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Cobalt in PDB 4ikr: Crystal Structure of Type 1 Human Methionine Aminopeptidase in Complex with 2-(4-(5-Chloro-6-Methyl-2-(Pyridin-2-Yl)Pyrimidin-4-Yl) Piperazin-1-Yl)Ethanol

Enzymatic activity of Crystal Structure of Type 1 Human Methionine Aminopeptidase in Complex with 2-(4-(5-Chloro-6-Methyl-2-(Pyridin-2-Yl)Pyrimidin-4-Yl) Piperazin-1-Yl)Ethanol

All present enzymatic activity of Crystal Structure of Type 1 Human Methionine Aminopeptidase in Complex with 2-(4-(5-Chloro-6-Methyl-2-(Pyridin-2-Yl)Pyrimidin-4-Yl) Piperazin-1-Yl)Ethanol:
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Type 1 Human Methionine Aminopeptidase in Complex with 2-(4-(5-Chloro-6-Methyl-2-(Pyridin-2-Yl)Pyrimidin-4-Yl) Piperazin-1-Yl)Ethanol, PDB code: 4ikr was solved by A.Addlagatta, C.Kishor, T.Arya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.39 / 1.78
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.345, 77.423, 48.023, 90.00, 91.03, 90.00
R / Rfree (%) 18 / 21.1

Other elements in 4ikr:

The structure of Crystal Structure of Type 1 Human Methionine Aminopeptidase in Complex with 2-(4-(5-Chloro-6-Methyl-2-(Pyridin-2-Yl)Pyrimidin-4-Yl) Piperazin-1-Yl)Ethanol also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Type 1 Human Methionine Aminopeptidase in Complex with 2-(4-(5-Chloro-6-Methyl-2-(Pyridin-2-Yl)Pyrimidin-4-Yl) Piperazin-1-Yl)Ethanol (pdb code 4ikr). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Crystal Structure of Type 1 Human Methionine Aminopeptidase in Complex with 2-(4-(5-Chloro-6-Methyl-2-(Pyridin-2-Yl)Pyrimidin-4-Yl) Piperazin-1-Yl)Ethanol, PDB code: 4ikr:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 4ikr

Go back to Cobalt Binding Sites List in 4ikr
Cobalt binding site 1 out of 3 in the Crystal Structure of Type 1 Human Methionine Aminopeptidase in Complex with 2-(4-(5-Chloro-6-Methyl-2-(Pyridin-2-Yl)Pyrimidin-4-Yl) Piperazin-1-Yl)Ethanol


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Type 1 Human Methionine Aminopeptidase in Complex with 2-(4-(5-Chloro-6-Methyl-2-(Pyridin-2-Yl)Pyrimidin-4-Yl) Piperazin-1-Yl)Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co401

b:15.4
occ:1.00
 O A:HOH587 1.9 16.2 1.0
OE2 A:GLU367 2.0 13.5 1.0
OD2 A:ASP240 2.1 15.0 1.0
NE2 A:HIS303 2.1 10.5 1.0
OE1 A:GLU336 2.2 17.1 1.0
CD A:GLU367 2.9 14.4 1.0
CG A:ASP240 3.0 14.8 1.0
CD A:GLU336 3.1 17.9 1.0
CO A:CO402 3.1 13.5 1.0
CD2 A:HIS303 3.1 12.9 1.0
CE1 A:HIS303 3.1 15.3 1.0
OE1 A:GLU367 3.2 16.3 1.0
OE2 A:GLU336 3.3 17.9 1.0
OD1 A:ASP240 3.3 12.8 1.0
OG1 A:THR334 3.7 16.0 1.0
O A:HOH585 3.7 13.9 1.0
CG2 A:THR334 3.9 16.9 1.0
CB A:THR334 4.1 16.1 1.0
O A:HOH546 4.2 14.6 1.0
ND1 A:HIS303 4.2 12.7 1.0
CG A:HIS303 4.2 15.2 1.0
CB A:ASP240 4.3 14.1 1.0
CG A:GLU367 4.3 14.0 1.0
CG A:GLU336 4.4 15.7 1.0
NE2 A:HIS310 4.6 15.6 1.0
O A:HOH586 4.8 18.1 1.0
CD2 A:HIS310 4.9 17.4 1.0
OD2 A:ASP229 4.9 14.8 1.0
CB A:GLU336 4.9 14.5 1.0

Cobalt binding site 2 out of 3 in 4ikr

Go back to Cobalt Binding Sites List in 4ikr
Cobalt binding site 2 out of 3 in the Crystal Structure of Type 1 Human Methionine Aminopeptidase in Complex with 2-(4-(5-Chloro-6-Methyl-2-(Pyridin-2-Yl)Pyrimidin-4-Yl) Piperazin-1-Yl)Ethanol


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Type 1 Human Methionine Aminopeptidase in Complex with 2-(4-(5-Chloro-6-Methyl-2-(Pyridin-2-Yl)Pyrimidin-4-Yl) Piperazin-1-Yl)Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co402

b:13.5
occ:1.00
 O A:HOH587 2.0 16.2 1.0
OD1 A:ASP240 2.0 12.8 1.0
OE1 A:GLU367 2.1 16.3 1.0
OD1 A:ASP229 2.1 11.4 1.0
O A:HOH546 2.2 14.6 1.0
OD2 A:ASP229 2.4 14.8 1.0
CG A:ASP229 2.6 12.9 1.0
CG A:ASP240 2.9 14.8 1.0
CD A:GLU367 3.0 14.4 1.0
CO A:CO401 3.1 15.4 1.0
OD2 A:ASP240 3.1 15.0 1.0
OE2 A:GLU367 3.3 13.5 1.0
O A:HOH585 3.8 13.9 1.0
OG1 A:THR231 3.9 13.9 1.0
ND2 A:ASN242 4.1 12.5 1.0
CB A:ASP229 4.1 12.7 1.0
O A:HOH588 4.1 13.7 1.0
OE2 A:GLU336 4.2 17.9 1.0
CB A:ASP240 4.4 14.1 1.0
CG A:GLU367 4.4 14.0 1.0
O A:HOH556 4.4 19.5 1.0
O A:LEU241 4.5 12.0 1.0
OE1 A:GLU336 4.6 17.1 1.0
O A:ILE230 4.6 12.2 1.0
O A:HOH518 4.6 13.8 1.0
O A:HOH586 4.6 18.1 1.0
N A:LEU241 4.6 13.5 1.0
CD A:GLU336 4.7 17.9 1.0
C A:LEU241 4.7 12.5 1.0
CA A:ASP229 4.8 12.8 1.0
C A:ASP240 4.8 14.1 1.0
CA A:ASP240 4.9 14.4 1.0
CB A:ASN242 4.9 12.7 1.0
N A:ILE230 4.9 11.0 1.0
CB A:GLU367 4.9 11.8 1.0
C A:ASP229 5.0 12.1 1.0
CA A:LEU241 5.0 12.7 1.0
CG A:ASN242 5.0 13.9 1.0
NE2 A:HIS303 5.0 10.5 1.0

Cobalt binding site 3 out of 3 in 4ikr

Go back to Cobalt Binding Sites List in 4ikr
Cobalt binding site 3 out of 3 in the Crystal Structure of Type 1 Human Methionine Aminopeptidase in Complex with 2-(4-(5-Chloro-6-Methyl-2-(Pyridin-2-Yl)Pyrimidin-4-Yl) Piperazin-1-Yl)Ethanol


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Type 1 Human Methionine Aminopeptidase in Complex with 2-(4-(5-Chloro-6-Methyl-2-(Pyridin-2-Yl)Pyrimidin-4-Yl) Piperazin-1-Yl)Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co403

b:17.4
occ:1.00
 N23 A:PVP404 2.2 15.6 1.0
O A:HOH585 2.2 13.9 1.0
N3 A:PVP404 2.2 16.7 1.0
NE2 A:HIS212 2.2 15.5 1.0
O A:HOH586 2.3 18.1 1.0
O A:HOH588 2.4 13.7 1.0
C5 A:PVP404 2.9 16.8 1.0
C6 A:PVP404 3.0 17.7 1.0
CD2 A:HIS212 3.1 15.8 1.0
C1 A:PVP404 3.1 13.9 1.0
C9 A:PVP404 3.2 21.1 1.0
CE1 A:HIS212 3.3 18.8 1.0
C16 A:PVP404 3.5 20.0 1.0
O A:HOH587 3.9 16.2 1.0
O A:HOH545 4.0 30.4 1.0
NE2 A:HIS310 4.0 15.6 1.0
O A:HOH546 4.2 14.6 1.0
C4 A:PVP404 4.2 14.4 1.0
N2 A:PVP404 4.3 21.1 1.0
CG A:HIS212 4.3 15.4 1.0
ND1 A:HIS212 4.3 16.7 1.0
CE1 A:HIS310 4.3 16.7 1.0
C2 A:PVP404 4.4 13.2 1.0
O A:HOH518 4.5 13.8 1.0
C8 A:PVP404 4.5 23.3 1.0
OD2 A:ASP229 4.7 14.8 1.0
C3 A:PVP404 4.9 12.6 1.0
O A:HOH556 4.9 19.5 1.0
C7 A:PVP404 4.9 23.6 1.0

Reference:

C.Kishor, T.Arya, R.Reddi, X.Chen, V.Saddanapu, A.K.Marapaka, R.Gumpena, D.Ma, J.O.Liu, A.Addlagatta. Identification, Biochemical and Structural Evaluation of Species-Specific Inhibitors Against Type I Methionine Aminopeptidases J.Med.Chem. V. 56 5295 2013.
ISSN: ISSN 0022-2623
PubMed: 23767698
DOI: 10.1021/JM400395P
Page generated: Tue Jul 30 17:10:51 2024

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