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Zinc in PDB 4gzn: Mouse ZFP57 Zinc Fingers in Complex with Methylated Dna

Protein crystallography data

The structure of Mouse ZFP57 Zinc Fingers in Complex with Methylated Dna, PDB code: 4gzn was solved by Y.Liu, X.Zhang, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.68 / 0.99
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 40.218, 60.641, 96.119, 90.00, 90.00, 90.00
R / Rfree (%) 13.1 / 14

Other elements in 4gzn:

The structure of Mouse ZFP57 Zinc Fingers in Complex with Methylated Dna also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Mouse ZFP57 Zinc Fingers in Complex with Methylated Dna (pdb code 4gzn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Mouse ZFP57 Zinc Fingers in Complex with Methylated Dna, PDB code: 4gzn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4gzn

Go back to Zinc Binding Sites List in 4gzn
Zinc binding site 1 out of 2 in the Mouse ZFP57 Zinc Fingers in Complex with Methylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mouse ZFP57 Zinc Fingers in Complex with Methylated Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn203

b:6.7
occ:1.00
NE2 C:HIS190 2.0 6.7 1.0
NE2 C:HIS186 2.1 6.4 1.0
SG C:CYS173 2.3 8.2 1.0
SG C:CYS170 2.3 6.7 1.0
CE1 C:HIS190 3.0 6.7 1.0
CD2 C:HIS186 3.0 5.8 1.0
CD2 C:HIS190 3.1 6.4 1.0
CE1 C:HIS186 3.1 6.3 1.0
CB C:CYS170 3.1 7.1 1.0
CB C:CYS173 3.3 9.1 1.0
N C:CYS173 3.7 9.5 1.0
CA C:CYS173 4.1 9.5 1.0
ND1 C:HIS190 4.1 6.7 1.0
CG C:HIS186 4.2 5.5 1.0
ND1 C:HIS186 4.2 5.9 1.0
CG C:HIS190 4.2 6.2 1.0
CB C:GLU172 4.3 9.8 0.5
CB C:GLU172 4.4 10.7 0.5
CG2 C:VAL189 4.5 7.8 0.5
O B:HOH262 4.5 26.8 1.0
CA C:CYS170 4.6 7.5 1.0
CG C:GLU172 4.7 10.1 0.5
C C:GLU172 4.7 10.3 1.0
OE1 C:GLU172 4.7 12.9 0.5
C C:CYS173 4.8 9.9 1.0
CB C:LYS175 4.8 9.8 0.4
CA C:GLU172 4.9 9.6 0.5
N C:GLY174 4.9 9.6 1.0
CA C:GLU172 4.9 9.9 0.5
CB C:LYS175 4.9 9.9 0.6
N C:GLU172 5.0 9.3 1.0

Zinc binding site 2 out of 2 in 4gzn

Go back to Zinc Binding Sites List in 4gzn
Zinc binding site 2 out of 2 in the Mouse ZFP57 Zinc Fingers in Complex with Methylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mouse ZFP57 Zinc Fingers in Complex with Methylated Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn204

b:8.4
occ:1.00
NE2 C:HIS162 2.0 7.9 1.0
NE2 C:HIS158 2.1 8.4 1.0
SG C:CYS145 2.3 7.3 1.0
SG C:CYS142 2.3 9.7 1.0
CD2 C:HIS162 2.9 7.8 1.0
CE1 C:HIS158 3.0 8.1 1.0
CD2 C:HIS158 3.0 8.2 1.0
CE1 C:HIS162 3.1 7.1 1.0
CB C:CYS142 3.1 8.5 1.0
CB C:CYS145 3.3 7.3 1.0
CB C:PHE144 3.7 9.3 0.5
N C:CYS145 3.8 7.5 1.0
CA C:CYS145 4.0 6.9 1.0
CG C:HIS162 4.1 6.9 1.0
ND1 C:HIS158 4.1 7.9 1.0
ND1 C:HIS162 4.1 7.0 1.0
CG C:HIS158 4.2 7.5 1.0
CG C:PHE144 4.5 9.0 0.5
CB C:LYS147 4.6 8.7 0.4
C C:CYS145 4.6 6.4 1.0
CA C:CYS142 4.6 7.5 1.0
C C:PHE144 4.6 9.0 0.5
CD2 C:PHE144 4.6 8.9 0.5
CA C:PHE144 4.7 9.9 0.5
N C:GLY146 4.7 6.8 1.0
C C:PHE144 4.7 8.1 0.5
CB C:LYS147 4.7 8.5 0.6
O C:HOH396 4.8 16.9 1.0
N C:LYS147 4.8 7.2 1.0
N C:PHE144 4.9 10.6 0.5
N C:PHE144 5.0 10.0 0.5

Reference:

Y.Liu, H.Toh, H.Sasaki, X.Zhang, X.Cheng. An Atomic Model of ZFP57 Recognition of Cpg Methylation Within A Specific Dna Sequence. Genes Dev. V. 26 2374 2012.
ISSN: ISSN 0890-9369
PubMed: 23059534
DOI: 10.1101/GAD.202200.112
Page generated: Wed Dec 16 05:21:17 2020

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