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Zinc in PDB 4ype: ASH1L Set Domain H2193F Mutant in Complex with S-Adenosyl Methionine (Sam)

Enzymatic activity of ASH1L Set Domain H2193F Mutant in Complex with S-Adenosyl Methionine (Sam)

All present enzymatic activity of ASH1L Set Domain H2193F Mutant in Complex with S-Adenosyl Methionine (Sam):
2.1.1.43;

Protein crystallography data

The structure of ASH1L Set Domain H2193F Mutant in Complex with S-Adenosyl Methionine (Sam), PDB code: 4ype 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) 42.56 / 2.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 58.838, 58.838, 232.152, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 26.3

Zinc Binding Sites:

The binding sites of Zinc atom in the ASH1L Set Domain H2193F Mutant in Complex with S-Adenosyl Methionine (Sam) (pdb code 4ype). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the ASH1L Set Domain H2193F Mutant in Complex with S-Adenosyl Methionine (Sam), PDB code: 4ype:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4ype

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Zinc binding site 1 out of 6 in the ASH1L Set Domain H2193F 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 H2193F Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2301

b:23.0
occ:0.87
 SG A:CYS2268 2.1 28.6 1.0
SG A:CYS2270 2.1 29.8 1.0
SG A:CYS2220 2.3 24.4 1.0
SG A:CYS2275 2.5 36.8 1.0
CB A:CYS2270 3.2 33.6 1.0
CB A:CYS2275 3.3 39.3 1.0
CB A:CYS2268 3.3 33.2 1.0
CB A:CYS2220 3.4 24.3 1.0
CA A:CYS2275 3.7 40.1 1.0
N A:CYS2220 3.8 23.1 1.0
N A:ARG2276 3.8 40.5 1.0
N A:CYS2270 3.9 33.8 1.0
CA A:CYS2270 4.1 34.0 1.0
C A:CYS2275 4.2 40.9 1.0
CA A:CYS2220 4.2 23.4 1.0
O A:HOH2434 4.4 26.2 1.0
NE2 A:HIS2218 4.4 24.1 1.0
C A:CYS2268 4.5 34.5 1.0
CA A:CYS2268 4.5 34.0 1.0
CD2 A:HIS2218 4.6 23.6 1.0
O A:CYS2268 4.6 34.1 1.0
N A:GLY2277 4.7 36.3 1.0
N A:GLY2271 4.7 35.1 1.0
C A:CYS2270 4.8 34.6 1.0
N A:LYS2269 4.8 33.5 1.0
C A:SER2219 4.9 23.9 1.0
CA A:ARG2276 5.0 40.0 1.0
N A:CYS2275 5.0 40.9 1.0

Zinc binding site 2 out of 6 in 4ype

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Zinc binding site 2 out of 6 in the ASH1L Set Domain H2193F 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 H2193F Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2302

b:19.2
occ:0.71
 SG A:CYS2128 1.9 27.7 1.0
SG A:CYS2117 2.2 29.1 1.0
SG A:CYS2122 2.4 36.4 1.0
SG A:CYS2104 2.5 42.6 1.0
CB A:CYS2117 3.1 27.0 1.0
CB A:CYS2104 3.2 52.8 1.0
CB A:CYS2128 3.4 36.9 1.0
CB A:CYS2122 3.6 38.6 1.0
ZN A:ZN2303 3.9 20.3 0.6
CA A:CYS2128 4.3 36.9 1.0
SG A:CYS2091 4.3 40.9 1.0
CB A:ASN2130 4.4 23.8 1.0
NE2 A:GLN2131 4.6 22.2 1.0
CA A:CYS2117 4.6 26.9 1.0
CA A:CYS2104 4.7 53.2 1.0
CB A:CYS2124 4.7 43.1 1.0
SG A:CYS2108 4.8 41.6 1.0
CA A:CYS2122 4.8 40.2 1.0
ND2 A:ASN2110 5.0 28.9 1.0

Zinc binding site 3 out of 6 in 4ype

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Zinc binding site 3 out of 6 in the ASH1L Set Domain H2193F 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 H2193F Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2303

b:20.3
occ:0.60
 SG A:CYS2104 2.1 42.6 1.0
SG A:CYS2091 2.1 40.9 1.0
SG A:CYS2093 2.2 46.8 1.0
SG A:CYS2108 2.4 41.6 1.0
CB A:CYS2091 2.8 48.6 1.0
CB A:CYS2104 3.2 52.8 1.0
CB A:CYS2093 3.2 50.4 1.0
CB A:CYS2108 3.4 45.7 1.0
CA A:CYS2104 3.8 53.2 1.0
ZN A:ZN2302 3.9 19.2 0.7
CA A:CYS2108 4.0 45.5 1.0
SG A:CYS2117 4.0 29.1 1.0
N A:CYS2093 4.2 50.6 1.0
CA A:CYS2091 4.3 49.4 1.0
CA A:CYS2093 4.3 51.0 1.0
ND2 A:ASN2110 4.5 28.9 1.0
N A:LEU2109 4.6 42.1 1.0
C A:CYS2108 4.7 43.9 1.0
N A:CYS2104 4.7 54.3 1.0
C A:CYS2091 4.7 49.9 1.0
C A:CYS2104 4.8 54.7 1.0
N A:CYS2091 4.9 51.4 1.0
O A:CYS2104 5.0 54.0 1.0
SG A:CYS2122 5.0 36.4 1.0

Zinc binding site 4 out of 6 in 4ype

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Zinc binding site 4 out of 6 in the ASH1L Set Domain H2193F 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 H2193F Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2301

b:19.7
occ:0.64
 SG B:CYS2270 2.0 26.7 1.0
SG B:CYS2220 2.3 30.0 1.0
SG B:CYS2268 2.3 29.0 1.0
SG B:CYS2275 2.3 35.1 1.0
CB B:CYS2270 3.2 35.2 1.0
CB B:CYS2268 3.2 38.0 1.0
CB B:CYS2220 3.3 26.6 1.0
CB B:CYS2275 3.4 34.0 1.0
CA B:CYS2275 3.8 34.8 1.0
N B:CYS2220 3.9 26.2 1.0
N B:CYS2270 4.0 36.4 1.0
N B:ARG2276 4.0 35.1 1.0
CA B:CYS2270 4.1 35.2 1.0
CA B:CYS2220 4.3 25.5 1.0
NE2 B:HIS2218 4.4 27.8 1.0
C B:CYS2275 4.4 34.8 1.0
CA B:CYS2268 4.5 38.5 1.0
CD2 B:HIS2218 4.6 26.9 1.0
N B:GLY2277 4.7 39.2 1.0
C B:CYS2268 4.7 38.8 1.0
N B:GLY2271 4.8 38.1 1.0
C B:CYS2270 4.9 36.6 1.0
C B:SER2219 4.9 26.8 1.0
O B:CYS2268 5.0 38.9 1.0

Zinc binding site 5 out of 6 in 4ype

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Zinc binding site 5 out of 6 in the ASH1L Set Domain H2193F 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 H2193F Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2302

b:25.7
occ:0.51
 SG B:CYS2128 1.9 38.9 1.0
SG B:CYS2117 2.1 32.9 1.0
SG B:CYS2122 2.3 50.4 1.0
CB B:CYS2117 3.1 31.1 1.0
CB B:CYS2104 3.3 70.1 1.0
ZN B:ZN2303 3.3 36.2 0.5
SG B:CYS2104 3.4 72.9 1.0
CB B:CYS2128 3.4 45.4 1.0
CB B:CYS2122 3.7 53.1 1.0
SG B:CYS2091 4.0 64.8 1.0
CB B:ASN2130 4.4 29.8 1.0
CA B:CYS2128 4.4 44.8 1.0
CA B:CYS2117 4.6 31.3 1.0
SG B:CYS2108 4.6 63.1 1.0
NE2 B:GLN2131 4.7 28.7 1.0
CA B:CYS2104 4.8 69.9 1.0
N B:ASN2130 4.8 33.3 1.0
CA B:CYS2122 4.9 52.9 1.0
ND2 B:ASN2130 4.9 26.9 1.0

Zinc binding site 6 out of 6 in 4ype

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Zinc binding site 6 out of 6 in the ASH1L Set Domain H2193F 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 H2193F Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2303

b:36.2
occ:0.50
 SG B:CYS2104 1.2 72.9 1.0
SG B:CYS2091 1.8 64.8 1.0
SG B:CYS2108 2.2 63.1 1.0
CB B:CYS2091 2.9 64.1 1.0
CB B:CYS2104 3.0 70.1 1.0
ZN B:ZN2302 3.3 25.7 0.5
CB B:CYS2108 3.6 61.9 1.0
SG B:CYS2117 3.6 32.9 1.0
CA B:CYS2104 4.1 69.9 1.0
CA B:CYS2108 4.2 61.5 1.0
CA B:CYS2091 4.3 64.5 1.0
SG B:CYS2122 4.5 50.4 1.0
C B:CYS2091 4.6 64.6 1.0
C B:CYS2104 4.8 69.9 1.0
N B:LEU2109 4.9 55.4 1.0
C B:CYS2108 5.0 59.1 1.0
O B:CYS2104 5.0 69.7 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: Sun Oct 27 11:20:38 2024

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