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Zinc in PDB 4ynp: ASH1L Set Domain S2259M Mutant in Complex with S-Adenosyl Methionine (Sam)

Enzymatic activity of ASH1L Set Domain S2259M Mutant in Complex with S-Adenosyl Methionine (Sam)

All present enzymatic activity of ASH1L Set Domain S2259M Mutant in Complex with S-Adenosyl Methionine (Sam):
2.1.1.43;

Protein crystallography data

The structure of ASH1L Set Domain S2259M Mutant in Complex with S-Adenosyl Methionine (Sam), PDB code: 4ynp 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) 47.00 / 2.90
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 59.262, 59.262, 233.924, 90.00, 90.00, 120.00
R / Rfree (%) 26.2 / 31.9

Zinc Binding Sites:

The binding sites of Zinc atom in the ASH1L Set Domain S2259M Mutant in Complex with S-Adenosyl Methionine (Sam) (pdb code 4ynp). 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 S2259M Mutant in Complex with S-Adenosyl Methionine (Sam), PDB code: 4ynp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4ynp

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Zinc binding site 1 out of 6 in the ASH1L Set Domain S2259M 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 S2259M Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2301

b:37.3
occ:0.87
 SG A:CYS2268 2.1 52.5 1.0
SG A:CYS2270 2.2 51.1 1.0
SG A:CYS2220 2.4 40.8 1.0
SG A:CYS2275 2.5 56.4 1.0
CB A:CYS2275 3.3 56.1 1.0
CB A:CYS2268 3.4 53.8 1.0
CB A:CYS2220 3.4 40.4 1.0
CB A:CYS2270 3.4 52.4 1.0
N A:CYS2220 3.8 40.4 1.0
CA A:CYS2275 3.8 56.1 1.0
NE2 A:HIS2218 4.0 41.7 1.0
N A:ARG2276 4.1 56.0 1.0
CA A:CYS2220 4.2 40.5 1.0
N A:CYS2270 4.2 52.6 1.0
CA A:CYS2270 4.3 52.6 1.0
C A:CYS2275 4.3 56.0 1.0
CD2 A:HIS2218 4.4 41.2 1.0
N A:GLY2277 4.5 55.8 1.0
CA A:CYS2268 4.6 53.9 1.0
C A:CYS2268 4.7 53.6 1.0
C A:SER2219 4.8 40.2 1.0
O A:CYS2268 4.9 53.5 1.0
N A:GLY2271 4.9 53.4 1.0
C A:CYS2270 5.0 53.0 1.0

Zinc binding site 2 out of 6 in 4ynp

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Zinc binding site 2 out of 6 in the ASH1L Set Domain S2259M 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 S2259M 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:CYS2128 2.1 57.0 1.0
SG A:CYS2117 2.2 53.1 1.0
SG A:CYS2122 2.4 58.4 1.0
SG A:CYS2104 2.4 68.4 1.0
CB A:CYS2117 3.1 54.1 1.0
CB A:CYS2128 3.2 57.8 1.0
SG A:CYS2091 3.4 72.1 1.0
CB A:CYS2104 3.5 69.6 1.0
ZN A:ZN2303 3.7 31.6 0.6
CB A:CYS2122 3.7 57.9 1.0
CB A:ASN2130 4.1 56.0 1.0
CA A:CYS2128 4.3 57.7 1.0
SG A:CYS2108 4.5 63.6 1.0
CA A:CYS2117 4.5 54.2 1.0
ND2 A:ASN2130 4.7 56.1 1.0
NE2 A:GLN2131 4.8 56.4 1.0
CA A:CYS2104 4.8 69.6 1.0
CA A:CYS2122 4.9 58.0 1.0
CB A:CYS2124 4.9 57.9 1.0
N A:ASN2130 4.9 56.4 1.0

Zinc binding site 3 out of 6 in 4ynp

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Zinc binding site 3 out of 6 in the ASH1L Set Domain S2259M 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 S2259M Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2303

b:31.6
occ:0.60
 SG A:CYS2108 2.1 63.6 1.0
SG A:CYS2091 2.1 72.1 1.0
SG A:CYS2093 2.2 73.2 1.0
SG A:CYS2104 2.4 68.4 1.0
CB A:CYS2091 2.8 72.3 1.0
CB A:CYS2104 3.2 69.6 1.0
CB A:CYS2108 3.2 63.9 1.0
ZN A:ZN2302 3.7 37.2 0.7
CA A:CYS2091 3.9 72.4 1.0
CB A:CYS2093 3.9 73.6 1.0
CA A:CYS2108 4.0 63.8 1.0
CA A:CYS2104 4.1 69.6 1.0
SG A:CYS2117 4.1 53.1 1.0
O A:CYS2093 4.6 73.8 1.0
N A:CYS2093 4.7 73.3 1.0
CA A:CYS2093 4.7 73.6 1.0
C A:CYS2108 4.8 63.2 1.0
C A:CYS2091 4.8 72.7 1.0
SG A:CYS2122 4.8 58.4 1.0
N A:LEU2109 4.8 62.4 1.0
N A:CYS2091 4.9 72.2 1.0
N A:CYS2104 5.0 70.3 1.0

Zinc binding site 4 out of 6 in 4ynp

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Zinc binding site 4 out of 6 in the ASH1L Set Domain S2259M 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 S2259M Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2301

b:38.9
occ:0.64
 SG B:CYS2270 2.1 75.9 1.0
SG B:CYS2268 2.2 76.3 1.0
SG B:CYS2220 2.2 53.0 1.0
SG B:CYS2275 2.3 78.1 1.0
CB B:CYS2275 3.2 78.2 1.0
CB B:CYS2270 3.3 76.0 1.0
CB B:CYS2220 3.5 52.2 1.0
CB B:CYS2268 3.5 76.7 1.0
N B:CYS2270 3.8 76.1 1.0
N B:CYS2220 3.8 52.0 1.0
CA B:CYS2275 4.0 78.2 1.0
CA B:CYS2270 4.1 76.0 1.0
CA B:CYS2220 4.3 52.1 1.0
N B:ARG2276 4.3 78.4 1.0
C B:CYS2268 4.5 76.6 1.0
NE2 B:HIS2218 4.5 50.6 1.0
N B:LYS2269 4.5 76.4 1.0
N B:GLY2277 4.6 78.3 1.0
C B:CYS2275 4.6 78.4 1.0
CD2 B:HIS2218 4.6 50.6 1.0
CA B:CYS2268 4.6 76.7 1.0
C B:SER2219 4.7 51.6 1.0
O B:CYS2268 4.8 76.5 1.0
C B:LYS2269 4.9 76.2 1.0
CA B:SER2219 4.9 51.4 1.0

Zinc binding site 5 out of 6 in 4ynp

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Zinc binding site 5 out of 6 in the ASH1L Set Domain S2259M 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 S2259M Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2302

b:77.9
occ:0.51
 SG B:CYS2104 1.6 81.9 1.0
SG B:CYS2122 2.1 71.3 1.0
SG B:CYS2117 2.3 70.8 1.0
ZN B:ZN2303 2.4 57.2 0.5
CB B:CYS2104 3.2 82.1 1.0
CD B:PRO2123 3.3 73.5 1.0
CG B:PRO2123 3.4 73.8 1.0
SG B:CYS2128 3.5 70.4 1.0
CB B:CYS2122 3.7 72.7 1.0
CA B:CYS2122 4.0 72.9 1.0
N B:PRO2123 4.0 73.5 1.0
CB B:CYS2117 4.1 70.7 1.0
SG B:CYS2108 4.3 79.4 1.0
SG B:CYS2124 4.3 74.6 1.0
CA B:CYS2104 4.4 82.1 1.0
C B:CYS2122 4.4 73.2 1.0
CB B:ASN2130 4.6 65.2 1.0
N B:CYS2104 4.6 82.1 1.0
CB B:PRO2123 4.7 73.8 1.0
CB B:CYS2128 4.7 70.2 1.0
ND2 B:ASN2110 4.8 76.4 1.0
N B:CYS2124 4.9 73.7 1.0

Zinc binding site 6 out of 6 in 4ynp

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Zinc binding site 6 out of 6 in the ASH1L Set Domain S2259M 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 S2259M Mutant in Complex with S-Adenosyl Methionine (Sam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2303

b:57.2
occ:0.50
 SG B:CYS2104 2.0 81.9 1.0
SG B:CYS2108 2.3 79.4 1.0
ZN B:ZN2302 2.4 77.9 0.5
CB B:CYS2104 3.2 82.1 1.0
CG B:PRO2123 3.4 73.8 1.0
CB B:CYS2108 3.7 80.1 1.0
CD B:PRO2123 3.8 73.5 1.0
SG B:CYS2117 4.1 70.8 1.0
CA B:CYS2104 4.2 82.1 1.0
SG B:CYS2122 4.5 71.3 1.0
ND2 B:ASN2110 4.6 76.4 1.0
CA B:CYS2108 4.6 80.1 1.0
N B:LEU2109 4.7 79.4 1.0
CB B:PRO2123 4.9 73.8 1.0
CB B:ASN2110 4.9 77.2 1.0
N B:ASN2110 5.0 77.9 1.0
N B:CYS2104 5.0 82.1 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: Sun Oct 27 11:19:51 2024

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