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Cobalt in PDB 3m5a: SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy

Enzymatic activity of SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy

All present enzymatic activity of SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy:
2.1.1.43;

Protein crystallography data

The structure of SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy, PDB code: 3m5a was solved by P.A.Del Rizzo, J.-F.Couture, M.S.Roiko, B.S.Strunk, J.S.Brunzelle, L.M.Dirk, R.L.Houtz, R.C.Trievel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.14 / 1.75
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.108, 83.108, 95.570, 90.00, 90.00, 120.00
R / Rfree (%) 19.6 / 21

Cobalt Binding Sites:

The binding sites of Cobalt atom in the SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy (pdb code 3m5a). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy, PDB code: 3m5a:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in 3m5a

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Cobalt binding site 1 out of 7 in the SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co367

b:0.8
occ:1.00
 N A:GLU351 3.3 41.5 1.0
CB A:GLU351 3.4 41.9 1.0
N A:TRP352 3.5 40.7 1.0
CA A:GLU351 3.7 41.3 1.0
CD1 A:TRP352 3.9 36.5 1.0
C A:GLU351 4.1 41.2 1.0
C A:PRO350 4.3 41.1 1.0
CB A:PRO350 4.3 40.7 1.0
CB A:TRP352 4.5 39.8 1.0
CA A:TRP352 4.6 40.0 1.0
CA A:PRO350 4.6 40.8 1.0
CG A:TRP352 4.6 38.2 1.0
NE1 A:TRP352 4.9 36.1 1.0

Cobalt binding site 2 out of 7 in 3m5a

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Cobalt binding site 2 out of 7 in the SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co2

b:1.0
occ:1.00
 O A:HOH99 3.9 33.1 1.0
NH2 A:ARG215 4.2 27.0 1.0
CB A:ASP150 4.3 20.9 1.0
NE A:ARG215 4.8 26.3 1.0
CG2 A:THR240 4.9 21.0 1.0
CA A:ASP150 4.9 21.1 1.0

Cobalt binding site 3 out of 7 in 3m5a

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Cobalt binding site 3 out of 7 in the SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co3

b:90.2
occ:1.00
 N A:ALA324 3.2 27.1 1.0
CB A:ARG323 3.7 27.6 0.6
CB A:ARG323 3.8 27.3 0.4
CB A:ALA324 3.8 27.4 1.0
CA A:ARG323 3.9 27.0 0.4
CA A:ARG323 3.9 27.1 0.6
C A:ARG323 4.1 27.4 1.0
CA A:ALA324 4.1 27.3 1.0
CG A:ARG323 4.2 26.8 0.4
CD A:ARG323 4.6 27.7 0.4
CG A:PRO238 4.7 24.6 1.0
CD A:PRO238 4.7 24.1 1.0
O A:ALA324 4.9 28.3 1.0

Cobalt binding site 4 out of 7 in 3m5a

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Cobalt binding site 4 out of 7 in the SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co4

b:0.5
occ:1.00
 N A:THR175 3.7 24.7 1.0
CA A:SER174 3.9 24.3 1.0
OG1 A:THR175 4.1 32.2 1.0
C A:SER174 4.3 24.8 1.0
CB A:SER174 4.3 25.2 1.0
O A:THR175 4.4 27.9 1.0
NH2 A:ARG152 4.6 42.5 1.0
CA A:THR175 4.7 26.5 1.0
NH1 A:ARG152 4.8 42.7 1.0
CB A:THR175 4.8 26.6 1.0
CG2 A:THR175 5.0 27.0 1.0
O A:MET173 5.0 23.6 1.0

Cobalt binding site 5 out of 7 in 3m5a

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Cobalt binding site 5 out of 7 in the SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co5

b:0.3
occ:1.00
 N A:TRP260 3.7 37.2 1.0
CD1 A:TRP260 3.8 38.7 1.0
NZ B:LYS187 4.0 38.5 1.0
CA A:ASP259 4.2 37.7 1.0
CB A:TRP260 4.3 37.1 1.0
CG A:TRP260 4.5 38.2 1.0
C A:ASP259 4.5 37.7 1.0
CB A:ASP259 4.6 37.9 1.0
CA A:TRP260 4.7 37.1 1.0
NE1 A:TRP260 4.9 39.1 1.0
CE B:LYS187 5.0 37.3 1.0

Cobalt binding site 6 out of 7 in 3m5a

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Cobalt binding site 6 out of 7 in the SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co7

b:64.3
occ:1.00
 O A:HOH60 3.5 34.2 1.0
OG A:SER285 3.7 31.2 1.0
ND1 A:HIS283 3.8 35.7 1.0
CB A:HIS283 4.1 29.0 1.0
N A:SER285 4.1 28.7 1.0
CB A:SER285 4.2 29.5 1.0
N A:VAL284 4.3 27.8 1.0
CG A:HIS283 4.4 32.0 1.0
CA A:HIS283 4.5 28.6 1.0
C A:HIS283 4.7 27.5 1.0
CA A:SER285 4.8 29.3 1.0
CE1 A:HIS283 4.9 37.2 1.0

Cobalt binding site 7 out of 7 in 3m5a

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Cobalt binding site 7 out of 7 in the SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of SET7/9 Y245A in Complex with TAF10-K189ME3 Peptide and Adohcy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co8

b:56.6
occ:1.00
 NE2 A:HIS283 2.1 37.1 1.0
CE1 A:HIS283 2.8 37.2 1.0
CD2 A:HIS283 3.3 34.9 1.0
ND1 A:HIS283 4.0 35.7 1.0
CG A:HIS283 4.3 32.0 1.0
ND2 A:ASN282 4.5 37.9 1.0
OD1 A:ASN282 4.9 34.6 1.0

Reference:

P.A.Del Rizzo, J.F.Couture, L.M.Dirk, B.S.Strunk, M.S.Roiko, J.S.Brunzelle, R.L.Houtz, R.C.Trievel. SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation. J.Biol.Chem. V. 285 31849 2010.
ISSN: ISSN 0021-9258
PubMed: 20675860
DOI: 10.1074/JBC.M110.114587
Page generated: Tue Jul 30 16:18:50 2024

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