Atomistry » Zinc » PDB 4m2u-4mgr » 4m9v
Atomistry »
  Zinc »
    PDB 4m2u-4mgr »
      4m9v »

Zinc in PDB 4m9v: ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna

Protein crystallography data

The structure of ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna, PDB code: 4m9v was solved by Y.Liu, Y.O.Olanrewaju, X.Zhang, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.46 / 0.97
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 36.388, 96.093, 36.408, 90.00, 113.14, 90.00
R / Rfree (%) 13 / 14.3

Other elements in 4m9v:

The structure of ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna (pdb code 4m9v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna, PDB code: 4m9v:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4m9v

Go back to Zinc Binding Sites List in 4m9v
Zinc binding site 1 out of 4 in the ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:7.7
occ:1.00
NE2 C:HIS186 2.0 7.4 1.0
NE2 C:HIS190 2.0 7.7 1.0
SG C:CYS173 2.3 9.3 1.0
SG C:CYS170 2.3 8.0 1.0
CD2 C:HIS186 3.0 7.0 1.0
CE1 C:HIS190 3.0 8.1 1.0
CD2 C:HIS190 3.0 7.5 1.0
CE1 C:HIS186 3.0 7.2 1.0
HB3 C:CYS170 3.1 10.3 1.0
H C:CYS173 3.1 12.7 0.5
CB C:CYS170 3.1 8.6 1.0
HD2 C:HIS186 3.2 8.4 1.0
HE1 C:HIS190 3.2 9.7 1.0
HB3 C:CYS173 3.2 12.3 1.0
HB2 C:CYS170 3.2 10.3 1.0
HD2 C:HIS190 3.2 9.0 1.0
HE1 C:HIS186 3.3 8.7 1.0
HB3 C:GLU172 3.3 13.3 0.5
CB C:CYS173 3.3 10.3 1.0
HB3 C:GLU172 3.4 13.9 0.5
N C:CYS173 3.7 10.6 1.0
CA C:CYS173 4.1 10.9 1.0
ND1 C:HIS190 4.1 8.1 1.0
HG22 C:VAL189 4.1 10.3 0.5
HB2 C:CYS173 4.1 12.3 1.0
ND1 C:HIS186 4.1 7.2 1.0
CG C:HIS186 4.2 6.8 1.0
CG C:HIS190 4.2 7.3 1.0
HB3 C:LYS175 4.2 12.8 1.0
HG21 C:VAL189 4.2 10.3 0.5
CB C:GLU172 4.2 11.1 0.5
H C:LYS175 4.2 12.1 1.0
CB C:GLU172 4.4 11.6 0.5
H C:GLU172 4.4 12.3 0.5
HG3 C:GLU172 4.4 13.8 0.5
HG23 C:VAL189 4.4 10.3 0.5
H C:GLU172 4.4 12.1 0.5
CG2 C:VAL189 4.5 8.6 0.5
O B:HOH236 4.5 28.7 1.0
HD23 C:LEU187 4.5 10.3 1.0
H C:GLY174 4.5 12.4 1.0
HA C:LEU187 4.5 8.3 1.0
HG2 C:GLU172 4.5 13.8 0.5
CA C:CYS170 4.6 8.9 1.0
OE2 C:GLU172 4.6 14.0 0.5
HB C:VAL189 4.6 9.7 0.6
C C:GLU172 4.6 11.0 0.5
CG C:GLU172 4.6 11.5 0.5
HB2 C:GLU172 4.7 13.9 0.5
C C:GLU172 4.7 10.7 0.5
HB2 C:LYS175 4.8 12.8 1.0
C C:CYS173 4.8 11.1 1.0
HB2 C:GLU172 4.8 13.3 0.5
N C:GLY174 4.9 10.3 1.0
CA C:GLU172 4.9 10.5 0.5
CA C:GLU172 4.9 10.8 0.5
HA C:CYS173 4.9 13.1 1.0
HD1 C:HIS190 4.9 9.7 1.0
N C:GLU172 4.9 10.2 0.5
CB C:LYS175 4.9 10.6 1.0
HA C:CYS170 4.9 10.7 1.0
HD1 C:HIS186 4.9 8.6 1.0
N C:GLU172 4.9 10.1 0.5
HE1 C:PHE177 5.0 11.0 1.0
C C:CYS170 5.0 9.0 1.0

Zinc binding site 2 out of 4 in 4m9v

Go back to Zinc Binding Sites List in 4m9v
Zinc binding site 2 out of 4 in the ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:8.8
occ:1.00
NE2 C:HIS158 2.0 8.7 1.0
NE2 C:HIS162 2.0 8.9 1.0
SG C:CYS145 2.3 8.2 1.0
SG C:CYS142 2.3 10.2 1.0
HB2 C:PHE144 2.8 12.1 0.5
CD2 C:HIS162 3.0 8.2 1.0
CE1 C:HIS158 3.0 8.5 1.0
CD2 C:HIS158 3.0 8.6 1.0
HD2 C:HIS162 3.1 9.9 1.0
HB3 C:CYS142 3.1 10.5 1.0
CE1 C:HIS162 3.1 8.2 1.0
CB C:CYS142 3.1 8.8 1.0
HE1 C:HIS158 3.2 10.2 1.0
HB3 C:CYS145 3.2 9.7 1.0
HD2 C:HIS158 3.2 10.3 1.0
HB2 C:CYS142 3.2 10.5 1.0
H C:CYS145 3.3 10.3 0.5
HE1 C:HIS162 3.3 9.8 1.0
CB C:CYS145 3.3 8.1 1.0
CB C:PHE144 3.7 10.1 0.5
HB2 C:LYS147 3.7 12.4 1.0
N C:CYS145 3.8 8.6 1.0
HB3 C:PHE144 3.8 12.1 0.5
H C:LYS147 4.0 9.8 1.0
O F:HOH324 4.0 11.5 1.0
CA C:CYS145 4.0 7.8 1.0
ND1 C:HIS158 4.1 8.5 1.0
HB2 C:CYS145 4.1 9.7 1.0
HB2 C:PHE144 4.1 11.6 0.5
CG C:HIS162 4.1 7.5 1.0
CG C:HIS158 4.1 8.3 1.0
HD1 C:PHE144 4.1 11.4 0.5
ND1 C:HIS162 4.2 7.5 1.0
H C:PHE144 4.2 14.3 0.5
HD3 C:LYS147 4.3 18.2 1.0
H C:PHE144 4.4 14.4 0.5
H C:GLY146 4.4 9.6 1.0
CG C:PHE144 4.5 9.7 0.5
CD1 C:PHE144 4.5 9.5 0.5
C C:CYS145 4.6 7.4 1.0
C C:PHE144 4.6 10.1 0.5
CA C:CYS142 4.6 8.1 1.0
CA C:PHE144 4.6 11.1 0.5
C C:PHE144 4.6 9.7 0.5
CB C:LYS147 4.7 10.4 1.0
N C:GLY146 4.7 8.0 1.0
O C:HOH369 4.7 17.8 0.8
N C:LYS147 4.8 8.2 1.0
H51 B:MPD101 4.8 10.3 1.0
HD1 C:HIS158 4.9 10.2 1.0
N C:PHE144 4.9 12.0 0.5
N C:PHE144 4.9 11.9 0.5
HA C:CYS145 4.9 9.4 1.0
HA C:CYS142 5.0 9.7 1.0
HD1 C:HIS162 5.0 9.0 1.0
CB C:PHE144 5.0 9.7 0.5

Zinc binding site 3 out of 4 in 4m9v

Go back to Zinc Binding Sites List in 4m9v
Zinc binding site 3 out of 4 in the ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:7.6
occ:1.00
NE2 F:HIS190 2.0 7.5 1.0
NE2 F:HIS186 2.1 7.3 1.0
SG F:CYS173 2.3 9.1 1.0
SG F:CYS170 2.3 8.0 1.0
CE1 F:HIS190 3.0 8.2 1.0
CD2 F:HIS186 3.0 6.9 1.0
H F:CYS173 3.0 12.9 0.5
CD2 F:HIS190 3.0 7.2 1.0
HB3 F:CYS170 3.1 10.1 1.0
CE1 F:HIS186 3.1 7.0 1.0
CB F:CYS170 3.1 8.4 1.0
HB3 F:CYS173 3.2 12.3 1.0
HE1 F:HIS190 3.2 9.8 1.0
HD2 F:HIS186 3.2 8.3 1.0
HB2 F:CYS170 3.2 10.1 1.0
HD2 F:HIS190 3.2 8.7 1.0
HE1 F:HIS186 3.3 8.4 1.0
HB3 F:GLU172 3.3 12.6 0.5
CB F:CYS173 3.3 10.3 1.0
HB3 F:GLU172 3.4 12.9 0.5
N F:CYS173 3.7 10.7 1.0
CA F:CYS173 4.0 10.7 1.0
HB2 F:CYS173 4.1 12.3 1.0
ND1 F:HIS190 4.1 7.7 1.0
HB3 F:LYS175 4.1 12.5 0.5
HB3 F:LYS175 4.2 12.5 0.5
HG22 F:VAL189 4.2 10.2 0.4
ND1 F:HIS186 4.2 7.0 1.0
CG F:HIS190 4.2 7.3 1.0
CG F:HIS186 4.2 6.6 1.0
HG21 F:VAL189 4.2 10.2 0.4
CB F:GLU172 4.2 10.5 0.5
H F:LYS175 4.2 11.8 0.5
H F:LYS175 4.2 11.9 0.5
CB F:GLU172 4.4 10.7 0.5
H F:GLU172 4.4 12.0 0.5
HG3 F:GLU172 4.4 13.4 0.5
HG23 F:VAL189 4.4 10.2 0.4
H F:GLU172 4.5 11.8 0.5
CG2 F:VAL189 4.5 8.5 0.4
HD23 F:LEU187 4.5 10.4 1.0
H F:GLY174 4.5 12.5 1.0
O E:HOH238 4.5 25.8 1.0
HA F:LEU187 4.5 7.9 1.0
HG2 F:GLU172 4.5 13.4 0.5
CA F:CYS170 4.6 8.9 1.0
C F:GLU172 4.6 11.0 0.5
OE2 F:GLU172 4.6 13.9 0.5
HB F:VAL189 4.6 9.7 0.6
CG F:GLU172 4.6 11.2 0.5
HB2 F:GLU172 4.7 12.9 0.5
C F:GLU172 4.7 10.8 0.5
C F:CYS173 4.8 10.7 1.0
HB2 F:LYS175 4.8 12.5 0.5
HB2 F:LYS175 4.8 12.5 0.5
HB2 F:GLU172 4.8 12.6 0.5
N F:GLY174 4.8 10.4 1.0
HA F:CYS173 4.9 12.8 1.0
CA F:GLU172 4.9 10.2 0.5
CA F:GLU172 4.9 10.4 0.5
CB F:LYS175 4.9 10.4 0.5
HA F:CYS170 4.9 10.6 1.0
HD1 F:HIS190 4.9 9.2 1.0
N F:GLU172 4.9 10.0 0.5
CB F:LYS175 4.9 10.4 0.5
N F:GLU172 4.9 9.8 0.5
HD1 F:HIS186 5.0 8.3 1.0
C F:CYS170 5.0 9.0 1.0
HE1 F:PHE177 5.0 10.3 1.0

Zinc binding site 4 out of 4 in 4m9v

Go back to Zinc Binding Sites List in 4m9v
Zinc binding site 4 out of 4 in the ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn202

b:8.7
occ:1.00
NE2 F:HIS162 2.0 8.5 1.0
NE2 F:HIS158 2.1 8.8 1.0
SG F:CYS145 2.3 8.0 1.0
SG F:CYS142 2.3 10.1 1.0
HB2 F:PHE144 2.8 12.1 0.5
CD2 F:HIS162 2.9 8.4 1.0
CE1 F:HIS158 3.0 8.5 1.0
CD2 F:HIS158 3.0 8.6 1.0
HD2 F:HIS162 3.0 10.0 1.0
CE1 F:HIS162 3.1 8.0 1.0
HB3 F:CYS142 3.1 10.2 1.0
CB F:CYS142 3.2 8.5 1.0
HB3 F:CYS145 3.2 9.7 1.0
HD2 F:HIS158 3.2 10.3 1.0
HE1 F:HIS158 3.2 10.2 1.0
HB2 F:CYS142 3.2 10.2 1.0
H F:CYS145 3.3 10.1 0.5
HE1 F:HIS162 3.3 9.6 1.0
CB F:CYS145 3.3 8.1 1.0
CB F:PHE144 3.7 10.1 0.5
HB2 F:LYS147 3.7 12.1 1.0
N F:CYS145 3.7 8.4 1.0
HB3 F:PHE144 3.8 12.1 0.5
H F:LYS147 4.0 9.7 1.0
CA F:CYS145 4.0 7.7 1.0
O C:HOH321 4.1 11.7 1.0
CG F:HIS162 4.1 7.8 1.0
HB2 F:PHE144 4.1 11.6 0.6
ND1 F:HIS158 4.1 8.4 1.0
HB2 F:CYS145 4.1 9.7 1.0
ND1 F:HIS162 4.1 7.7 1.0
HD1 F:PHE144 4.2 10.9 0.5
CG F:HIS158 4.2 8.3 1.0
H F:PHE144 4.2 13.9 0.6
HD3 F:LYS147 4.3 17.9 1.0
H F:PHE144 4.4 14.1 0.5
H F:GLY146 4.4 9.3 1.0
CG F:PHE144 4.4 9.4 0.5
CD1 F:PHE144 4.5 9.1 0.5
C F:CYS145 4.6 7.6 1.0
C F:PHE144 4.6 9.7 0.5
CA F:CYS142 4.6 8.0 1.0
CA F:PHE144 4.6 10.9 0.5
C F:PHE144 4.6 9.4 0.6
CB F:LYS147 4.7 10.0 1.0
N F:GLY146 4.7 7.7 1.0
O F:HOH365 4.7 13.9 0.7
HO4 E:MPD101 4.8 51.8 1.0
N F:LYS147 4.8 8.1 1.0
N F:PHE144 4.9 11.7 0.5
N F:PHE144 4.9 11.6 0.6
HD1 F:HIS158 4.9 10.1 1.0
HA F:CYS145 4.9 9.2 1.0
HD1 F:HIS162 4.9 9.2 1.0
HA F:CYS142 5.0 9.6 1.0
CB F:PHE144 5.0 9.6 0.6

Reference:

Y.Liu, Y.O.Olanrewaju, X.Zhang, X.Cheng. Dna Recognition of 5-Carboxylcytosine By A ZFP57 Mutant at An Atomic Resolution of 0.97 Angstrom. Biochemistry V. 52 9310 2013.
ISSN: ISSN 0006-2960
PubMed: 24236546
DOI: 10.1021/BI401360N
Page generated: Wed Dec 16 05:34:21 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy