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Zinc in PDB 2ysm: Solution Structure of the Second and Third Phd Domain From Histone- Lysine N-Methyltransferase 2C (KMT2C/MLL3)

Enzymatic activity of Solution Structure of the Second and Third Phd Domain From Histone- Lysine N-Methyltransferase 2C (KMT2C/MLL3)

All present enzymatic activity of Solution Structure of the Second and Third Phd Domain From Histone- Lysine N-Methyltransferase 2C (KMT2C/MLL3):
2.1.1.43;

Zinc Binding Sites:

The binding sites of Zinc atom in the Solution Structure of the Second and Third Phd Domain From Histone- Lysine N-Methyltransferase 2C (KMT2C/MLL3) (pdb code 2ysm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Solution Structure of the Second and Third Phd Domain From Histone- Lysine N-Methyltransferase 2C (KMT2C/MLL3), PDB code: 2ysm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2ysm

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Zinc binding site 1 out of 4 in the Solution Structure of the Second and Third Phd Domain From Histone- Lysine N-Methyltransferase 2C (KMT2C/MLL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Solution Structure of the Second and Third Phd Domain From Histone- Lysine N-Methyltransferase 2C (KMT2C/MLL3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:0.0
occ:1.00
ND1 A:HIS33 2.0 0.0 1.0
SG A:CYS36 2.2 0.0 1.0
SG A:CYS10 2.3 0.0 1.0
SG A:CYS13 2.4 0.0 1.0
CE1 A:HIS33 2.8 0.0 1.0
HE1 A:HIS33 3.0 0.0 1.0
HB3 A:CYS13 3.0 0.0 1.0
CB A:CYS10 3.1 0.0 1.0
HB2 A:HIS33 3.1 0.0 1.0
HB2 A:CYS10 3.1 0.0 1.0
HB3 A:CYS10 3.1 0.0 1.0
CG A:HIS33 3.1 0.0 1.0
H A:HIS33 3.1 0.0 1.0
HB2 A:CYS36 3.2 0.0 1.0
H A:CYS13 3.3 0.0 1.0
CB A:CYS13 3.3 0.0 1.0
CB A:CYS36 3.3 0.0 1.0
HB3 A:CYS36 3.6 0.0 1.0
CB A:HIS33 3.7 0.0 1.0
HB A:VAL12 3.7 0.0 1.0
N A:CYS13 3.9 0.0 1.0
NE2 A:HIS33 4.0 0.0 1.0
N A:HIS33 4.0 0.0 1.0
HB2 A:CYS13 4.1 0.0 1.0
CD2 A:HIS33 4.1 0.0 1.0
CA A:CYS13 4.2 0.0 1.0
HA A:TYR32 4.4 0.0 1.0
H A:ASP14 4.4 0.0 1.0
H A:SER15 4.5 0.0 1.0
CA A:HIS33 4.5 0.0 1.0
HB3 A:HIS33 4.5 0.0 1.0
H A:VAL12 4.5 0.0 1.0
HB3 A:SER15 4.6 0.0 1.0
CA A:CYS10 4.6 0.0 1.0
H A:CYS36 4.6 0.0 1.0
CA A:CYS36 4.7 0.0 1.0
HG13 A:VAL12 4.7 0.0 1.0
CB A:VAL12 4.8 0.0 1.0
HE2 A:HIS33 4.8 0.0 1.0
HA A:CYS10 4.9 0.0 1.0
HA A:CYS36 4.9 0.0 1.0
N A:ASP14 4.9 0.0 1.0
C A:VAL12 5.0 0.0 1.0
O A:SER15 5.0 0.0 1.0

Zinc binding site 2 out of 4 in 2ysm

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Zinc binding site 2 out of 4 in the Solution Structure of the Second and Third Phd Domain From Histone- Lysine N-Methyltransferase 2C (KMT2C/MLL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Solution Structure of the Second and Third Phd Domain From Histone- Lysine N-Methyltransferase 2C (KMT2C/MLL3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:0.0
occ:1.00
SG A:CYS51 2.2 0.0 1.0
SG A:CYS25 2.2 0.0 1.0
SG A:CYS28 2.3 0.0 1.0
SG A:CYS54 2.4 0.0 1.0
HB2 A:CYS54 2.7 0.0 1.0
H A:CYS28 2.8 0.0 1.0
CB A:CYS54 3.1 0.0 1.0
HB3 A:CYS28 3.1 0.0 1.0
CB A:CYS25 3.1 0.0 1.0
HB3 A:CYS25 3.1 0.0 1.0
HB3 A:CYS51 3.2 0.0 1.0
HB2 A:CYS25 3.2 0.0 1.0
CB A:CYS28 3.3 0.0 1.0
CB A:CYS51 3.3 0.0 1.0
HB A:THR27 3.4 0.0 1.0
H A:CYS51 3.6 0.0 1.0
N A:CYS28 3.6 0.0 1.0
H A:CYS54 3.6 0.0 1.0
H A:GLY29 3.7 0.0 1.0
HB2 A:GLU53 3.8 0.0 1.0
HB3 A:CYS54 3.8 0.0 1.0
N A:CYS54 4.0 0.0 1.0
CA A:CYS28 4.1 0.0 1.0
H A:GLN30 4.1 0.0 1.0
HB2 A:CYS51 4.1 0.0 1.0
CA A:CYS54 4.2 0.0 1.0
HB2 A:CYS28 4.2 0.0 1.0
HB2 A:GLN30 4.2 0.0 1.0
N A:CYS51 4.2 0.0 1.0
CA A:CYS51 4.3 0.0 1.0
H A:THR27 4.4 0.0 1.0
CB A:THR27 4.5 0.0 1.0
N A:GLY29 4.5 0.0 1.0
H A:GLU53 4.5 0.0 1.0
CA A:CYS25 4.6 0.0 1.0
HG22 A:THR27 4.6 0.0 1.0
HA A:CYS54 4.7 0.0 1.0
HE1 A:TYR32 4.7 0.0 1.0
O A:CYS51 4.7 0.0 1.0
C A:THR27 4.8 0.0 1.0
C A:GLU53 4.8 0.0 1.0
C A:CYS51 4.8 0.0 1.0
C A:CYS28 4.8 0.0 1.0
CB A:GLU53 4.8 0.0 1.0
HG2 A:GLN30 4.9 0.0 1.0
N A:THR27 4.9 0.0 1.0
HA A:CYS25 4.9 0.0 1.0
H A:THR26 4.9 0.0 1.0
H A:LYS55 4.9 0.0 1.0
HA A:CYS28 4.9 0.0 1.0
CA A:THR27 5.0 0.0 1.0
HE21 A:GLN50 5.0 0.0 1.0

Zinc binding site 3 out of 4 in 2ysm

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Zinc binding site 3 out of 4 in the Solution Structure of the Second and Third Phd Domain From Histone- Lysine N-Methyltransferase 2C (KMT2C/MLL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Solution Structure of the Second and Third Phd Domain From Histone- Lysine N-Methyltransferase 2C (KMT2C/MLL3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:0.0
occ:1.00
ND1 A:HIS80 2.1 0.0 1.0
SG A:CYS60 2.3 0.0 1.0
SG A:CYS83 2.3 0.0 1.0
SG A:CYS57 2.4 0.0 1.0
HB2 A:HIS80 2.8 0.0 1.0
CE1 A:HIS80 2.9 0.0 1.0
CG A:HIS80 3.0 0.0 1.0
HB3 A:CYS57 3.0 0.0 1.0
CB A:CYS57 3.1 0.0 1.0
HB3 A:CYS60 3.1 0.0 1.0
HB2 A:CYS57 3.2 0.0 1.0
HE1 A:HIS80 3.2 0.0 1.0
HE2 A:PHE82 3.2 0.0 1.0
H A:CYS60 3.2 0.0 1.0
HB2 A:CYS83 3.2 0.0 1.0
CB A:CYS83 3.3 0.0 1.0
CB A:CYS60 3.3 0.0 1.0
CB A:HIS80 3.4 0.0 1.0
HB2 A:ASN59 3.5 0.0 1.0
HB3 A:CYS83 3.5 0.0 1.0
H A:HIS80 3.6 0.0 1.0
N A:CYS60 3.9 0.0 1.0
CE2 A:PHE82 3.9 0.0 1.0
NE2 A:HIS80 4.0 0.0 1.0
CD2 A:HIS80 4.1 0.0 1.0
HB3 A:HIS80 4.1 0.0 1.0
HB2 A:CYS60 4.1 0.0 1.0
CA A:CYS60 4.2 0.0 1.0
H A:LYS61 4.2 0.0 1.0
N A:HIS80 4.4 0.0 1.0
H A:GLN62 4.4 0.0 1.0
HZ A:PHE82 4.4 0.0 1.0
HB2 A:GLN62 4.5 0.0 1.0
CZ A:PHE82 4.5 0.0 1.0
CB A:ASN59 4.5 0.0 1.0
H A:ASN59 4.6 0.0 1.0
CA A:HIS80 4.6 0.0 1.0
CA A:CYS57 4.6 0.0 1.0
HD2 A:PHE82 4.6 0.0 1.0
CD2 A:PHE82 4.6 0.0 1.0
OD1 A:ASN59 4.7 0.0 1.0
CA A:CYS83 4.7 0.0 1.0
N A:LYS61 4.8 0.0 1.0
HE2 A:HIS80 4.8 0.0 1.0
C A:ASN59 4.9 0.0 1.0
C A:CYS60 4.9 0.0 1.0
H A:CYS83 4.9 0.0 1.0
HA A:CYS57 5.0 0.0 1.0

Zinc binding site 4 out of 4 in 2ysm

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Zinc binding site 4 out of 4 in the Solution Structure of the Second and Third Phd Domain From Histone- Lysine N-Methyltransferase 2C (KMT2C/MLL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Solution Structure of the Second and Third Phd Domain From Histone- Lysine N-Methyltransferase 2C (KMT2C/MLL3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:0.0
occ:1.00
SG A:CYS98 2.2 0.0 1.0
SG A:CYS75 2.2 0.0 1.0
SG A:CYS72 2.3 0.0 1.0
SG A:CYS101 2.4 0.0 1.0
HB2 A:CYS101 2.7 0.0 1.0
H A:CYS75 2.9 0.0 1.0
H A:CYS98 3.1 0.0 1.0
HB2 A:CYS72 3.1 0.0 1.0
HB3 A:CYS75 3.1 0.0 1.0
CB A:CYS101 3.1 0.0 1.0
CB A:CYS72 3.1 0.0 1.0
HB3 A:CYS72 3.1 0.0 1.0
HB3 A:CYS98 3.1 0.0 1.0
CB A:CYS75 3.3 0.0 1.0
CB A:CYS98 3.3 0.0 1.0
HB A:THR74 3.6 0.0 1.0
N A:CYS75 3.7 0.0 1.0
HB3 A:CYS101 3.8 0.0 1.0
N A:CYS98 3.8 0.0 1.0
H A:CYS101 3.9 0.0 1.0
H A:ASP76 4.0 0.0 1.0
HE2 A:TYR79 4.1 0.0 1.0
CA A:CYS75 4.1 0.0 1.0
HB2 A:CYS75 4.1 0.0 1.0
HG2 A:LYS97 4.1 0.0 1.0
CA A:CYS98 4.1 0.0 1.0
N A:CYS101 4.2 0.0 1.0
HB2 A:CYS98 4.2 0.0 1.0
CA A:CYS101 4.2 0.0 1.0
H A:THR74 4.2 0.0 1.0
HB2 A:ASN100 4.4 0.0 1.0
H A:LYS77 4.4 0.0 1.0
HB2 A:LYS77 4.5 0.0 1.0
HA A:LYS97 4.5 0.0 1.0
HA A:CYS101 4.5 0.0 1.0
CA A:CYS72 4.6 0.0 1.0
CB A:THR74 4.7 0.0 1.0
N A:ASP76 4.7 0.0 1.0
C A:CYS98 4.7 0.0 1.0
HH A:TYR79 4.7 0.0 1.0
HA A:CYS72 4.8 0.0 1.0
O A:CYS98 4.9 0.0 1.0
C A:THR74 4.9 0.0 1.0
C A:CYS75 4.9 0.0 1.0
HA A:CYS75 5.0 0.0 1.0
H A:ASP73 5.0 0.0 1.0
N A:THR74 5.0 0.0 1.0
C A:LYS97 5.0 0.0 1.0

Reference:

X.R.Qin, F.Hayashi, S.Yokoyama. Solution Structure of the First and Second Phd Domain From Myeloid/Lymphoid or Mixed-Lineage Leukemia Protein 3 Homolog To Be Published.
Page generated: Wed Dec 16 04:03:00 2020

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