Zinc in PDB 8jwu: Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker

Enzymatic activity of Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker

All present enzymatic activity of Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker:
2.3.2.23; 2.3.2.24;

Protein crystallography data

The structure of Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker, PDB code: 8jwu was solved by H.S.Lee, I.Bang, H.-J.Choi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.89 / 3.58
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 210.54, 102.05, 78.64, 90, 95.92, 90
R / Rfree (%) 21.6 / 26.5

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Zinc atom in the Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker (pdb code 8jwu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 23 binding sites of Zinc where determined in the Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker, PDB code: 8jwu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 23 in 8jwu

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Zinc binding site 1 out of 23 in the Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:106.3
occ:1.00
 ND1 A:HIS45 2.1 134.7 1.0
SG A:CYS23 2.3 119.4 1.0
SG A:CYS20 2.3 120.8 1.0
SG A:CYS48 2.3 116.8 1.0
CB A:CYS20 2.8 121.5 1.0
CG A:HIS45 2.9 110.8 1.0
CE1 A:HIS45 3.1 140.8 1.0
CB A:HIS45 3.2 101.2 1.0
CB A:CYS23 3.3 109.1 1.0
CB A:CYS48 3.4 108.5 1.0
N A:CYS23 3.9 147.2 1.0
N A:HIS45 3.9 102.9 1.0
CD2 A:HIS45 4.0 109.4 1.0
NE2 A:HIS45 4.1 124.2 1.0
CA A:HIS45 4.2 109.6 1.0
CA A:CYS23 4.2 121.8 1.0
CA A:CYS20 4.3 147.9 1.0
CA A:CYS48 4.8 105.2 1.0
CD1 A:LEU33 4.8 116.0 1.0
C A:CYS23 4.9 129.4 1.0
C A:CYS20 5.0 156.4 1.0

Zinc binding site 2 out of 23 in 8jwu

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Zinc binding site 2 out of 23 in the Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:121.8
occ:1.00
 ND1 A:HIS107 2.0 103.0 1.0
SG A:CYS85 2.3 132.9 1.0
SG A:CYS88 2.3 152.2 1.0
SG A:CYS110 2.3 126.5 1.0
CE1 A:HIS107 2.9 124.1 1.0
CG A:HIS107 3.0 103.3 1.0
CB A:CYS85 3.1 141.8 1.0
CB A:HIS107 3.3 113.3 1.0
CB A:CYS88 3.4 153.6 1.0
CB A:CYS110 3.5 122.7 1.0
N A:CYS88 3.9 135.0 1.0
NE2 A:HIS107 4.0 135.7 1.0
CD2 A:HIS107 4.1 127.3 1.0
CA A:CYS88 4.2 144.6 1.0
N A:HIS107 4.4 117.2 1.0
CB A:VAL87 4.5 115.1 1.0
CA A:HIS107 4.6 109.7 1.0
CA A:CYS85 4.6 142.0 1.0
CA A:CYS110 4.8 121.5 1.0
C A:VAL87 4.8 125.6 1.0
N A:VAL87 4.8 134.9 1.0
C A:CYS88 5.0 136.7 1.0

Zinc binding site 3 out of 23 in 8jwu

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Zinc binding site 3 out of 23 in the Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:111.0
occ:1.00
 ND1 A:HIS131 2.1 134.3 1.0
SG A:CYS128 2.3 155.4 1.0
SG A:CYS102 2.3 140.2 1.0
SG A:CYS97 2.3 121.5 1.0
CB A:CYS102 2.9 150.3 1.0
CG A:HIS131 3.1 139.4 1.0
CE1 A:HIS131 3.1 149.0 1.0
CB A:HIS131 3.4 132.8 1.0
CB A:CYS128 3.5 123.9 1.0
CB A:CYS97 3.5 108.2 1.0
N A:CYS128 4.0 124.7 1.0
NE2 A:HIS131 4.2 167.6 1.0
N A:HIS131 4.2 148.0 1.0
CD2 A:HIS131 4.2 153.7 1.0
CA A:CYS128 4.3 108.2 1.0
CA A:HIS131 4.4 136.1 1.0
CB A:ASN99 4.4 122.0 1.0
CA A:CYS102 4.4 134.5 1.0
O A:HIS131 4.6 153.1 1.0
CB A:GLN104 4.8 126.9 1.0
CG A:GLN104 4.8 138.0 1.0
CA A:CYS97 4.8 119.1 1.0
ND2 A:ASN99 4.9 126.1 1.0

Zinc binding site 4 out of 23 in 8jwu

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Zinc binding site 4 out of 23 in the Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:139.7
occ:1.00
 ND1 A:HIS173 2.1 111.0 1.0
SG A:CYS150 2.3 144.2 1.0
SG A:CYS176 2.3 112.8 1.0
SG A:CYS147 2.3 116.5 1.0
CB A:CYS147 2.7 107.8 1.0
CG A:HIS173 2.9 122.6 1.0
CE1 A:HIS173 3.1 137.6 1.0
CB A:CYS150 3.1 140.2 1.0
CB A:HIS173 3.2 135.6 1.0
CB A:CYS176 3.4 110.9 1.0
N A:HIS173 3.8 113.2 1.0
N A:CYS150 3.8 106.0 1.0
CD2 A:HIS173 4.1 120.7 1.0
CA A:HIS173 4.1 114.1 1.0
CA A:CYS150 4.1 129.6 1.0
NE2 A:HIS173 4.1 132.2 1.0
CA A:CYS147 4.2 111.6 1.0
O A:CYS147 4.5 139.9 1.0
C A:CYS147 4.6 113.0 1.0
CA A:CYS176 4.8 120.3 1.0
CB A:LEU149 4.8 124.2 1.0
C A:LEU149 4.9 118.7 1.0
C A:TYR172 4.9 102.3 1.0
O A:HIS173 4.9 89.4 1.0
C A:CYS150 5.0 143.2 1.0
N A:CYS147 5.0 138.7 1.0
C A:HIS173 5.0 95.1 1.0

Zinc binding site 5 out of 23 in 8jwu

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Zinc binding site 5 out of 23 in the Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:117.5
occ:1.00
 SG A:CYS194 2.3 152.6 1.0
SG A:CYS191 2.3 122.6 1.0
SG A:CYS167 2.3 155.3 1.0
SG A:CYS166 2.3 136.0 1.0
N A:CYS167 3.0 149.7 1.0
CB A:CYS167 3.2 136.9 1.0
CB A:CYS194 3.2 119.2 1.0
CB A:CYS191 3.2 111.6 1.0
CB A:CYS166 3.4 130.4 1.0
CA A:CYS167 3.5 139.2 1.0
O A:CYS167 3.5 158.6 1.0
N A:CYS194 3.7 119.0 1.0
C A:CYS166 3.8 159.6 1.0
C A:CYS167 3.9 159.8 1.0
CA A:CYS194 4.0 123.4 1.0
CA A:CYS166 4.2 137.9 1.0
CB A:ASN196 4.4 113.1 1.0
OG A:SER164 4.5 129.9 1.0
O A:CYS166 4.6 173.0 1.0
C A:CYS194 4.7 137.5 1.0
CA A:CYS191 4.7 104.0 1.0
N A:ASN196 4.9 121.5 1.0
CB A:GLN193 4.9 109.5 1.0
N A:ASN195 4.9 140.3 1.0
C A:GLN193 4.9 122.2 1.0

Zinc binding site 6 out of 23 in 8jwu

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Zinc binding site 6 out of 23 in the Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:180.4
occ:1.00
 SG A:CYS284 2.3 272.7 1.0
SG A:CYS263 2.3 197.1 1.0
SG A:CYS287 2.3 182.5 1.0
SG A:CYS260 2.3 214.4 1.0
CB A:CYS263 3.2 206.4 1.0
CB A:CYS287 3.3 213.3 1.0
CB A:CYS284 3.4 248.7 1.0
CB A:CYS260 3.4 205.7 1.0
N A:CYS263 3.5 201.5 1.0
N A:CYS284 3.7 245.4 1.0
CA A:CYS263 3.9 197.8 1.0
CA A:CYS284 4.1 246.8 1.0
CB A:THR262 4.1 179.7 1.0
N A:CYS287 4.3 219.0 1.0
CD2 A:HIS266 4.3 197.0 1.0
CA A:CYS287 4.4 210.2 1.0
C A:THR262 4.5 178.0 1.0
OE1 A:GLU286 4.7 199.6 1.0
N A:GLY264 4.7 181.4 1.0
CA A:THR262 4.7 171.4 1.0
C A:CYS284 4.7 250.2 1.0
CB A:HIS266 4.7 180.4 1.0
N A:THR262 4.8 175.8 1.0
C A:CYS263 4.8 186.4 1.0
O A:CYS284 4.8 257.6 1.0
CG2 A:THR262 4.8 163.6 1.0
CA A:CYS260 4.8 200.4 1.0
C A:GLU283 4.9 221.9 1.0
CG A:HIS266 4.9 194.6 1.0
OG1 A:THR262 5.0 193.6 1.0

Zinc binding site 7 out of 23 in 8jwu

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Zinc binding site 7 out of 23 in the Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:275.6
occ:1.00
 ND1 A:HIS269 2.1 228.8 1.0
SG A:CYS240 2.3 281.2 1.0
SG A:CYS272 2.3 288.7 1.0
SG A:CYS235 2.3 288.0 1.0
N A:HIS269 2.6 229.7 1.0
CG A:HIS269 3.0 227.4 1.0
CE1 A:HIS269 3.1 222.3 1.0
CB A:CYS235 3.1 285.8 1.0
CB A:HIS269 3.2 227.8 1.0
CB A:CYS272 3.3 268.3 1.0
CB A:CYS240 3.4 264.5 1.0
CA A:HIS269 3.5 224.7 1.0
CA A:CYS240 3.9 264.7 1.0
N A:LEU241 3.9 250.7 1.0
CD2 A:HIS269 4.1 228.7 1.0
NE2 A:HIS269 4.1 224.8 1.0
C A:CYS240 4.4 271.0 1.0
C A:HIS269 4.5 233.2 1.0
CA A:CYS235 4.6 279.4 1.0
O A:HIS269 4.6 237.3 1.0
N A:TYR242 4.7 243.9 1.0
CA A:CYS272 4.7 277.2 1.0
CA A:LEU241 5.0 245.4 1.0

Zinc binding site 8 out of 23 in 8jwu

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Zinc binding site 8 out of 23 in the Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn508

b:111.4
occ:1.00
 OD1 A:ASP213 2.0 98.0 1.0
OD1 B:ASP213 2.0 108.4 1.0
NE2 B:HIS187 2.3 107.6 1.0
NE2 A:HIS187 2.3 124.0 1.0
CG B:ASP213 2.7 115.7 1.0
CG A:ASP213 2.8 109.0 1.0
OD2 B:ASP213 2.8 124.1 1.0
OD2 A:ASP213 2.9 123.2 1.0
CD2 A:HIS187 3.0 109.8 1.0
CE1 B:HIS187 3.3 124.3 1.0
CD2 B:HIS187 3.3 98.8 1.0
CE1 A:HIS187 3.4 128.4 1.0
CB B:ASP213 4.2 117.7 1.0
CB A:ASP213 4.2 116.7 1.0
CG A:HIS187 4.2 104.6 1.0
ND1 B:HIS187 4.4 118.5 1.0
ND1 A:HIS187 4.4 122.2 1.0
CG B:HIS187 4.4 99.7 1.0
CA B:ASP213 4.7 106.8 1.0
CA A:ASP213 4.8 93.9 1.0
CG A:LYS186 4.9 120.9 1.0
C B:ASP213 5.0 104.6 1.0

Zinc binding site 9 out of 23 in 8jwu

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Zinc binding site 9 out of 23 in the Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:204.0
occ:1.00
 ND1 B:HIS45 2.1 190.3 1.0
SG B:CYS23 2.3 177.4 1.0
SG B:CYS20 2.3 200.9 1.0
SG B:CYS48 2.3 174.4 1.0
CB B:CYS20 2.7 193.3 1.0
CG B:HIS45 2.9 177.2 1.0
CE1 B:HIS45 3.1 190.4 1.0
CB B:HIS45 3.2 192.9 1.0
CB B:CYS23 3.3 198.7 1.0
CB B:CYS48 3.4 183.8 1.0
N B:CYS23 4.0 203.7 1.0
N B:HIS45 4.0 210.9 1.0
CD2 B:HIS45 4.0 168.4 1.0
NE2 B:HIS45 4.1 179.6 1.0
CA B:CYS20 4.2 195.9 1.0
CA B:CYS23 4.2 211.5 1.0
CA B:HIS45 4.2 196.9 1.0
CA B:CYS48 4.8 176.3 1.0
O B:GLN25 4.9 193.3 1.0
C B:CYS23 5.0 212.4 1.0
C B:CYS20 5.0 194.8 1.0

Zinc binding site 10 out of 23 in 8jwu

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Zinc binding site 10 out of 23 in the Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Phd Finger Protein 7 (PHF7) Fused to UBE2D2 Via A (Gsgg)3 Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:289.4
occ:1.00
 ND1 B:HIS107 2.2 259.4 1.0
SG B:CYS85 2.3 316.4 1.0
SG B:CYS88 2.3 272.7 1.0
SG B:CYS110 2.3 281.0 1.0
CE1 B:HIS107 3.0 247.3 1.0
CG B:HIS107 3.0 262.0 1.0
CB B:CYS85 3.0 307.8 1.0
CB B:HIS107 3.4 262.5 1.0
CB B:CYS88 3.6 252.5 1.0
CB B:CYS110 3.7 248.5 1.0
NE2 B:HIS107 4.0 243.0 1.0
CD2 B:HIS107 4.0 253.4 1.0
N B:HIS107 4.4 262.7 1.0
CA B:CYS85 4.4 311.9 1.0
CA B:HIS107 4.5 256.7 1.0
N B:CYS85 4.7 318.2 1.0
N B:CYS88 4.7 246.2 1.0
CA B:CYS88 4.7 245.3 1.0

Reference:

H.S.Lee, I.Bang, J.You, T.K.Jeong, C.R.Kim, M.Hwang, J.S.Kim, S.H.Baek, J.J.Song, H.J.Choi. Molecular Basis For PHF7-Mediated Ubiquitination of Histone H3. Genes Dev. 2023.
ISSN: ISSN 0890-9369
PubMed: 37993255
DOI: 10.1101/GAD.350989.123
Page generated: Thu Oct 31 08:28:40 2024

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