Zinc in PDB 6mon: Crystal Structure of Human SMYD2 in Complex with Nle-Peptide Inhibitor

Enzymatic activity of Crystal Structure of Human SMYD2 in Complex with Nle-Peptide Inhibitor

All present enzymatic activity of Crystal Structure of Human SMYD2 in Complex with Nle-Peptide Inhibitor:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of Human SMYD2 in Complex with Nle-Peptide Inhibitor, PDB code: 6mon was solved by N.Spellmon, E.Cornett, J.Brunzelle, S.Rothbart, Z.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.24 / 2.71
Space group P 42
Cell size a, b, c (Å), α, β, γ (°) 153.728, 153.728, 53.457, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 22.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human SMYD2 in Complex with Nle-Peptide Inhibitor (pdb code 6mon). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Human SMYD2 in Complex with Nle-Peptide Inhibitor, PDB code: 6mon:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6mon

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Zinc binding site 1 out of 6 in the Crystal Structure of Human SMYD2 in Complex with Nle-Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human SMYD2 in Complex with Nle-Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:68.6
occ:1.00
 SG A:CYS78 2.3 65.8 1.0
SG A:CYS74 2.3 66.0 1.0
SG A:CYS55 2.3 69.5 1.0
SG A:CYS52 2.4 68.6 1.0
CB A:CYS52 3.2 67.7 1.0
CB A:CYS74 3.2 71.1 1.0
CB A:CYS78 3.4 68.4 1.0
CB A:CYS55 3.5 56.5 1.0
N A:CYS74 3.9 68.9 1.0
N A:CYS55 3.9 58.1 1.0
CA A:CYS74 4.1 72.9 1.0
CA A:CYS55 4.3 56.7 1.0
OG1 A:THR57 4.5 70.3 1.0
CA A:CYS52 4.7 63.2 1.0
CB A:THR57 4.7 63.9 1.0
CB A:TYR54 4.7 62.4 1.0
CA A:CYS78 4.8 74.3 1.0
C A:CYS55 4.9 50.4 1.0
C A:TYR54 5.0 58.0 1.0
CD1 A:TYR54 5.0 62.7 1.0

Zinc binding site 2 out of 6 in 6mon

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Zinc binding site 2 out of 6 in the Crystal Structure of Human SMYD2 in Complex with Nle-Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human SMYD2 in Complex with Nle-Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:63.9
occ:1.00
 NE2 A:HIS86 2.1 54.6 1.0
SG A:CYS68 2.3 58.7 1.0
SG A:CYS90 2.3 62.0 1.0
SG A:CYS65 2.4 67.8 1.0
CD2 A:HIS86 3.0 59.2 1.0
CE1 A:HIS86 3.1 58.0 1.0
CB A:CYS90 3.3 57.9 1.0
CB A:CYS68 3.4 62.1 1.0
CB A:CYS65 3.5 69.1 1.0
N A:CYS68 3.7 70.3 1.0
CA A:CYS90 4.0 51.0 1.0
CA A:CYS68 4.1 68.1 1.0
CG A:HIS86 4.1 57.6 1.0
ND1 A:HIS86 4.2 58.5 1.0
CB A:ARG67 4.5 76.3 1.0
CB A:ALA71 4.7 65.6 1.0
NH1 A:ARG67 4.8 92.3 1.0
C A:ARG67 4.8 71.4 1.0
C A:CYS90 4.9 60.2 1.0
CA A:CYS65 4.9 73.3 1.0
CZ3 A:TRP83 4.9 63.8 1.0
N A:ARG67 4.9 73.1 1.0
N A:LYS69 5.0 71.6 1.0
CA A:ARG67 5.0 70.6 1.0

Zinc binding site 3 out of 6 in 6mon

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Zinc binding site 3 out of 6 in the Crystal Structure of Human SMYD2 in Complex with Nle-Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human SMYD2 in Complex with Nle-Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:65.7
occ:1.00
 SG A:CYS267 2.3 65.6 1.0
SG A:CYS262 2.3 61.8 1.0
SG A:CYS209 2.3 51.8 1.0
SG A:CYS264 2.3 64.4 1.0
CB A:CYS209 3.1 67.7 1.0
CB A:CYS262 3.2 55.3 1.0
CB A:CYS267 3.5 72.9 1.0
CB A:CYS264 3.5 59.9 1.0
N A:CYS209 3.6 55.4 1.0
CA A:CYS209 4.0 63.1 1.0
N A:CYS267 4.0 73.7 1.0
N A:CYS264 4.0 65.5 1.0
NH2 A:ARG250 4.1 66.2 1.0
CA A:CYS264 4.3 65.4 1.0
CA A:CYS267 4.3 75.9 1.0
CA A:CYS262 4.5 60.2 1.0
C A:CYS262 4.5 65.6 1.0
NE A:ARG250 4.6 65.3 1.0
C A:SER208 4.7 56.2 1.0
NE2 A:HIS207 4.7 58.0 1.0
CB A:GLU266 4.8 82.8 1.0
O A:CYS262 4.8 70.2 1.0
N A:GLU263 4.8 64.8 1.0
C A:CYS264 4.9 69.7 1.0
CZ A:ARG250 4.9 69.0 1.0
CD2 A:HIS207 4.9 52.8 1.0
O A:CYS264 5.0 72.1 1.0

Zinc binding site 4 out of 6 in 6mon

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Zinc binding site 4 out of 6 in the Crystal Structure of Human SMYD2 in Complex with Nle-Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human SMYD2 in Complex with Nle-Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:76.7
occ:1.00
 SG B:CYS78 2.2 75.8 1.0
SG B:CYS55 2.3 72.6 1.0
SG B:CYS74 2.4 92.5 1.0
SG B:CYS52 2.4 73.4 1.0
CB B:CYS74 3.2 78.5 1.0
CB B:CYS52 3.3 68.2 1.0
CB B:CYS78 3.4 81.7 1.0
CB B:CYS55 3.5 72.5 1.0
N B:CYS74 3.9 79.7 1.0
N B:CYS55 3.9 64.8 1.0
CA B:CYS74 4.1 82.7 1.0
CA B:CYS55 4.3 63.5 1.0
OG1 B:THR57 4.5 72.0 1.0
CB B:THR57 4.7 71.4 1.0
CB B:TYR54 4.7 72.7 1.0
CA B:CYS78 4.8 80.0 1.0
CA B:CYS52 4.8 65.8 1.0
CD1 B:TYR54 4.9 74.4 1.0
C B:TYR54 5.0 66.5 1.0
C B:CYS55 5.0 58.9 1.0

Zinc binding site 5 out of 6 in 6mon

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Zinc binding site 5 out of 6 in the Crystal Structure of Human SMYD2 in Complex with Nle-Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Human SMYD2 in Complex with Nle-Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:64.6
occ:1.00
 NE2 B:HIS86 2.0 65.6 1.0
SG B:CYS68 2.2 64.8 1.0
SG B:CYS90 2.3 67.9 1.0
SG B:CYS65 2.4 71.5 1.0
CD2 B:HIS86 2.9 62.1 1.0
CE1 B:HIS86 3.1 64.4 1.0
CB B:CYS90 3.4 63.8 1.0
CB B:CYS68 3.4 60.5 1.0
CB B:CYS65 3.6 81.7 1.0
N B:CYS68 3.8 78.5 1.0
CA B:CYS90 4.0 59.7 1.0
CG B:HIS86 4.1 62.9 1.0
ND1 B:HIS86 4.2 58.8 1.0
CA B:CYS68 4.2 75.4 1.0
CB B:ALA71 4.6 70.0 1.0
CB B:ARG67 4.6 86.4 1.0
NH1 B:ARG67 4.8 95.9 1.0
C B:CYS90 4.9 59.1 1.0
CZ3 B:TRP83 4.9 69.8 1.0
C B:ARG67 4.9 84.1 1.0
CA B:CYS65 4.9 76.4 1.0

Zinc binding site 6 out of 6 in 6mon

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Zinc binding site 6 out of 6 in the Crystal Structure of Human SMYD2 in Complex with Nle-Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Human SMYD2 in Complex with Nle-Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:66.7
occ:1.00
 SG B:CYS262 2.2 56.7 1.0
SG B:CYS267 2.3 72.6 1.0
SG B:CYS209 2.3 63.3 1.0
SG B:CYS264 2.4 78.1 1.0
CB B:CYS209 3.1 69.0 1.0
CB B:CYS262 3.1 53.2 1.0
CB B:CYS267 3.5 73.8 1.0
CB B:CYS264 3.5 70.3 1.0
N B:CYS209 3.6 60.0 1.0
N B:CYS264 4.0 68.9 1.0
CA B:CYS209 4.0 64.6 1.0
N B:CYS267 4.0 70.5 1.0
CA B:CYS264 4.2 70.8 1.0
NH2 B:ARG250 4.3 73.0 1.0
CA B:CYS267 4.3 69.0 1.0
CA B:CYS262 4.4 60.1 1.0
C B:CYS262 4.4 70.7 1.0
C B:SER208 4.7 60.5 1.0
NE2 B:HIS207 4.7 53.3 1.0
NE B:ARG250 4.7 68.8 1.0
O B:CYS262 4.7 72.1 1.0
N B:GLU263 4.8 67.4 1.0
C B:CYS264 4.8 74.8 1.0
CB B:GLU266 4.9 78.0 1.0
O B:CYS264 4.9 76.5 1.0
CD2 B:HIS207 4.9 53.0 1.0
CA B:SER208 5.0 60.8 1.0
CZ B:ARG250 5.0 70.0 1.0

Reference:

E.M.Cornett, B.M.Dickson, K.Krajewski, N.Spellmon, A.Umstead, R.M.Vaughan, K.M.Shaw, P.P.Versluis, M.W.Cowles, J.Brunzelle, Z.Yang, I.E.Vega, Z.W.Sun, S.B.Rothbart. A Functional Proteomics Platform to Reveal the Sequence Determinants of Lysine Methyltransferase Substrate Selectivity. Sci Adv V. 4 V2623 2018.
ISSN: ESSN 2375-2548
PubMed: 30498785
DOI: 10.1126/SCIADV.AAV2623
Page generated: Wed Dec 16 12:20:11 2020

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