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Zinc in PDB 4ypu: ASH1L Set Domain K2264L Mutant in Complex with S-Adenosyl Methionine (Sam)

Enzymatic activity of ASH1L Set Domain K2264L Mutant in Complex with S-Adenosyl Methionine (Sam)

All present enzymatic activity of ASH1L Set Domain K2264L Mutant in Complex with S-Adenosyl Methionine (Sam):
2.1.1.43;

Protein crystallography data

The structure of ASH1L Set Domain K2264L Mutant in Complex with S-Adenosyl Methionine (Sam), PDB code: 4ypu 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) 75.35 / 2.60
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 59.108, 59.108, 226.043, 90.00, 90.00, 120.00
R / Rfree (%) 23.8 / 30.5

Zinc Binding Sites:

The binding sites of Zinc atom in the ASH1L Set Domain K2264L Mutant in Complex with S-Adenosyl Methionine (Sam) (pdb code 4ypu). 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 K2264L Mutant in Complex with S-Adenosyl Methionine (Sam), PDB code: 4ypu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4ypu

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Zinc binding site 1 out of 6 in the ASH1L Set Domain K2264L 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 K2264L Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2301

b:37.0
occ:0.87
 SG A:CYS2270 1.8 43.9 1.0
SG A:CYS2268 2.1 48.4 1.0
SG A:CYS2220 2.3 45.3 1.0
SG A:CYS2275 2.4 61.3 1.0
CB A:CYS2275 3.2 61.4 1.0
CB A:CYS2270 3.3 49.7 1.0
CB A:CYS2220 3.3 44.1 1.0
CB A:CYS2268 3.4 51.2 1.0
CA A:CYS2275 3.8 61.7 1.0
N A:CYS2220 3.8 44.8 1.0
N A:CYS2270 3.9 49.8 1.0
N A:ARG2276 4.1 62.2 1.0
CA A:CYS2270 4.1 49.6 1.0
CA A:CYS2220 4.2 44.1 1.0
C A:CYS2275 4.3 61.8 1.0
NE2 A:HIS2218 4.4 47.2 1.0
CD2 A:HIS2218 4.5 47.6 1.0
CA A:CYS2268 4.6 51.2 1.0
C A:CYS2268 4.6 50.9 1.0
N A:GLY2277 4.6 63.5 1.0
N A:LYS2269 4.6 50.3 1.0
C A:CYS2270 4.9 50.9 1.0
C A:SER2219 4.9 44.9 1.0
N A:GLY2271 4.9 51.8 1.0
CB A:PHE2272 5.0 56.3 1.0

Zinc binding site 2 out of 6 in 4ypu

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Zinc binding site 2 out of 6 in the ASH1L Set Domain K2264L 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 K2264L Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2302

b:37.2
occ:0.71
 SG A:CYS2117 2.1 48.1 1.0
SG A:CYS2122 2.1 64.7 1.0
SG A:CYS2128 2.2 51.5 1.0
SG A:CYS2104 2.4 59.8 1.0
CB A:CYS2117 3.1 48.3 1.0
CB A:CYS2128 3.4 54.7 1.0
CB A:CYS2104 3.4 63.4 1.0
CB A:CYS2122 3.6 65.4 1.0
ZN A:ZN2303 3.7 36.9 0.6
SG A:CYS2091 4.3 56.8 1.0
CA A:CYS2128 4.4 54.5 1.0
CB A:ASN2130 4.4 45.1 1.0
NE2 A:GLN2131 4.5 43.4 1.0
CA A:CYS2117 4.6 48.3 1.0
SG A:CYS2108 4.6 58.6 1.0
CA A:CYS2122 4.8 65.4 1.0
CA A:CYS2104 4.8 63.7 1.0
CB A:CYS2124 4.9 63.5 1.0
SG A:CYS2124 4.9 66.4 1.0
N A:ASN2130 5.0 47.5 1.0

Zinc binding site 3 out of 6 in 4ypu

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Zinc binding site 3 out of 6 in the ASH1L Set Domain K2264L 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 K2264L Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2303

b:36.9
occ:0.60
 SG A:CYS2091 2.0 56.8 1.0
SG A:CYS2108 2.3 58.6 1.0
SG A:CYS2104 2.3 59.8 1.0
SG A:CYS2093 2.4 65.1 1.0
CB A:CYS2091 3.2 60.9 1.0
CB A:CYS2104 3.3 63.4 1.0
CB A:CYS2093 3.3 64.5 1.0
CB A:CYS2108 3.4 59.2 1.0
ZN A:ZN2302 3.7 37.2 0.7
SG A:CYS2117 3.9 48.1 1.0
CA A:CYS2104 4.0 63.7 1.0
CA A:CYS2108 4.1 59.2 1.0
N A:CYS2093 4.4 64.0 1.0
CA A:CYS2093 4.5 64.9 1.0
CA A:CYS2091 4.6 61.5 1.0
SG A:CYS2122 4.6 64.7 1.0
C A:CYS2108 4.9 57.8 1.0
C A:CYS2091 4.9 62.3 1.0
N A:LEU2109 4.9 56.2 1.0
N A:CYS2104 4.9 64.8 1.0

Zinc binding site 4 out of 6 in 4ypu

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Zinc binding site 4 out of 6 in the ASH1L Set Domain K2264L 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 K2264L Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2301

b:37.6
occ:0.64
 SG B:CYS2270 1.9 53.7 1.0
SG B:CYS2268 2.1 57.1 1.0
SG B:CYS2220 2.2 53.5 1.0
SG B:CYS2275 2.7 68.1 1.0
CB B:CYS2220 3.1 48.5 1.0
CB B:CYS2270 3.2 57.1 1.0
CB B:CYS2275 3.5 69.0 1.0
N B:CYS2220 3.6 47.0 1.0
CB B:CYS2268 3.6 62.9 1.0
N B:CYS2270 3.9 58.3 1.0
CA B:CYS2220 3.9 48.3 1.0
CA B:CYS2275 4.0 69.2 1.0
CA B:CYS2270 4.1 57.8 1.0
NE2 B:HIS2218 4.2 41.7 1.0
N B:ARG2276 4.4 70.7 1.0
CD2 B:HIS2218 4.4 43.3 1.0
C B:CYS2275 4.7 69.9 1.0
C B:SER2219 4.7 45.6 1.0
C B:CYS2268 4.7 62.3 1.0
N B:GLY2271 4.8 59.1 1.0
CA B:CYS2268 4.8 62.9 1.0
C B:CYS2270 4.8 58.5 1.0
CB B:PHE2272 4.9 63.3 1.0
N B:LYS2269 4.9 61.1 1.0

Zinc binding site 5 out of 6 in 4ypu

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Zinc binding site 5 out of 6 in the ASH1L Set Domain K2264L 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 K2264L Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2302

b:51.7
occ:0.51
 SG B:CYS2128 1.7 80.5 1.0
SG B:CYS2122 1.8 84.5 1.0
SG B:CYS2117 2.3 74.0 1.0
SG B:CYS2104 2.7 91.5 1.0
CB B:CYS2117 3.0 71.5 1.0
CB B:CYS2104 3.0 92.2 1.0
CB B:CYS2128 3.3 81.2 1.0
CB B:CYS2122 3.3 86.1 1.0
CB B:ASN2130 3.9 69.1 1.0
CA B:CYS2128 4.0 80.8 1.0
N B:ASN2130 4.2 71.3 1.0
C B:CYS2128 4.4 79.5 1.0
ZN B:ZN2303 4.4 76.9 0.5
CA B:CYS2122 4.4 86.4 1.0
N B:CYS2129 4.5 77.4 1.0
CA B:CYS2117 4.5 71.7 1.0
CA B:CYS2104 4.5 92.3 1.0
CA B:ASN2130 4.6 68.7 1.0
SG B:CYS2108 4.7 87.4 1.0
O B:ASN2130 4.8 66.5 1.0
NE2 B:GLN2131 4.8 63.2 1.0
SG B:CYS2124 4.9 90.2 1.0
CD B:PRO2123 4.9 87.7 1.0
ND2 B:ASN2130 4.9 69.9 1.0
C B:ASN2130 5.0 66.4 1.0

Zinc binding site 6 out of 6 in 4ypu

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Zinc binding site 6 out of 6 in the ASH1L Set Domain K2264L 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 K2264L Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2303

b:76.9
occ:0.50
 SG B:CYS2108 2.0 87.4 1.0
SG B:CYS2104 2.2 91.5 1.0
CD2 B:LEU2109 3.3 84.9 1.0
CG B:LEU2109 3.3 85.6 1.0
CB B:CYS2104 3.6 92.2 1.0
N B:LEU2109 3.6 86.5 1.0
CB B:CYS2108 3.6 87.8 1.0
CD B:PRO2123 3.9 87.7 1.0
CG B:PRO2123 4.0 88.1 1.0
CA B:CYS2108 4.1 88.0 1.0
CA B:CYS2104 4.1 92.3 1.0
SG B:CYS2117 4.2 74.0 1.0
C B:CYS2108 4.3 87.4 1.0
CD1 B:LEU2109 4.3 85.0 1.0
CB B:LEU2109 4.3 85.3 1.0
ZN B:ZN2302 4.4 51.7 0.5
CA B:LEU2109 4.5 85.5 1.0
N B:ASN2110 4.7 83.3 1.0
SG B:CYS2122 4.7 84.5 1.0
ND2 B:ASN2110 4.8 78.3 1.0
CB B:PRO2123 4.8 87.9 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 11:22:43 2024

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