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Zinc in PDB 4ynm: ASH1L Wild-Type Set Domain in Complex with S-Adenosyl Methionine (Sam)

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

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

Protein crystallography data

The structure of ASH1L Wild-Type Set Domain in Complex with S-Adenosyl Methionine (Sam), PDB code: 4ynm 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) 46.82 / 2.19
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 59.141, 59.141, 230.983, 90.00, 90.00, 120.00
R / Rfree (%) 24.2 / 27.8

Zinc Binding Sites:

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

Zinc binding site 1 out of 6 in 4ynm

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

b:30.4
occ:0.87
 SG A:CYS2270 2.2 34.9 1.0
SG A:CYS2268 2.2 37.2 1.0
SG A:CYS2275 2.3 41.4 1.0
SG A:CYS2220 2.3 35.3 1.0
CB A:CYS2275 3.1 46.2 1.0
CB A:CYS2270 3.3 40.0 1.0
CB A:CYS2220 3.3 33.9 1.0
CB A:CYS2268 3.4 41.7 1.0
CA A:CYS2275 3.7 47.1 1.0
N A:CYS2220 3.9 34.6 1.0
N A:CYS2270 3.9 41.3 1.0
N A:ARG2276 4.1 47.4 1.0
O A:HOH2415 4.1 32.1 1.0
CA A:CYS2270 4.1 40.5 1.0
CA A:CYS2220 4.2 34.2 1.0
C A:CYS2275 4.3 47.6 1.0
NE2 A:HIS2218 4.4 33.6 1.0
C A:CYS2268 4.5 42.3 1.0
CA A:CYS2268 4.6 42.0 1.0
CD2 A:HIS2218 4.6 31.7 1.0
N A:GLY2277 4.6 47.6 1.0
O A:CYS2268 4.7 42.0 1.0
N A:GLY2271 4.8 42.3 1.0
C A:CYS2270 4.8 41.2 1.0
N A:LYS2269 4.9 42.8 1.0
C A:SER2219 5.0 33.8 1.0

Zinc binding site 2 out of 6 in 4ynm

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

b:33.3
occ:0.71
 SG A:CYS2128 2.0 52.5 1.0
SG A:CYS2117 2.1 49.8 1.0
SG A:CYS2122 2.2 61.8 1.0
SG A:CYS2104 2.3 70.8 1.0
CB A:CYS2117 3.0 44.2 1.0
CB A:CYS2104 3.1 75.9 1.0
CB A:CYS2128 3.4 58.1 1.0
CB A:CYS2122 3.5 65.2 1.0
ZN A:ZN2303 3.7 37.5 0.6
O A:HOH2431 4.1 38.3 1.0
SG A:CYS2091 4.1 61.8 1.0
CA A:CYS2128 4.2 57.6 1.0
CB A:ASN2130 4.3 43.6 1.0
CA A:CYS2117 4.5 43.9 1.0
NE2 A:GLN2131 4.6 47.4 1.0
CA A:CYS2104 4.6 76.2 1.0
CA A:CYS2122 4.6 65.1 1.0
SG A:CYS2108 4.7 68.6 1.0
CB A:CYS2124 4.9 66.1 1.0
ND2 A:ASN2130 5.0 39.9 1.0
N A:ASN2130 5.0 46.7 1.0

Zinc binding site 3 out of 6 in 4ynm

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

b:37.5
occ:0.60
 SG A:CYS2091 2.0 61.8 1.0
SG A:CYS2104 2.2 70.8 1.0
SG A:CYS2108 2.3 68.6 1.0
SG A:CYS2093 2.3 67.2 1.0
CB A:CYS2091 3.0 67.8 1.0
CB A:CYS2093 3.1 69.3 1.0
CB A:CYS2108 3.2 70.8 1.0
CB A:CYS2104 3.2 75.9 1.0
CA A:CYS2104 3.7 76.2 1.0
ZN A:ZN2302 3.7 33.3 0.7
CA A:CYS2108 3.8 70.9 1.0
SG A:CYS2117 4.0 49.8 1.0
N A:CYS2093 4.3 69.0 1.0
CA A:CYS2093 4.3 69.5 1.0
N A:LEU2109 4.4 66.2 1.0
CA A:CYS2091 4.4 68.3 1.0
C A:CYS2108 4.4 68.8 1.0
O A:HOH2431 4.5 38.3 1.0
N A:CYS2104 4.6 76.6 1.0
C A:CYS2104 4.8 77.3 1.0
SG A:CYS2122 4.9 61.8 1.0
C A:CYS2091 4.9 68.7 1.0

Zinc binding site 4 out of 6 in 4ynm

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

b:28.2
occ:0.64
 SG B:CYS2270 2.0 36.0 1.0
SG B:CYS2268 2.2 37.3 1.0
SG B:CYS2220 2.2 38.0 1.0
SG B:CYS2275 2.5 43.2 1.0
CB B:CYS2220 3.2 34.0 1.0
CB B:CYS2270 3.2 40.8 1.0
CB B:CYS2275 3.3 46.1 1.0
CB B:CYS2268 3.4 42.1 1.0
CA B:CYS2275 3.7 47.3 1.0
N B:CYS2220 3.8 34.6 1.0
N B:CYS2270 4.0 41.8 1.0
CA B:CYS2220 4.1 35.0 1.0
N B:ARG2276 4.1 47.8 1.0
CA B:CYS2270 4.1 40.8 1.0
NE2 B:HIS2218 4.2 33.8 1.0
C B:CYS2275 4.3 47.8 1.0
CD2 B:HIS2218 4.5 31.5 1.0
C B:CYS2268 4.5 42.7 1.0
CA B:CYS2268 4.6 42.4 1.0
N B:GLY2277 4.6 48.4 1.0
O B:CYS2268 4.7 43.1 1.0
N B:GLY2271 4.8 42.8 1.0
C B:SER2219 4.8 34.0 1.0
C B:CYS2270 4.9 41.2 1.0
N B:LYS2269 4.9 42.7 1.0

Zinc binding site 5 out of 6 in 4ynm

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

b:53.3
occ:0.51
 SG B:CYS2128 1.7 54.9 1.0
SG B:CYS2122 1.8 63.5 1.0
SG B:CYS2104 2.2 72.3 1.0
SG B:CYS2117 2.5 51.9 1.0
CB B:CYS2117 3.1 44.5 1.0
CB B:CYS2104 3.2 76.0 1.0
CB B:CYS2122 3.3 65.6 1.0
CB B:CYS2128 3.4 58.6 1.0
ZN B:ZN2303 3.5 79.3 0.5
CA B:CYS2128 4.0 58.3 1.0
CA B:CYS2122 4.3 65.6 1.0
NE2 B:GLN2131 4.3 48.1 1.0
CB B:ASN2130 4.5 43.8 1.0
CA B:CYS2117 4.6 44.4 1.0
CA B:CYS2104 4.6 76.5 1.0
SG B:CYS2108 4.7 71.0 1.0
CB B:CYS2124 4.8 66.4 1.0
SG B:CYS2124 4.8 69.0 1.0
CD B:PRO2123 4.9 67.0 1.0
N B:CYS2104 4.9 76.6 1.0
C B:CYS2128 4.9 57.1 1.0
C B:CYS2122 5.0 66.4 1.0
N B:CYS2129 5.0 54.9 1.0

Zinc binding site 6 out of 6 in 4ynm

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

b:79.3
occ:0.50
 SG B:CYS2104 2.0 72.3 1.0
SG B:CYS2108 2.7 71.0 1.0
ZN B:ZN2302 3.5 53.3 0.5
CB B:CYS2104 3.5 76.0 1.0
SG B:CYS2117 3.6 51.9 1.0
CB B:CYS2108 4.1 71.2 1.0
CA B:CYS2104 4.3 76.5 1.0
CG B:PRO2123 4.3 66.9 1.0
CD B:PRO2123 4.4 67.0 1.0
SG B:CYS2122 4.4 63.5 1.0
CA B:CYS2108 4.6 71.5 1.0
SG B:CYS2124 4.8 69.0 1.0
N B:LEU2109 4.8 66.8 1.0
N B:CYS2104 5.0 76.6 1.0
ND2 B:ASN2110 5.0 51.4 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 11:19:51 2024

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