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Cobalt in PDB 2g6p: Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with Pyridyl Pyrimidine Derivative

Enzymatic activity of Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with Pyridyl Pyrimidine Derivative

All present enzymatic activity of Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with Pyridyl Pyrimidine Derivative:
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with Pyridyl Pyrimidine Derivative, PDB code: 2g6p was solved by A.Addlagatta, X.Hu, J.O.Liu, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.386, 77.522, 47.720, 90.00, 90.82, 90.00
R / Rfree (%) 19.3 / 24.1

Other elements in 2g6p:

The structure of Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with Pyridyl Pyrimidine Derivative 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 Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with Pyridyl Pyrimidine Derivative (pdb code 2g6p). 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 Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with Pyridyl Pyrimidine Derivative, PDB code: 2g6p:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 2g6p

Go back to Cobalt Binding Sites List in 2g6p
Cobalt binding site 1 out of 3 in the Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with Pyridyl Pyrimidine Derivative


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 Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with Pyridyl Pyrimidine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co401

b:16.9
occ:1.00
 OE2 A:GLU367 1.9 15.3 1.0
O A:HOH624 2.0 2.7 1.0
OD2 A:ASP240 2.0 12.7 1.0
NE2 A:HIS303 2.2 20.3 1.0
OE1 A:GLU336 2.2 20.1 1.0
CD A:GLU367 2.9 14.1 1.0
CO A:CO402 3.0 17.7 1.0
CG A:ASP240 3.0 21.4 1.0
CD A:GLU336 3.1 24.7 1.0
CE1 A:HIS303 3.1 24.7 1.0
OE1 A:GLU367 3.1 16.9 1.0
CD2 A:HIS303 3.1 18.5 1.0
OE2 A:GLU336 3.4 21.4 1.0
OD1 A:ASP240 3.4 18.8 1.0
OG1 A:THR334 3.7 15.8 1.0
O A:HOH500 3.7 14.1 1.0
CG2 A:THR334 3.9 15.0 1.0
CB A:THR334 4.1 19.4 1.0
O A:HOH514 4.2 14.4 1.0
ND1 A:HIS303 4.2 15.2 1.0
CG A:HIS303 4.3 23.1 1.0
CG A:GLU367 4.3 12.4 1.0
CB A:ASP240 4.3 13.5 1.0
CG A:GLU336 4.5 13.1 1.0
NE2 A:HIS310 4.7 22.4 1.0
O A:HOH502 4.8 21.9 1.0
CD2 A:HIS310 4.9 21.5 1.0
CB A:GLU336 4.9 12.7 1.0

Cobalt binding site 2 out of 3 in 2g6p

Go back to Cobalt Binding Sites List in 2g6p
Cobalt binding site 2 out of 3 in the Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with Pyridyl Pyrimidine Derivative


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 Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with Pyridyl Pyrimidine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co402

b:17.7
occ:1.00
 OD1 A:ASP240 1.9 18.8 1.0
O A:HOH624 2.0 2.7 1.0
OE1 A:GLU367 2.1 16.9 1.0
OD1 A:ASP229 2.2 16.1 1.0
O A:HOH514 2.3 14.4 1.0
OD2 A:ASP229 2.6 20.2 1.0
CG A:ASP229 2.7 19.1 1.0
CG A:ASP240 2.8 21.4 1.0
OD2 A:ASP240 3.0 12.7 1.0
CD A:GLU367 3.0 14.1 1.0
CO A:CO401 3.0 16.9 1.0
OE2 A:GLU367 3.2 15.3 1.0
O A:HOH500 3.7 14.1 1.0
OG1 A:THR231 4.0 15.9 1.0
ND2 A:ASN242 4.0 16.9 1.0
O A:HOH501 4.1 14.2 1.0
OE2 A:GLU336 4.2 21.4 1.0
CB A:ASP229 4.2 17.9 1.0
CB A:ASP240 4.3 13.5 1.0
O A:HOH510 4.4 26.6 1.0
CG A:GLU367 4.4 12.4 1.0
OE1 A:GLU336 4.5 20.1 1.0
O A:ILE230 4.5 14.6 1.0
O A:LEU241 4.5 14.2 1.0
N A:LEU241 4.6 16.7 1.0
CD A:GLU336 4.6 24.7 1.0
O A:HOH502 4.7 21.9 1.0
O A:HOH507 4.7 18.3 1.0
C A:LEU241 4.8 15.0 1.0
C A:ASP240 4.8 22.2 1.0
CA A:ASP240 4.9 17.9 1.0
CB A:GLU367 5.0 13.3 1.0
CB A:ASN242 5.0 14.0 1.0
NE2 A:HIS303 5.0 20.3 1.0
CA A:ASP229 5.0 13.9 1.0

Cobalt binding site 3 out of 3 in 2g6p

Go back to Cobalt Binding Sites List in 2g6p
Cobalt binding site 3 out of 3 in the Crystal Structure of Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with Pyridyl Pyrimidine Derivative


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 Truncated (Delta 1-89) Human Methionine Aminopeptidase Type 1 in Complex with Pyridyl Pyrimidine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co403

b:20.8
occ:1.00
 N1 A:HM2410 2.1 24.1 1.0
NE2 A:HIS212 2.2 18.7 1.0
O A:HOH500 2.2 14.1 1.0
O A:HOH502 2.2 21.9 1.0
N3 A:HM2410 2.3 23.4 1.0
O A:HOH501 2.4 14.2 1.0
C5 A:HM2410 3.1 23.0 1.0
CD2 A:HIS212 3.1 18.2 1.0
C6 A:HM2410 3.2 15.4 1.0
CE1 A:HIS212 3.2 19.8 1.0
C1 A:HM2410 3.2 18.5 1.0
C8 A:HM2410 3.2 20.2 1.0
C18 A:HM2410 3.4 21.6 1.0
O A:HOH624 3.9 2.7 1.0
NE2 A:HIS310 4.1 22.4 1.0
ND1 A:HIS212 4.3 11.9 1.0
CG A:HIS212 4.3 19.7 1.0
O A:HOH514 4.3 14.4 1.0
C4 A:HM2410 4.4 23.2 1.0
O A:HOH507 4.4 18.3 1.0
N2 A:HM2410 4.5 30.3 1.0
C2 A:HM2410 4.5 18.1 1.0
OD2 A:ASP229 4.6 20.2 1.0
CE1 A:HIS310 4.6 23.6 1.0
C9 A:HM2410 4.6 25.9 1.0
OE2 A:GLU336 4.9 21.4 1.0
O A:HOH510 5.0 26.6 1.0
C3 A:HM2410 5.0 18.4 1.0

Reference:

X.Hu, A.Addlagatta, B.W.Matthews, J.O.Liu. Identification of Pyridinylpyrimidines As Inhibitors of Human Methionine Aminopeptidases. Angew.Chem.Int.Ed.Engl. V. 45 3772 2006.
ISSN: ISSN 1433-7851
PubMed: 16724298
DOI: 10.1002/ANIE.200600757
Page generated: Tue Jul 30 15:11:45 2024

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