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Zinc in PDB 3qmb: Structural Basis of Selective Binding of Nonmethylated Cpg Islands By the Cxxc Domain of CFP1

Protein crystallography data

The structure of Structural Basis of Selective Binding of Nonmethylated Cpg Islands By the Cxxc Domain of CFP1, PDB code: 3qmb was solved by R.Lam, C.Xu, C.B.Bian, J.Kania, C.Bountra, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, J.Min, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.55 / 2.06
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 37.375, 71.965, 115.600, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 23.5

Other elements in 3qmb:

The structure of Structural Basis of Selective Binding of Nonmethylated Cpg Islands By the Cxxc Domain of CFP1 also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Basis of Selective Binding of Nonmethylated Cpg Islands By the Cxxc Domain of CFP1 (pdb code 3qmb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structural Basis of Selective Binding of Nonmethylated Cpg Islands By the Cxxc Domain of CFP1, PDB code: 3qmb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3qmb

Go back to Zinc Binding Sites List in 3qmb
Zinc binding site 1 out of 2 in the Structural Basis of Selective Binding of Nonmethylated Cpg Islands By the Cxxc Domain of CFP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis of Selective Binding of Nonmethylated Cpg Islands By the Cxxc Domain of CFP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:52.0
occ:1.00
SG A:CYS212 2.3 51.9 1.0
SG A:CYS173 2.4 58.0 1.0
SG A:CYS176 2.4 51.0 1.0
SG A:CYS179 2.4 50.0 1.0
CB A:CYS179 3.3 50.9 1.0
CB A:CYS212 3.3 49.6 1.0
N A:CYS173 3.4 58.2 1.0
CB A:CYS173 3.4 60.9 1.0
CB A:CYS176 3.4 56.9 1.0
CA A:CYS212 3.7 49.0 1.0
N A:CYS176 3.8 59.3 1.0
CA A:CYS173 3.8 60.1 1.0
N A:GLY174 3.8 59.5 1.0
N A:GLN213 4.0 53.5 1.0
N A:CYS179 4.2 49.8 1.0
CA A:CYS176 4.2 57.8 1.0
C A:CYS173 4.2 61.3 1.0
C A:CYS212 4.2 51.5 1.0
N A:GLU175 4.3 62.0 1.0
CA A:CYS179 4.3 49.9 1.0
C A:MET172 4.5 58.3 1.0
N A:LEU214 4.6 58.2 1.0
CA A:MET172 4.7 56.7 1.0
CA A:GLY174 4.8 60.4 1.0
O A:CYS176 4.8 54.3 1.0
C A:CYS176 4.8 56.3 1.0
C A:GLU175 4.9 62.1 1.0
N A:CYS212 5.0 46.9 1.0
C A:GLY174 5.0 62.0 1.0

Zinc binding site 2 out of 2 in 3qmb

Go back to Zinc Binding Sites List in 3qmb
Zinc binding site 2 out of 2 in the Structural Basis of Selective Binding of Nonmethylated Cpg Islands By the Cxxc Domain of CFP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis of Selective Binding of Nonmethylated Cpg Islands By the Cxxc Domain of CFP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:53.3
occ:1.00
SG A:CYS207 2.3 49.2 1.0
SG A:CYS185 2.3 57.4 1.0
SG A:CYS188 2.4 56.0 1.0
SG A:CYS191 2.4 53.4 1.0
CB A:CYS207 3.3 45.5 1.0
CB A:CYS185 3.3 58.3 1.0
CB A:CYS191 3.4 54.6 1.0
CB A:CYS188 3.4 59.7 1.0
N A:CYS185 3.4 54.7 1.0
CA A:CYS207 3.6 45.2 1.0
N A:GLY186 3.7 58.8 1.0
CA A:CYS185 3.8 57.8 1.0
N A:CYS188 3.9 63.3 1.0
N A:ARG208 3.9 47.4 1.0
C A:CYS207 4.2 45.6 1.0
C A:CYS185 4.2 59.6 1.0
CA A:CYS188 4.2 62.4 1.0
N A:HIS187 4.3 63.7 1.0
N A:CYS191 4.4 54.6 1.0
CA A:CYS191 4.4 54.7 1.0
C A:ASP184 4.5 53.8 1.0
CA A:GLY186 4.7 60.6 1.0
N A:LEU209 4.7 47.8 1.0
N A:CYS207 4.9 43.5 1.0
CA A:ASP184 4.9 52.0 1.0
C A:CYS188 4.9 61.9 1.0
CA A:ARG208 5.0 48.7 1.0
CG A:LEU209 5.0 54.1 1.0

Reference:

C.Xu, C.Bian, R.Lam, A.Dong, J.Min. The Structural Basis For Selective Binding of Non-Methylated Cpg Islands By the CFP1 Cxxc Domain. Nat Commun V. 2 227 2011.
ISSN: ESSN 2041-1723
PubMed: 21407193
DOI: 10.1038/NCOMMS1237
Page generated: Wed Dec 16 04:45:31 2020

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