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Zinc in PDB 4ypa: ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam)

Enzymatic activity of ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam)

All present enzymatic activity of ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam):
2.1.1.43;

Protein crystallography data

The structure of ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam), PDB code: 4ypa was solved by D.S.Rogawski, J.Ndoj, H.J.Cho, I.Maillard, J.Grembecka, T.Cierpicki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.04 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 53.682, 61.773, 73.233, 91.57, 93.83, 90.46
R / Rfree (%) 24.9 / 30.3

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam) (pdb code 4ypa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam), PDB code: 4ypa:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 4ypa

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Zinc binding site 1 out of 12 in the ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3001

b:39.5
occ:1.00
 SG A:CYS2093 1.6 48.5 1.0
SG A:CYS2104 1.8 45.8 1.0
SG A:CYS2091 2.4 47.0 1.0
SG A:CYS2108 2.4 37.3 1.0
CB A:CYS2104 2.9 49.9 1.0
CB A:CYS2093 3.1 53.6 1.0
CB A:CYS2091 3.3 53.2 1.0
CB A:CYS2108 3.4 40.0 1.0
CA A:CYS2104 3.6 50.0 1.0
ZN A:ZN3002 3.7 46.7 1.0
CA A:CYS2108 4.0 40.5 1.0
SG A:CYS2117 4.0 32.4 1.0
CA A:CYS2093 4.3 54.1 1.0
N A:CYS2093 4.4 53.9 1.0
N A:CYS2104 4.5 51.1 1.0
C A:CYS2104 4.6 50.3 1.0
N A:LEU2109 4.6 38.4 1.0
C A:CYS2108 4.7 39.8 1.0
CA A:CYS2091 4.8 54.1 1.0
O A:CYS2104 4.9 49.9 1.0
ND2 A:ASN2110 4.9 33.7 1.0

Zinc binding site 2 out of 12 in 4ypa

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Zinc binding site 2 out of 12 in the ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3002

b:46.7
occ:1.00
 SG A:CYS2117 2.3 32.4 1.0
SG A:CYS2128 2.4 35.4 1.0
SG A:CYS2122 2.5 36.0 1.0
SG A:CYS2104 2.6 45.8 1.0
CB A:CYS2117 3.0 29.6 1.0
CB A:CYS2128 3.3 37.2 1.0
CB A:CYS2104 3.4 49.9 1.0
CB A:CYS2122 3.7 39.1 1.0
ZN A:ZN3001 3.7 39.5 1.0
SG A:CYS2091 4.5 47.0 1.0
CA A:CYS2117 4.5 30.0 1.0
CA A:CYS2128 4.6 37.2 1.0
CB A:ASN2130 4.6 28.8 1.0
NE2 A:GLN2131 4.7 28.8 1.0
CB A:CYS2124 4.7 42.1 1.0
SG A:CYS2108 4.8 37.3 1.0
CA A:CYS2122 4.8 39.4 1.0
CA A:CYS2104 4.8 50.0 1.0
SG A:CYS2093 4.8 48.5 1.0

Zinc binding site 3 out of 12 in 4ypa

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Zinc binding site 3 out of 12 in the ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3003

b:29.2
occ:1.00
 SG A:CYS2220 2.2 24.0 1.0
SG A:CYS2270 2.3 23.1 1.0
SG A:CYS2268 2.3 27.7 1.0
SG A:CYS2275 2.3 36.6 1.0
CB A:CYS2275 3.2 38.7 1.0
CB A:CYS2220 3.2 24.8 1.0
CB A:CYS2270 3.4 25.1 1.0
CB A:CYS2268 3.4 30.8 1.0
CA A:CYS2275 3.7 38.6 1.0
N A:CYS2220 3.8 23.3 1.0
N A:ARG2276 4.0 39.0 1.0
N A:CYS2270 4.1 26.4 1.0
CA A:CYS2220 4.1 23.9 1.0
C A:CYS2275 4.2 38.6 1.0
CA A:CYS2270 4.3 25.7 1.0
NE2 A:HIS2218 4.5 23.1 1.0
N A:GLY2277 4.5 40.9 1.0
CD2 A:HIS2218 4.6 19.8 1.0
N A:GLY2271 4.6 28.8 1.0
CA A:CYS2268 4.7 30.7 1.0
C A:CYS2268 4.7 30.2 1.0
N A:LYS2269 4.9 28.8 1.0
C A:SER2219 4.9 22.4 1.0
C A:CYS2270 4.9 27.5 1.0

Zinc binding site 4 out of 12 in 4ypa

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Zinc binding site 4 out of 12 in the ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2301

b:38.6
occ:1.00
 SG B:CYS2091 0.7 52.8 1.0
SG B:CYS2108 2.2 37.6 1.0
SG B:CYS2093 2.3 54.0 1.0
SG B:CYS2104 2.3 38.8 1.0
CB B:CYS2091 2.7 51.5 1.0
CB B:CYS2104 2.9 44.5 1.0
CB B:CYS2108 3.2 36.1 1.0
CB B:CYS2093 3.4 56.6 1.0
CA B:CYS2104 3.4 44.9 1.0
ZN B:ZN2302 3.8 40.4 1.0
CA B:CYS2091 4.1 53.2 1.0
N B:CYS2104 4.3 47.2 1.0
CA B:CYS2108 4.3 36.5 1.0
SG B:CYS2117 4.4 32.4 1.0
N B:CYS2093 4.5 56.1 1.0
CA B:CYS2093 4.5 56.9 1.0
C B:CYS2104 4.6 45.2 1.0
N B:LEU2109 4.7 32.8 1.0
N B:ASN2092 4.8 54.0 1.0
SG B:CYS2122 4.9 45.6 1.0
C B:CYS2108 4.9 35.1 1.0
C B:CYS2091 4.9 53.5 1.0

Zinc binding site 5 out of 12 in 4ypa

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Zinc binding site 5 out of 12 in the ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2302

b:40.4
occ:1.00
 SG B:CYS2122 2.3 45.6 1.0
SG B:CYS2104 2.3 38.8 1.0
SG B:CYS2128 2.4 42.6 1.0
SG B:CYS2117 2.5 32.4 1.0
CB B:CYS2117 3.3 32.3 1.0
CB B:CYS2122 3.3 45.9 1.0
CB B:CYS2128 3.4 42.2 1.0
CB B:CYS2104 3.4 44.5 1.0
ZN B:ZN2301 3.8 38.6 1.0
SG B:CYS2091 4.0 52.8 1.0
CB B:ASN2130 4.3 29.4 1.0
CA B:CYS2128 4.3 41.8 1.0
CB B:CYS2091 4.4 51.5 1.0
CA B:CYS2122 4.6 45.6 1.0
NE2 B:GLN2131 4.7 30.9 1.0
CA B:CYS2117 4.8 32.5 1.0
CB B:CYS2124 4.8 48.7 1.0
CA B:CYS2104 4.8 44.9 1.0
N B:ASN2130 4.9 30.7 1.0

Zinc binding site 6 out of 12 in 4ypa

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Zinc binding site 6 out of 12 in the ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2303

b:28.9
occ:1.00
 SG B:CYS2270 2.3 27.2 1.0
SG B:CYS2268 2.3 29.8 1.0
SG B:CYS2220 2.3 24.9 1.0
SG B:CYS2275 2.4 33.7 1.0
CB B:CYS2220 3.2 21.6 1.0
CB B:CYS2275 3.3 36.4 1.0
CB B:CYS2270 3.3 28.6 1.0
CB B:CYS2268 3.5 33.3 1.0
CA B:CYS2275 3.6 36.1 1.0
N B:CYS2220 3.9 21.0 1.0
N B:CYS2270 4.1 29.4 1.0
N B:ARG2276 4.1 36.2 1.0
CA B:CYS2220 4.2 21.8 1.0
O B:HOH2419 4.2 35.0 1.0
CA B:CYS2270 4.2 28.9 1.0
C B:CYS2275 4.3 35.8 1.0
NE2 B:HIS2218 4.4 22.0 1.0
CD2 B:HIS2218 4.6 21.8 1.0
N B:GLY2277 4.6 37.5 1.0
C B:CYS2268 4.6 32.2 1.0
CA B:CYS2268 4.7 33.1 1.0
N B:GLY2271 4.7 29.4 1.0
O B:CYS2268 4.8 32.4 1.0
N B:CYS2275 4.8 36.2 1.0
C B:CYS2270 4.9 29.1 1.0
C B:SER2219 4.9 20.0 1.0
N B:LYS2269 4.9 31.0 1.0

Zinc binding site 7 out of 12 in 4ypa

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Zinc binding site 7 out of 12 in the ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2301

b:30.4
occ:1.00
 SG C:CYS2093 2.2 43.5 1.0
SG C:CYS2091 2.2 41.4 1.0
SG C:CYS2108 2.3 32.8 1.0
SG C:CYS2104 2.4 42.6 1.0
CB C:CYS2093 3.0 48.5 1.0
CB C:CYS2104 3.2 46.1 1.0
CB C:CYS2108 3.2 38.4 1.0
CB C:CYS2091 3.3 49.2 1.0
CA C:CYS2104 3.7 46.1 1.0
ZN C:ZN2302 3.8 25.9 1.0
CA C:CYS2108 3.8 38.8 1.0
SG C:CYS2117 4.0 28.9 1.0
CA C:CYS2093 4.3 49.3 1.0
O C:HOH2448 4.3 29.2 1.0
N C:CYS2093 4.4 49.3 1.0
N C:CYS2104 4.5 46.8 1.0
N C:LEU2109 4.6 37.4 1.0
CA C:CYS2091 4.6 49.6 1.0
C C:CYS2108 4.6 38.0 1.0
SG C:CYS2122 4.9 35.0 1.0
C C:CYS2104 4.9 47.1 1.0

Zinc binding site 8 out of 12 in 4ypa

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Zinc binding site 8 out of 12 in the ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2302

b:25.9
occ:1.00
 SG C:CYS2104 2.2 42.6 1.0
SG C:CYS2122 2.2 35.0 1.0
SG C:CYS2128 2.4 31.2 1.0
SG C:CYS2117 2.4 28.9 1.0
CB C:CYS2117 3.1 27.2 1.0
CB C:CYS2128 3.3 34.0 1.0
CB C:CYS2122 3.4 36.4 1.0
CB C:CYS2104 3.5 46.1 1.0
ZN C:ZN2301 3.8 30.4 1.0
SG C:CYS2091 4.4 41.4 1.0
CA C:CYS2128 4.4 34.2 1.0
CA C:CYS2117 4.6 27.3 1.0
CB C:CYS2124 4.6 37.9 1.0
CA C:CYS2122 4.6 36.3 1.0
CB C:ASN2130 4.6 26.6 1.0
SG C:CYS2108 4.6 32.8 1.0
NE2 C:GLN2131 4.8 27.4 1.0
CA C:CYS2104 4.8 46.1 1.0
SG C:CYS2124 5.0 32.7 1.0

Zinc binding site 9 out of 12 in 4ypa

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Zinc binding site 9 out of 12 in the ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2303

b:27.0
occ:1.00
 SG C:CYS2270 2.2 22.2 1.0
SG C:CYS2268 2.3 31.4 1.0
SG C:CYS2220 2.4 28.6 1.0
SG C:CYS2275 2.4 38.3 1.0
CB C:CYS2220 3.3 25.4 1.0
CB C:CYS2275 3.3 39.4 1.0
CB C:CYS2270 3.4 26.5 1.0
CB C:CYS2268 3.4 31.0 1.0
CA C:CYS2275 3.7 39.7 1.0
N C:CYS2220 3.8 23.9 1.0
N C:ARG2276 4.1 39.4 1.0
N C:CYS2270 4.1 26.9 1.0
CA C:CYS2220 4.2 24.4 1.0
O C:HOH2439 4.2 32.4 1.0
CA C:CYS2270 4.3 26.2 1.0
C C:CYS2275 4.3 39.9 1.0
NE2 C:HIS2218 4.5 22.6 1.0
C C:CYS2268 4.5 31.1 1.0
CA C:CYS2268 4.6 31.7 1.0
O C:CYS2268 4.6 30.5 1.0
N C:GLY2277 4.6 40.5 1.0
CD2 C:HIS2218 4.6 21.1 1.0
N C:GLY2271 4.7 30.2 1.0
C C:SER2219 4.8 22.0 1.0
N C:LYS2269 4.9 30.2 1.0
C C:CYS2270 4.9 28.4 1.0

Zinc binding site 10 out of 12 in 4ypa

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Zinc binding site 10 out of 12 in the ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of ASH1L Set Domain Q2265A Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2301

b:38.7
occ:1.00
 SG D:CYS2091 1.4 52.4 1.0
SG D:CYS2093 1.6 49.7 1.0
SG D:CYS2104 2.4 38.2 1.0
SG D:CYS2108 2.4 33.4 1.0
CB D:CYS2091 3.0 53.5 1.0
CB D:CYS2093 3.1 53.9 1.0
CB D:CYS2108 3.2 33.5 1.0
CB D:CYS2104 3.3 42.4 1.0
ZN D:ZN2302 3.7 35.7 1.0
CA D:CYS2104 3.8 42.4 1.0
CA D:CYS2108 3.9 33.5 1.0
CA D:CYS2091 4.1 53.6 1.0
SG D:CYS2117 4.1 32.2 1.0
CA D:CYS2093 4.3 53.9 1.0
N D:CYS2093 4.3 53.4 1.0
C D:CYS2108 4.6 33.1 1.0
N D:CYS2104 4.6 45.2 1.0
N D:LEU2109 4.6 31.8 1.0
N D:CYS2091 4.8 54.1 1.0
C D:CYS2104 4.9 42.6 1.0
SG D:CYS2122 4.9 47.9 1.0
N D:ASN2092 5.0 53.1 1.0

Reference:

D.S.Rogawski, J.Ndoj, H.J.Cho, I.Maillard, J.Grembecka, T.Cierpicki. Two Loops Undergoing Concerted Dynamics Regulate the Activity of the ASH1L Histone Methyltransferase. Biochemistry V. 54 5401 2015.
ISSN: ISSN 0006-2960
PubMed: 26292256
DOI: 10.1021/ACS.BIOCHEM.5B00697
Page generated: Wed Dec 16 05:58:05 2020

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