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Zinc in PDB 8jwj: Phd Finger Protein 7 (PHF7) in Complex with UBE2D2

Enzymatic activity of Phd Finger Protein 7 (PHF7) in Complex with UBE2D2

All present enzymatic activity of Phd Finger Protein 7 (PHF7) in Complex with UBE2D2:
2.3.2.23; 2.3.2.24;

Protein crystallography data

The structure of Phd Finger Protein 7 (PHF7) in Complex with UBE2D2, PDB code: 8jwj 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) 47.35 / 2.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 102.304, 106.825, 145.759, 90, 90, 90
R / Rfree (%) 19.4 / 22.2

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Phd Finger Protein 7 (PHF7) in Complex with UBE2D2 (pdb code 8jwj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Phd Finger Protein 7 (PHF7) in Complex with UBE2D2, PDB code: 8jwj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 8jwj

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Zinc binding site 1 out of 14 in the Phd Finger Protein 7 (PHF7) in Complex with UBE2D2


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) in Complex with UBE2D2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:85.2
occ:1.00
 ND1 A:HIS58 2.1 104.0 1.0
SG A:CYS36 2.3 103.3 1.0
SG A:CYS61 2.3 83.1 1.0
SG A:CYS33 2.3 84.4 1.0
CG A:HIS58 3.0 85.7 1.0
CE1 A:HIS58 3.0 99.5 1.0
CB A:CYS33 3.1 100.5 1.0
CB A:CYS36 3.2 85.9 1.0
CB A:HIS58 3.3 74.1 1.0
CB A:CYS61 3.4 74.0 1.0
N A:CYS36 3.9 88.8 1.0
NE2 A:HIS58 4.0 94.0 1.0
CD2 A:HIS58 4.0 84.4 1.0
N A:HIS58 4.0 85.4 1.0
CA A:CYS36 4.1 93.8 1.0
CA A:HIS58 4.3 84.7 1.0
CA A:CYS33 4.6 106.6 1.0
CA A:CYS61 4.8 80.2 1.0
C A:CYS36 4.9 102.7 1.0
C A:LEU35 4.9 91.4 1.0
N A:LEU37 5.0 101.3 1.0

Zinc binding site 2 out of 14 in 8jwj

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Zinc binding site 2 out of 14 in the Phd Finger Protein 7 (PHF7) in Complex with UBE2D2


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) in Complex with UBE2D2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:98.5
occ:1.00
 ND1 A:HIS120 2.1 93.1 1.0
SG A:CYS123 2.3 117.3 1.0
SG A:CYS101 2.3 119.1 1.0
SG A:CYS98 2.3 102.4 1.0
CE1 A:HIS120 3.0 84.1 1.0
CB A:CYS98 3.0 99.0 1.0
CG A:HIS120 3.1 89.5 1.0
CB A:CYS123 3.2 109.9 1.0
CB A:CYS101 3.4 109.8 1.0
CB A:HIS120 3.5 80.3 1.0
N A:CYS101 3.8 110.8 1.0
N A:HIS120 4.1 95.5 1.0
NE2 A:HIS120 4.1 85.9 1.0
CA A:CYS101 4.1 116.1 1.0
CD2 A:HIS120 4.2 88.0 1.0
CA A:HIS120 4.4 83.9 1.0
CA A:CYS98 4.5 94.8 1.0
CB A:VAL100 4.5 112.0 1.0
CA A:CYS123 4.7 107.3 1.0
C A:VAL100 4.9 126.5 1.0
C A:CYS101 4.9 122.3 1.0

Zinc binding site 3 out of 14 in 8jwj

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Zinc binding site 3 out of 14 in the Phd Finger Protein 7 (PHF7) in Complex with UBE2D2


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) in Complex with UBE2D2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:119.9
occ:1.00
 ND1 A:HIS144 2.1 136.5 1.0
SG A:CYS115 2.3 165.1 1.0
SG A:CYS141 2.3 121.9 1.0
SG A:CYS110 2.3 103.0 1.0
CE1 A:HIS144 2.8 144.3 1.0
CB A:CYS115 2.9 139.4 1.0
CG A:HIS144 3.2 136.3 1.0
CB A:CYS110 3.2 103.1 1.0
CB A:CYS141 3.5 120.0 1.0
CB A:HIS144 3.7 142.7 1.0
NE2 A:HIS144 4.0 150.5 1.0
N A:CYS141 4.0 120.5 1.0
CD2 A:HIS144 4.2 127.4 1.0
CA A:CYS141 4.3 115.1 1.0
CA A:CYS115 4.4 140.8 1.0
CB A:ASN112 4.5 135.5 1.0
N A:HIS144 4.6 129.1 1.0
CA A:CYS110 4.7 100.1 1.0
CA A:HIS144 4.8 131.1 1.0
CG A:GLN117 4.8 120.3 1.0
CB A:GLN117 4.9 100.5 1.0
C A:CYS141 4.9 124.6 1.0

Zinc binding site 4 out of 14 in 8jwj

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Zinc binding site 4 out of 14 in the Phd Finger Protein 7 (PHF7) in Complex with UBE2D2


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) in Complex with UBE2D2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:113.8
occ:1.00
 ND1 A:HIS186 2.2 107.5 1.0
SG A:CYS163 2.3 136.7 1.0
SG A:CYS189 2.3 106.4 1.0
SG A:CYS160 2.3 94.3 1.0
CG A:HIS186 2.9 112.2 1.0
CB A:CYS160 3.0 122.6 1.0
CE1 A:HIS186 3.1 128.0 1.0
CB A:CYS163 3.1 127.9 1.0
CB A:HIS186 3.2 114.5 1.0
CB A:CYS189 3.4 97.9 1.0
N A:CYS163 3.8 118.3 1.0
CD2 A:HIS186 4.0 114.3 1.0
CA A:CYS163 4.0 122.3 1.0
NE2 A:HIS186 4.1 125.2 1.0
N A:HIS186 4.2 103.2 1.0
CA A:HIS186 4.3 100.8 1.0
CA A:CYS160 4.4 130.4 1.0
O A:CYS160 4.4 131.0 1.0
C A:CYS160 4.6 134.8 1.0
CA A:CYS189 4.7 96.9 1.0
CB A:LEU162 4.8 104.6 1.0
C A:LEU162 4.8 119.8 1.0
C A:CYS163 4.9 136.1 1.0
N A:CYS189 4.9 89.4 1.0

Zinc binding site 5 out of 14 in 8jwj

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Zinc binding site 5 out of 14 in the Phd Finger Protein 7 (PHF7) in Complex with UBE2D2


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) in Complex with UBE2D2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:170.5
occ:1.00
 SG A:CYS179 2.3 202.9 1.0
SG A:CYS207 2.3 138.7 1.0
SG A:CYS204 2.3 125.8 1.0
SG A:CYS180 2.3 205.3 1.0
CB A:CYS179 3.0 189.8 1.0
CB A:CYS207 3.2 142.3 1.0
CB A:CYS204 3.4 137.2 1.0
CB A:CYS180 3.4 195.2 1.0
N A:CYS180 3.5 195.1 1.0
N A:CYS207 3.7 133.5 1.0
C A:CYS179 3.9 199.6 1.0
CA A:CYS180 3.9 200.3 1.0
CA A:CYS207 4.0 136.4 1.0
CA A:CYS179 4.0 195.1 1.0
O A:CYS180 4.2 192.8 1.0
C A:CYS180 4.5 198.3 1.0
O A:CYS179 4.6 210.0 1.0
CB A:GLN206 4.7 114.6 1.0
CB A:ASN209 4.7 139.3 1.0
C A:CYS207 4.8 139.1 1.0
CA A:CYS204 4.8 129.1 1.0
C A:GLN206 4.8 131.1 1.0
N A:CYS179 4.9 192.8 1.0
OE1 A:GLN206 4.9 152.2 1.0
OG A:SER177 4.9 166.4 1.0

Zinc binding site 6 out of 14 in 8jwj

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Zinc binding site 6 out of 14 in the Phd Finger Protein 7 (PHF7) in Complex with UBE2D2


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) in Complex with UBE2D2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:152.9
occ:1.00
 ND1 A:HIS282 2.1 157.3 1.0
SG A:CYS285 2.3 159.2 1.0
SG A:CYS248 2.3 195.6 1.0
SG A:CYS253 2.3 156.1 1.0
CG A:HIS282 2.9 151.3 1.0
CE1 A:HIS282 3.1 156.7 1.0
CB A:HIS282 3.1 147.3 1.0
CB A:CYS248 3.3 153.5 1.0
CB A:CYS253 3.4 128.3 1.0
CB A:CYS285 3.6 160.4 1.0
CA A:CYS253 3.6 145.1 1.0
N A:HIS282 3.9 144.7 1.0
N A:LEU254 3.9 175.4 1.0
CD2 A:HIS282 4.0 146.9 1.0
CA A:HIS282 4.1 146.8 1.0
NE2 A:HIS282 4.1 150.8 1.0
C A:CYS253 4.2 168.8 1.0
OG1 A:THR281 4.2 155.4 1.0
CA A:CYS248 4.7 152.2 1.0
CB A:TYR255 4.8 188.7 1.0
O A:HIS282 4.8 171.5 1.0
N A:CYS253 4.9 141.3 1.0
C A:HIS282 4.9 160.9 1.0
CA A:CYS285 4.9 181.2 1.0
N A:TYR255 5.0 184.5 1.0
CG A:ARG259 5.0 153.9 1.0

Zinc binding site 7 out of 14 in 8jwj

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Zinc binding site 7 out of 14 in the Phd Finger Protein 7 (PHF7) in Complex with UBE2D2


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) in Complex with UBE2D2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:127.0
occ:1.00
 SG A:CYS297 2.3 133.6 1.0
SG A:CYS276 2.3 101.3 1.0
SG A:CYS273 2.3 125.4 1.0
SG A:CYS300 2.4 96.7 1.0
CB A:CYS273 3.1 114.4 1.0
CB A:CYS276 3.2 102.2 1.0
CB A:CYS300 3.4 147.8 1.0
CB A:CYS297 3.7 145.4 1.0
N A:CYS276 3.8 110.8 1.0
N A:CYS300 4.0 136.3 1.0
OG1 A:THR275 4.1 125.8 1.0
CA A:CYS276 4.1 107.3 1.0
N A:CYS297 4.2 134.9 1.0
CA A:CYS300 4.4 127.3 1.0
CA A:CYS297 4.4 142.0 1.0
CB A:HIS279 4.5 126.9 1.0
CA A:CYS273 4.5 126.0 1.0
CB A:GLU299 4.8 162.3 1.0
N A:GLY277 4.8 98.2 1.0
OE1 A:GLU299 4.8 181.4 1.0
C A:CYS276 4.9 110.8 1.0
C A:CYS297 5.0 148.8 1.0
C A:GLU299 5.0 149.1 1.0

Zinc binding site 8 out of 14 in 8jwj

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Zinc binding site 8 out of 14 in the Phd Finger Protein 7 (PHF7) in Complex with UBE2D2


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) in Complex with UBE2D2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:94.0
occ:1.00
 ND1 C:HIS58 2.2 87.8 1.0
SG C:CYS61 2.3 84.9 1.0
SG C:CYS36 2.3 116.1 1.0
SG C:CYS33 2.3 97.0 1.0
CG C:HIS58 3.0 85.1 1.0
CB C:CYS36 3.0 113.8 1.0
CE1 C:HIS58 3.1 100.7 1.0
CB C:CYS33 3.1 94.5 1.0
CB C:CYS61 3.3 82.9 1.0
CB C:HIS58 3.4 75.3 1.0
N C:CYS36 3.7 98.8 1.0
CA C:CYS36 3.9 109.6 1.0
NE2 C:HIS58 4.1 87.3 1.0
CD2 C:HIS58 4.1 95.0 1.0
N C:HIS58 4.1 88.2 1.0
CA C:HIS58 4.4 76.1 1.0
CA C:CYS33 4.6 103.9 1.0
C C:CYS36 4.7 110.0 1.0
CA C:CYS61 4.7 77.5 1.0
C C:LEU35 4.8 96.5 1.0
N C:LEU37 4.9 106.2 1.0
CG C:PRO122 4.9 88.9 1.0
CD1 C:LEU46 4.9 78.7 1.0
CD C:PRO122 5.0 85.9 1.0
CB C:LEU35 5.0 98.7 1.0

Zinc binding site 9 out of 14 in 8jwj

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Zinc binding site 9 out of 14 in the Phd Finger Protein 7 (PHF7) in Complex with UBE2D2


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) in Complex with UBE2D2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:109.1
occ:1.00
 ND1 C:HIS120 2.1 101.0 1.0
SG C:CYS123 2.3 112.2 1.0
SG C:CYS101 2.3 146.8 1.0
SG C:CYS98 2.3 96.3 1.0
CE1 C:HIS120 2.9 108.6 1.0
CB C:CYS98 3.0 110.3 1.0
CB C:CYS123 3.2 108.8 1.0
CG C:HIS120 3.2 119.6 1.0
CB C:CYS101 3.3 105.2 1.0
N C:CYS101 3.6 116.0 1.0
CB C:HIS120 3.7 88.5 1.0
CA C:CYS101 4.0 120.4 1.0
NE2 C:HIS120 4.1 120.1 1.0
N C:HIS120 4.1 88.2 1.0
CD2 C:HIS120 4.3 123.9 1.0
CB C:VAL100 4.5 129.2 1.0
CA C:CYS98 4.5 101.4 1.0
CA C:HIS120 4.5 92.7 1.0
CA C:CYS123 4.7 116.9 1.0
C C:VAL100 4.7 122.5 1.0
O C:LYS103 4.7 124.2 1.0
C C:CYS101 4.8 134.4 1.0
N C:VAL100 4.9 124.8 1.0
N C:LYS102 4.9 132.0 1.0
CA C:VAL100 4.9 129.8 1.0

Zinc binding site 10 out of 14 in 8jwj

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Zinc binding site 10 out of 14 in the Phd Finger Protein 7 (PHF7) in Complex with UBE2D2


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) in Complex with UBE2D2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn503

b:98.3
occ:1.00
 ND1 C:HIS144 2.1 83.2 1.0
SG C:CYS110 2.3 104.1 1.0
SG C:CYS115 2.3 96.5 1.0
SG C:CYS141 2.3 96.4 1.0
CE1 C:HIS144 2.9 100.5 1.0
CB C:CYS115 3.0 121.0 1.0
CG C:HIS144 3.2 95.4 1.0
CB C:CYS110 3.3 96.3 1.0
CB C:HIS144 3.7 99.8 1.0
CB C:CYS141 3.7 93.2 1.0
NE2 C:HIS144 4.1 114.7 1.0
N C:CYS141 4.1 88.4 1.0
CD2 C:HIS144 4.2 101.2 1.0
CB C:ASN112 4.3 117.3 1.0
N C:HIS144 4.4 104.2 1.0
CA C:CYS141 4.4 90.3 1.0
CA C:CYS115 4.4 124.0 1.0
CA C:HIS144 4.6 104.2 1.0
CB C:GLN117 4.7 103.8 1.0
CA C:CYS110 4.7 83.0 1.0
C C:CYS141 4.9 95.7 1.0
CB C:LYS143 4.9 100.6 1.0
O C:CYS141 5.0 88.1 1.0
ND2 C:ASN112 5.0 134.3 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 08:28:32 2024

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