Zinc in PDB 7z36: Crystal Structure of the KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain

Enzymatic activity of Crystal Structure of the KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain

All present enzymatic activity of Crystal Structure of the KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain:
2.3.2.27; 3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of the KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain, PDB code: 7z36 was solved by G.A.Stoll, Y.Modis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.79 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 190.283, 68.583, 149.111, 90, 114.05, 90
R / Rfree (%) 22.7 / 27.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain (pdb code 7z36). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain, PDB code: 7z36:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7z36

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Zinc binding site 1 out of 8 in the Crystal Structure of the KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain


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 KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:66.3
occ:1.00
 ND1 A:HIS216 2.3 41.4 1.0
SG A:CYS251 2.3 81.6 1.0
SG A:CYS214 2.3 70.6 1.0
SG A:CYS248 2.3 70.7 1.0
HB2 A:HIS216 2.7 74.7 1.0
HB2 A:CYS251 2.9 85.3 1.0
CB A:CYS251 3.1 71.1 1.0
CG A:HIS216 3.2 62.8 1.0
CB A:CYS248 3.2 74.4 1.0
HB2 A:CYS248 3.2 89.3 1.0
H A:CYS251 3.2 75.8 1.0
HB3 A:CYS248 3.3 89.3 1.0
CE1 A:HIS216 3.3 46.2 1.0
HB2 A:CYS214 3.4 56.3 1.0
CB A:HIS216 3.4 62.2 1.0
HE1 A:HIS216 3.5 55.5 1.0
CB A:CYS214 3.5 47.0 1.0
HB A:VAL250 3.7 59.2 1.0
N A:CYS251 3.8 63.1 1.0
HB3 A:HIS216 3.8 74.7 1.0
HB3 A:CYS251 3.9 85.3 1.0
H A:HIS216 4.0 59.9 1.0
HB3 A:CYS214 4.0 56.3 1.0
CA A:CYS251 4.1 61.9 1.0
O A:CYS214 4.1 70.2 1.0
CD2 A:HIS216 4.3 57.8 1.0
NE2 A:HIS216 4.4 52.5 1.0
H A:VAL250 4.4 79.2 1.0
C A:CYS214 4.6 55.1 1.0
HB2 A:GLN253 4.6 82.0 1.0
N A:HIS216 4.6 49.9 1.0
HA A:CYS251 4.6 74.3 1.0
CA A:HIS216 4.6 51.5 1.0
HD22 A:LEU212 4.6 88.1 1.0
CA A:CYS214 4.6 56.7 1.0
CB A:VAL250 4.6 49.4 1.0
HG12 A:VAL250 4.7 57.7 1.0
H A:GLN253 4.7 75.6 1.0
CA A:CYS248 4.7 78.8 1.0
HB2 A:LEU212 4.7 76.4 1.0
HD23 A:LEU212 4.8 88.1 1.0
H A:CYS214 4.8 68.1 1.0
C A:VAL250 4.9 64.0 1.0
HB3 A:LEU212 5.0 76.4 1.0

Zinc binding site 2 out of 8 in 7z36

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Zinc binding site 2 out of 8 in the Crystal Structure of the KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain


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 KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:77.6
occ:1.00
 SG A:CYS196 2.2 78.6 1.0
SG A:CYS219 2.3 62.7 1.0
SG A:CYS199 2.3 74.5 1.0
SG A:CYS222 2.4 79.7 1.0
HB2 A:CYS219 2.9 78.6 1.0
HB2 A:CYS196 3.1 65.7 1.0
CB A:CYS196 3.1 54.7 1.0
HB3 A:CYS196 3.2 65.7 1.0
HB3 A:CYS199 3.2 87.7 1.0
CB A:CYS219 3.2 65.5 1.0
H A:CYS219 3.2 87.6 1.0
H A:CYS199 3.3 67.0 1.0
CB A:CYS199 3.4 73.1 1.0
HG13 A:VAL198 3.6 79.8 1.0
HG12 A:VAL198 3.8 79.8 1.0
HB2 A:CYS222 3.8 89.8 1.0
CB A:CYS222 3.9 74.8 1.0
HB3 A:CYS219 3.9 78.6 1.0
N A:CYS219 4.0 73.0 1.0
N A:CYS199 4.0 55.8 1.0
CG1 A:VAL198 4.1 66.5 1.0
HB2 A:CYS199 4.1 87.7 1.0
CA A:CYS219 4.2 75.4 1.0
CA A:CYS199 4.3 66.4 1.0
HB3 A:CYS222 4.3 89.8 1.0
HB2 A:GLU201 4.4 83.0 1.0
HH21 A:ARG207 4.4 124.1 1.0
HG11 A:VAL198 4.5 79.8 1.0
H A:VAL198 4.5 64.4 1.0
H A:GLU201 4.5 70.1 1.0
CA A:CYS196 4.6 49.6 1.0
HB1 A:ALA218 4.7 54.8 1.0
H A:CYS222 4.8 99.5 1.0
H A:ARG200 4.8 77.8 1.0
HA A:CYS219 4.9 90.5 1.0
HA A:ALA218 4.9 68.9 1.0
HB3 A:ALA221 4.9 97.7 1.0
HA A:CYS196 4.9 59.5 1.0
NH2 A:ARG207 4.9 103.4 1.0

Zinc binding site 3 out of 8 in 7z36

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Zinc binding site 3 out of 8 in the Crystal Structure of the KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain


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 KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:138.0
occ:1.00
 HG A:CYS278 1.4 157.9 1.0
SG A:CYS298 2.3 105.3 1.0
SG A:CYS278 2.3 131.6 1.0
SG A:CYS301 2.3 120.8 1.0
ND1 A:HIS281 2.4 116.3 1.0
HB A:VAL280 2.7 162.9 1.0
HB2 A:HIS281 3.0 156.8 1.0
H A:HIS281 3.1 169.9 1.0
CG A:HIS281 3.3 122.6 1.0
CE1 A:HIS281 3.3 120.7 1.0
HB2 A:CYS301 3.4 131.9 1.0
H A:CYS301 3.5 128.2 1.0
HE1 A:HIS281 3.5 144.9 1.0
CB A:CYS301 3.5 109.9 1.0
CB A:HIS281 3.6 130.7 1.0
CB A:VAL280 3.6 135.8 1.0
N A:HIS281 3.6 141.6 1.0
HB3 A:CYS298 3.6 130.2 1.0
CB A:CYS298 3.7 108.5 1.0
HG12 A:VAL280 3.7 139.6 1.0
H A:CYS298 3.8 121.3 1.0
H A:VAL280 4.0 159.7 1.0
CB A:CYS278 4.0 123.5 1.0
N A:CYS301 4.0 106.8 1.0
HB2 A:ASP300 4.1 142.2 1.0
CG1 A:VAL280 4.1 116.3 1.0
HB2 A:CYS278 4.1 148.1 1.0
HB3 A:CYS278 4.2 148.1 1.0
HB2 A:GLU284 4.2 177.2 1.0
CA A:HIS281 4.2 139.1 1.0
HG11 A:VAL280 4.3 139.6 1.0
HB3 A:CYS301 4.3 131.9 1.0
CA A:CYS301 4.3 105.3 1.0
C A:VAL280 4.3 133.8 1.0
HB2 A:CYS298 4.3 130.2 1.0
CA A:VAL280 4.4 135.3 1.0
HB3 A:HIS281 4.4 156.8 1.0
NE2 A:HIS281 4.4 132.3 1.0
CD2 A:HIS281 4.4 125.0 1.0
HG3 A:GLU284 4.4 217.0 1.0
HG21 A:VAL280 4.5 145.6 1.0
CG2 A:VAL280 4.5 121.3 1.0
HG23 A:VAL280 4.5 145.6 1.0
HA A:CYS301 4.5 126.3 1.0
N A:CYS298 4.6 101.1 1.0
N A:VAL280 4.6 133.0 1.0
CA A:CYS298 4.7 109.0 1.0
HB3 A:GLU284 4.7 177.2 1.0
CB A:GLU284 4.9 147.7 1.0
HA A:HIS281 4.9 166.9 1.0
HD23 A:LEU286 4.9 132.1 1.0
H A:ASP300 4.9 123.7 1.0
CB A:ASP300 4.9 118.5 1.0
C A:ASP300 4.9 113.5 1.0

Zinc binding site 4 out of 8 in 7z36

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Zinc binding site 4 out of 8 in the Crystal Structure of the KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain


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 KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:132.9
occ:1.00
 SG A:CYS293 2.3 140.0 1.0
SG A:CYS290 2.3 97.5 1.0
ND1 A:HIS306 2.3 116.6 1.0
ND1 A:HIS309 2.4 119.7 1.0
HB3 A:HIS306 2.6 144.7 1.0
CG A:HIS306 2.9 126.3 1.0
CE1 A:HIS309 3.2 118.3 1.0
HE1 A:HIS309 3.2 141.9 1.0
CE1 A:HIS306 3.2 115.0 1.0
CB A:HIS306 3.2 120.6 1.0
HB2 A:CYS293 3.4 148.3 1.0
HB3 A:SER292 3.5 142.4 1.0
CG A:HIS309 3.5 117.7 1.0
CB A:CYS293 3.5 123.6 1.0
HE1 A:HIS306 3.5 137.9 1.0
HB2 A:HIS309 3.6 129.1 1.0
HE22 A:GLN302 3.8 126.0 1.0
CD2 A:HIS306 3.9 111.5 1.0
HB2 A:HIS306 3.9 144.7 1.0
CB A:HIS309 4.0 107.6 1.0
HA A:HIS306 4.0 135.4 1.0
NE2 A:HIS306 4.0 107.7 1.0
H A:CYS293 4.0 144.2 1.0
CB A:CYS290 4.0 107.3 1.0
HB3 A:HIS309 4.0 129.1 1.0
HB3 A:CYS293 4.2 148.3 1.0
HB3 A:CYS290 4.2 128.7 1.0
CA A:HIS306 4.2 112.8 1.0
HB2 A:CYS290 4.3 128.7 1.0
N A:CYS293 4.3 120.2 1.0
NE2 A:HIS309 4.3 127.2 1.0
CB A:SER292 4.4 118.7 1.0
HG A:SER292 4.4 129.7 1.0
CA A:CYS293 4.5 118.8 1.0
OG A:SER292 4.5 108.1 1.0
CD2 A:HIS309 4.5 121.6 1.0
NE2 A:GLN302 4.6 105.0 1.0
HD2 A:HIS306 4.6 133.7 1.0
HE2 A:HIS306 4.7 129.2 1.0
O A:HIS306 4.8 119.8 1.0
C A:SER292 4.9 120.6 1.0
HA A:CYS293 4.9 142.5 1.0
HB2 A:SER292 5.0 142.4 1.0

Zinc binding site 5 out of 8 in 7z36

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Zinc binding site 5 out of 8 in the Crystal Structure of the KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:40.0
occ:1.00
 ND1 B:HIS216 2.2 33.2 1.0
SG B:CYS214 2.3 33.9 1.0
SG B:CYS248 2.3 41.4 1.0
SG B:CYS251 2.3 41.0 1.0
O B:VAL250 2.5 78.4 1.0
HB2 B:HIS216 2.8 44.2 1.0
HB3 B:CYS248 3.2 58.3 1.0
CG B:HIS216 3.2 50.1 1.0
CE1 B:HIS216 3.2 33.6 1.0
HB2 B:CYS214 3.2 47.2 1.0
CB B:CYS248 3.2 48.5 1.0
HB2 B:CYS248 3.4 58.3 1.0
HE1 B:HIS216 3.4 40.3 1.0
CB B:CYS214 3.4 39.3 1.0
CB B:HIS216 3.5 36.8 1.0
HB3 B:CYS251 3.8 42.6 1.0
HB B:VAL250 3.8 54.9 1.0
C B:VAL250 3.8 66.6 1.0
CB B:CYS251 3.8 35.5 1.0
H B:HIS216 3.9 41.4 1.0
HB3 B:CYS214 3.9 47.2 1.0
HB3 B:HIS216 4.0 44.2 1.0
HB3 B:GLN253 4.1 40.2 1.0
H B:GLN253 4.2 53.1 1.0
NE2 B:HIS216 4.3 37.0 1.0
CD2 B:HIS216 4.3 39.5 1.0
H B:VAL250 4.4 51.3 1.0
O B:CYS214 4.4 29.0 1.0
HD22 B:LEU212 4.5 46.1 1.0
HB2 B:CYS251 4.5 42.6 1.0
N B:HIS216 4.5 34.5 1.0
CA B:HIS216 4.6 36.5 1.0
CB B:VAL250 4.6 45.8 1.0
HB2 B:GLN253 4.6 40.2 1.0
CA B:CYS214 4.6 27.8 1.0
C B:CYS214 4.6 35.9 1.0
HG12 B:VAL250 4.6 50.3 1.0
CA B:CYS251 4.7 43.7 1.0
N B:CYS251 4.7 36.2 1.0
CA B:VAL250 4.7 48.0 1.0
CA B:CYS248 4.7 55.7 1.0
HD23 B:LEU212 4.8 46.1 1.0
CB B:GLN253 4.8 33.5 1.0
HB2 B:LEU212 4.8 38.0 1.0
H B:CYS214 4.8 45.6 1.0
H B:LYS252 4.8 46.0 1.0
N B:VAL250 4.9 42.8 1.0
HA B:CYS248 5.0 66.9 1.0
C B:CYS251 5.0 34.9 1.0

Zinc binding site 6 out of 8 in 7z36

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Zinc binding site 6 out of 8 in the Crystal Structure of the KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:39.2
occ:1.00
 SG B:CYS196 2.3 46.2 1.0
SG B:CYS219 2.3 45.8 1.0
SG B:CYS222 2.3 41.5 1.0
SG B:CYS199 2.3 46.0 1.0
HB2 B:CYS219 2.8 50.2 1.0
HB3 B:CYS196 3.0 48.2 1.0
HB2 B:CYS196 3.0 48.2 1.0
CB B:CYS196 3.0 40.2 1.0
CB B:CYS219 3.1 41.9 1.0
H B:CYS219 3.2 51.3 1.0
H B:CYS199 3.3 53.0 1.0
HB3 B:CYS199 3.3 56.0 1.0
HH21 B:ARG207 3.4 65.9 1.0
CB B:CYS199 3.4 46.7 1.0
HB2 B:CYS222 3.5 58.2 1.0
CB B:CYS222 3.6 48.5 1.0
HB B:VAL198 3.8 52.5 1.0
HB3 B:CYS219 3.8 50.2 1.0
N B:CYS199 4.0 44.1 1.0
N B:CYS219 4.0 42.8 1.0
HB3 B:CYS222 4.0 58.2 1.0
HB2 B:GLU201 4.1 71.0 1.0
NH2 B:ARG207 4.1 54.9 1.0
CA B:CYS219 4.2 38.4 1.0
HB2 B:CYS199 4.2 56.0 1.0
CA B:CYS199 4.3 44.7 1.0
H B:GLU201 4.3 53.5 1.0
HH22 B:ARG207 4.4 65.9 1.0
H B:VAL198 4.4 48.0 1.0
CA B:CYS196 4.5 46.9 1.0
HE B:ARG207 4.5 71.0 1.0
HB1 B:ALA218 4.6 57.1 1.0
H B:CYS222 4.7 71.5 1.0
H B:ARG200 4.8 57.5 1.0
CB B:VAL198 4.8 43.7 1.0
HA B:CYS219 4.8 46.1 1.0
HA B:CYS196 4.9 56.3 1.0
CA B:CYS222 4.9 47.9 1.0
HA B:ALA218 4.9 50.5 1.0
C B:CYS199 5.0 44.9 1.0
N B:CYS222 5.0 59.5 1.0

Zinc binding site 7 out of 8 in 7z36

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Zinc binding site 7 out of 8 in the Crystal Structure of the KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:91.3
occ:1.00
 SG B:CYS278 2.3 91.4 1.0
ND1 B:HIS281 2.3 104.9 1.0
SG B:CYS301 2.3 86.1 1.0
SG B:CYS298 2.3 66.9 1.0
HB2 B:HIS281 3.0 118.1 1.0
CE1 B:HIS281 3.2 93.7 1.0
HB2 B:CYS278 3.2 88.2 1.0
HB2 B:CYS301 3.2 98.6 1.0
CG B:HIS281 3.2 94.8 1.0
H B:CYS301 3.2 97.8 1.0
CB B:CYS278 3.3 73.5 1.0
H B:HIS281 3.3 103.2 1.0
HE1 B:HIS281 3.3 112.4 1.0
CB B:CYS301 3.4 82.2 1.0
HB3 B:CYS278 3.4 88.2 1.0
CB B:HIS281 3.6 98.4 1.0
N B:CYS301 3.8 81.5 1.0
HB B:VAL280 3.8 109.5 1.0
H B:CYS298 3.8 84.4 1.0
CB B:CYS298 3.9 93.5 1.0
HB3 B:CYS298 3.9 112.2 1.0
HB2 B:ASP300 4.1 111.6 1.0
CA B:CYS301 4.1 82.9 1.0
N B:HIS281 4.1 86.0 1.0
HB3 B:CYS301 4.2 98.6 1.0
NE2 B:HIS281 4.3 106.2 1.0
HA B:CYS301 4.3 99.5 1.0
HB3 B:HIS281 4.3 118.1 1.0
CD2 B:HIS281 4.3 101.2 1.0
CA B:HIS281 4.5 94.7 1.0
H B:VAL280 4.5 126.6 1.0
HB2 B:CYS298 4.6 112.2 1.0
N B:CYS298 4.6 70.3 1.0
CA B:CYS278 4.7 68.9 1.0
CA B:CYS298 4.7 76.4 1.0
C B:ASP300 4.7 82.6 1.0
CB B:VAL280 4.8 91.2 1.0
O B:CYS298 4.9 65.9 1.0
CB B:ASP300 4.9 93.0 1.0
HA B:CYS278 4.9 82.7 1.0
HB2 B:GLU284 4.9 119.7 1.0
HG23 B:VAL280 4.9 111.7 1.0
H B:ASP300 5.0 94.1 1.0

Zinc binding site 8 out of 8 in 7z36

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Zinc binding site 8 out of 8 in the Crystal Structure of the KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the KAP1 Tripartite Motif in Complex with the ZNF93 Krab Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:74.3
occ:1.00
 HE2 B:HIS309 1.8 123.6 1.0
ND1 B:HIS306 2.2 76.6 1.0
HD2 B:HIS309 2.2 116.5 1.0
NE2 B:HIS309 2.3 103.0 1.0
SG B:CYS293 2.3 105.7 1.0
SG B:CYS290 2.3 64.3 1.0
CD2 B:HIS309 2.5 97.1 1.0
CE1 B:HIS306 2.9 70.7 1.0
HB2 B:CYS293 2.9 84.2 1.0
HB3 B:HIS306 3.0 107.3 1.0
CG B:HIS306 3.0 90.4 1.0
HE1 B:HIS306 3.2 84.9 1.0
CB B:CYS293 3.2 70.2 1.0
CB B:HIS306 3.5 89.4 1.0
CE1 B:HIS309 3.5 93.8 1.0
H B:CYS293 3.6 91.2 1.0
CB B:CYS290 3.6 65.2 1.0
HB3 B:CYS290 3.6 78.2 1.0
HB2 B:CYS290 3.8 78.2 1.0
CG B:HIS309 3.8 92.0 1.0
HB2 B:SER292 3.8 108.9 1.0
HE22 B:GLN302 3.8 99.8 1.0
NE2 B:HIS306 3.9 74.7 1.0
HB3 B:CYS293 3.9 84.2 1.0
CD2 B:HIS306 3.9 85.2 1.0
N B:CYS293 3.9 76.0 1.0
HE1 B:HIS309 4.1 112.5 1.0
CA B:CYS293 4.2 77.4 1.0
ND1 B:HIS309 4.2 98.7 1.0
HA B:HIS306 4.2 105.0 1.0
HB2 B:HIS306 4.2 107.3 1.0
CA B:HIS306 4.5 87.5 1.0
HG21 B:THR297 4.5 57.9 1.0
HE2 B:HIS306 4.6 89.7 1.0
NE2 B:GLN302 4.6 83.2 1.0
CB B:SER292 4.6 90.7 1.0
HA B:CYS293 4.7 92.9 1.0
C B:SER292 4.7 73.1 1.0
HB3 B:SER292 4.7 108.9 1.0
HD2 B:HIS306 4.7 102.3 1.0
HB2 B:HIS309 4.8 124.4 1.0
OE1 B:GLN302 4.8 60.0 1.0
O B:HIS306 4.8 89.8 1.0
CB B:HIS309 4.9 103.7 1.0
CA B:CYS290 4.9 51.2 1.0

Reference:

G.A.Stoll, N.Pandiloski, C.H.Douse, Y.Modis. Structure and Functional Mapping of the Krab-KAP1 Repressor Complex. Embo J. V. 41 11179 2022.
ISSN: ESSN 1460-2075
PubMed: 36341546
DOI: 10.15252/EMBJ.2022111179
Page generated: Wed Oct 30 16:14:05 2024

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