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Zinc in PDB 3c6w: Crystal Structure of the ING5 Phd Finger in Complex with H3K4ME3 Peptide

Protein crystallography data

The structure of Crystal Structure of the ING5 Phd Finger in Complex with H3K4ME3 Peptide, PDB code: 3c6w was solved by K.S.Champagne, P.V.Pena, K.Johnson, T.G.Kutateladze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.00 / 1.75
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 68.140, 68.140, 28.250, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 19.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the ING5 Phd Finger in Complex with H3K4ME3 Peptide (pdb code 3c6w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the ING5 Phd Finger in Complex with H3K4ME3 Peptide, PDB code: 3c6w:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3c6w

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Zinc binding site 1 out of 4 in the Crystal Structure of the ING5 Phd Finger in Complex with H3K4ME3 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 the ING5 Phd Finger in Complex with H3K4ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:15.9
occ:1.00
SG A:CYS216 2.3 11.0 1.0
SG A:CYS191 2.3 8.1 1.0
SG A:CYS189 2.4 8.5 1.0
ND1 A:HIS213 2.8 10.5 1.0
CB A:CYS189 3.0 10.3 1.0
CB A:CYS216 3.2 13.8 1.0
CB A:CYS191 3.4 8.8 1.0
CB A:HIS213 3.6 9.9 1.0
CG A:HIS213 3.6 10.8 1.0
CE1 A:HIS213 3.9 7.9 1.0
O A:HOH239 4.0 12.2 1.0
N A:CYS191 4.1 9.4 1.0
N A:HIS213 4.1 9.6 1.0
CA A:CYS191 4.3 9.8 1.0
CA A:HIS213 4.4 10.2 1.0
CA A:CYS189 4.5 8.9 1.0
O A:HOH254 4.5 19.5 1.0
N A:LEU190 4.6 10.0 1.0
OH A:TYR196 4.6 14.8 1.0
CA A:CYS216 4.6 14.7 1.0
CD2 A:HIS213 4.8 5.8 1.0
C A:CYS189 4.9 9.9 1.0
NE2 A:HIS213 4.9 11.9 1.0
O A:HIS213 4.9 10.4 1.0
O A:TYR188 5.0 9.7 1.0

Zinc binding site 2 out of 4 in 3c6w

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Zinc binding site 2 out of 4 in the Crystal Structure of the ING5 Phd Finger in Complex with H3K4ME3 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 the ING5 Phd Finger in Complex with H3K4ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:15.3
occ:1.00
SG A:CYS207 2.3 10.6 1.0
SG A:CYS229 2.3 9.8 1.0
SG A:CYS232 2.3 10.5 1.0
SG A:CYS202 2.3 8.2 1.0
CB A:CYS207 3.1 10.2 1.0
CB A:CYS202 3.2 8.2 1.0
CB A:CYS232 3.3 11.1 1.0
CB A:CYS229 3.4 9.3 1.0
N A:CYS229 4.0 10.2 1.0
N A:CYS232 4.1 10.5 1.0
CA A:CYS207 4.2 10.9 1.0
CA A:CYS229 4.2 10.9 1.0
CA A:CYS232 4.3 11.7 1.0
CZ A:PHE212 4.4 11.1 1.0
CE1 A:PHE212 4.5 11.8 1.0
CB A:ASN204 4.6 9.3 1.0
CA A:CYS202 4.7 8.8 1.0
C A:CYS229 4.8 11.7 1.0
O A:CYS229 4.8 10.4 1.0
CD A:ARG231 4.9 24.3 1.0
ND2 A:ASN204 5.0 9.4 1.0

Zinc binding site 3 out of 4 in 3c6w

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Zinc binding site 3 out of 4 in the Crystal Structure of the ING5 Phd Finger in Complex with H3K4ME3 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 the ING5 Phd Finger in Complex with H3K4ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3

b:16.8
occ:1.00
CD2 C:HIS213 2.2 7.5 1.0
SG C:CYS216 2.3 11.5 1.0
SG C:CYS189 2.3 9.4 1.0
SG C:CYS191 2.3 9.9 1.0
CB C:CYS189 3.0 10.0 1.0
CG C:HIS213 3.1 10.6 1.0
CB C:CYS216 3.2 11.6 1.0
NE2 C:HIS213 3.3 13.4 1.0
CB C:CYS191 3.4 12.4 1.0
CB C:HIS213 3.5 10.3 1.0
O C:HOH250 4.0 18.5 1.0
N C:HIS213 4.0 8.7 1.0
N C:CYS191 4.0 12.8 1.0
ND1 C:HIS213 4.3 12.5 1.0
CA C:CYS191 4.3 13.2 1.0
CA C:HIS213 4.4 9.5 1.0
CE1 C:HIS213 4.4 6.7 1.0
CA C:CYS189 4.5 11.3 1.0
N C:LEU190 4.5 13.5 1.0
O C:HOH253 4.6 21.2 1.0
CA C:CYS216 4.6 11.5 1.0
OH C:TYR196 4.6 17.2 1.0
C C:CYS189 4.8 12.6 1.0
O C:HIS213 4.9 9.3 1.0
O C:TYR188 4.9 12.4 1.0

Zinc binding site 4 out of 4 in 3c6w

Go back to Zinc Binding Sites List in 3c6w
Zinc binding site 4 out of 4 in the Crystal Structure of the ING5 Phd Finger in Complex with H3K4ME3 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 the ING5 Phd Finger in Complex with H3K4ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn4

b:17.3
occ:1.00
SG C:CYS207 2.3 11.3 1.0
SG C:CYS232 2.3 12.0 1.0
SG C:CYS229 2.3 11.9 1.0
SG C:CYS202 2.3 10.4 1.0
CB C:CYS207 3.1 13.8 1.0
CB C:CYS202 3.2 11.4 1.0
CB C:CYS232 3.3 13.6 1.0
CB C:CYS229 3.4 11.8 1.0
N C:CYS229 4.0 11.2 1.0
CA C:CYS207 4.1 15.1 1.0
N C:CYS232 4.2 13.7 1.0
CA C:CYS229 4.2 12.1 1.0
CA C:CYS232 4.4 13.7 1.0
CZ C:PHE212 4.4 10.7 1.0
CB C:ASN204 4.5 12.8 1.0
CE1 C:PHE212 4.5 8.9 1.0
CA C:CYS202 4.6 11.7 1.0
O C:CYS229 4.8 12.6 1.0
C C:CYS229 4.8 13.4 1.0
CD C:ARG231 4.9 28.6 1.0
ND2 C:ASN204 4.9 13.7 1.0

Reference:

K.S.Champagne, N.Saksouk, P.V.Pena, K.Johnson, M.Ullah, X.J.Yang, J.Cote, T.G.Kutateladze. The Crystal Structure of the ING5 Phd Finger in Complex with An H3K4ME3 Histone Peptide. Proteins V. 72 1371 2008.
ISSN: ISSN 0887-3585
PubMed: 18623064
DOI: 10.1002/PROT.22140
Page generated: Sat Sep 26 05:45:46 2020
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