Platform For Tgf-Beta Access to Master Regulators Cell(Cambridge,Mass.) V. 147 1511 2011.
ISSN: ISSN 0092-8674
PubMed: 22196728
DOI: 10.1016/J.CELL.2011.11.032
Page generated: Wed Dec 16 04:53:27 2020

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