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Manganese in PDB 1woi: Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily

Enzymatic activity of Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily

All present enzymatic activity of Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily:
3.5.3.11;

Protein crystallography data

The structure of Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily, PDB code: 1woi was solved by H.J.Ahn, K.H.Kim, J.Lee, J.-Y.Ha, H.H.Lee, D.Kim, H.-J.Yoon, A.-R.Kwon, S.W.Suh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.99 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.764, 130.759, 168.746, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 24.1

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily (pdb code 1woi). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily, PDB code: 1woi:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 1woi

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Manganese binding site 1 out of 12 in the Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1501

b:28.2
occ:1.00
 ND1 A:HIS121 2.0 13.2 1.0
OD2 A:ASP147 2.1 22.5 1.0
OD2 A:ASP143 2.1 14.9 1.0
OD2 A:ASP229 2.2 11.7 1.0
O A:HOH1636 2.4 25.6 1.0
CE1 A:HIS121 2.9 11.5 1.0
CG A:ASP143 2.9 15.1 1.0
MN A:MN1502 3.0 21.5 1.0
OD1 A:ASP143 3.1 12.1 1.0
CG A:HIS121 3.1 13.4 1.0
CG A:ASP147 3.2 17.8 1.0
CG A:ASP229 3.3 11.3 1.0
CB A:HIS121 3.6 13.1 1.0
CB A:ASP229 3.7 9.6 1.0
OD1 A:ASP147 3.8 19.4 1.0
NE2 A:HIS121 4.0 14.0 1.0
CD2 A:HIS121 4.2 12.5 1.0
CB A:ASP143 4.3 12.1 1.0
OD1 A:ASP229 4.4 13.7 1.0
CB A:ASP147 4.4 15.6 1.0
O A:HIS145 4.7 12.1 1.0
ND1 A:HIS145 4.7 12.8 1.0
CG A:GLU274 4.7 12.8 1.0
NE2 A:GLN141 4.8 10.5 1.0
OD2 A:ASP231 4.8 15.2 1.0
CB A:HIS145 4.8 13.0 1.0
OD1 A:ASP231 4.9 9.7 1.0
O A:ASN159 4.9 10.8 1.0

Manganese binding site 2 out of 12 in 1woi

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Manganese binding site 2 out of 12 in the Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1502

b:21.5
occ:1.00
 OD2 A:ASP231 2.2 15.2 1.0
OD1 A:ASP143 2.3 12.1 1.0
ND1 A:HIS145 2.3 12.8 1.0
OD2 A:ASP229 2.3 11.7 1.0
OD1 A:ASP231 2.4 9.7 1.0
O A:HOH1636 2.6 25.6 1.0
CG A:ASP231 2.6 13.3 1.0
MN A:MN1501 3.0 28.2 1.0
CG A:ASP229 3.1 11.3 1.0
CE1 A:HIS145 3.1 16.8 1.0
CG A:ASP143 3.3 15.1 1.0
CG A:HIS145 3.4 14.3 1.0
OD1 A:ASP229 3.5 13.7 1.0
OD2 A:ASP143 3.6 14.9 1.0
CB A:HIS145 3.8 13.0 1.0
N A:HIS145 3.9 11.0 1.0
N A:ALA144 4.1 10.8 1.0
CB A:ASP229 4.1 9.6 1.0
CB A:ASP231 4.2 11.0 1.0
NE2 A:HIS145 4.3 15.5 1.0
OD2 A:ASP147 4.4 22.5 1.0
CA A:HIS145 4.4 12.3 1.0
CD2 A:HIS145 4.5 13.6 1.0
CB A:ASP143 4.6 12.1 1.0
O A:HOH1520 4.7 12.0 1.0
CB A:ALA144 4.7 10.1 1.0
C A:ALA144 4.8 10.1 1.0
CA A:ALA144 4.8 11.1 1.0
CA A:ASP143 4.8 11.3 1.0
ND1 A:HIS121 4.9 13.2 1.0
C A:ASP143 4.9 10.8 1.0
OD1 A:ASP147 5.0 19.4 1.0
CG A:GLU274 5.0 12.8 1.0

Manganese binding site 3 out of 12 in 1woi

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Manganese binding site 3 out of 12 in the Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1503

b:42.2
occ:1.00
 OD2 B:ASP147 2.1 25.1 1.0
ND1 B:HIS121 2.1 18.1 1.0
OD2 B:ASP229 2.1 14.6 1.0
OD2 B:ASP143 2.3 19.5 1.0
O B:HOH1601 2.6 31.4 1.0
MN B:MN1504 2.9 35.4 1.0
CE1 B:HIS121 3.0 15.8 1.0
CG B:ASP143 3.1 16.7 1.0
OD1 B:ASP143 3.2 16.9 1.0
CG B:HIS121 3.2 17.3 1.0
CG B:ASP147 3.2 20.1 1.0
CG B:ASP229 3.2 17.2 1.0
CB B:HIS121 3.6 16.8 1.0
CB B:ASP229 3.7 16.2 1.0
OD1 B:ASP147 3.8 22.4 1.0
NE2 B:HIS121 4.1 18.9 1.0
CD2 B:HIS121 4.2 15.7 1.0
OD1 B:ASP229 4.3 16.6 1.0
CB B:ASP147 4.4 18.3 1.0
CB B:ASP143 4.5 16.0 1.0
CG B:GLU274 4.6 15.8 1.0
O B:ASN159 4.7 14.7 1.0
OD2 B:ASP231 4.8 19.1 1.0
NE2 B:GLN141 4.8 20.6 1.0
O B:HIS145 4.8 16.8 1.0
CB B:HIS145 4.9 20.5 1.0
ND1 B:HIS145 4.9 24.7 1.0
O B:HOH1581 4.9 32.3 1.0
OD1 B:ASP231 5.0 17.8 1.0

Manganese binding site 4 out of 12 in 1woi

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Manganese binding site 4 out of 12 in the Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1504

b:35.4
occ:1.00
 OD2 B:ASP231 2.3 19.1 1.0
OD1 B:ASP143 2.4 16.9 1.0
OD2 B:ASP229 2.4 14.6 1.0
OD1 B:ASP231 2.5 17.8 1.0
ND1 B:HIS145 2.6 24.7 1.0
CG B:ASP231 2.7 16.0 1.0
O B:HOH1601 2.9 31.4 1.0
MN B:MN1503 2.9 42.2 1.0
CG B:ASP229 3.1 17.2 1.0
CG B:ASP143 3.4 16.7 1.0
CE1 B:HIS145 3.5 24.7 1.0
OD1 B:ASP229 3.5 16.6 1.0
CG B:HIS145 3.6 23.4 1.0
OD2 B:ASP143 3.7 19.5 1.0
CB B:HIS145 3.9 20.5 1.0
N B:HIS145 4.0 14.8 1.0
CB B:ASP229 4.1 16.2 1.0
N B:ALA144 4.2 14.8 1.0
CB B:ASP231 4.2 14.1 1.0
OD2 B:ASP147 4.2 25.1 1.0
CA B:HIS145 4.6 17.1 1.0
NE2 B:HIS145 4.6 24.1 1.0
CB B:ASP143 4.7 16.0 1.0
CD2 B:HIS145 4.7 22.6 1.0
O B:HOH1521 4.8 18.1 1.0
ND1 B:HIS121 4.8 18.1 1.0
CB B:ALA144 4.8 14.7 1.0
C B:ALA144 4.9 14.2 1.0
CA B:ASP143 4.9 15.8 1.0
CG B:GLU274 4.9 15.8 1.0
CA B:ALA144 4.9 13.2 1.0

Manganese binding site 5 out of 12 in 1woi

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Manganese binding site 5 out of 12 in the Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1505

b:36.2
occ:1.00
 ND1 C:HIS121 2.0 15.9 1.0
OD2 C:ASP229 2.1 14.6 1.0
OD2 C:ASP147 2.1 22.4 1.0
OD2 C:ASP143 2.2 18.0 1.0
O C:HOH1630 2.6 31.4 1.0
CE1 C:HIS121 2.9 12.8 1.0
MN C:MN1506 2.9 32.6 1.0
CG C:ASP143 3.0 15.6 1.0
OD1 C:ASP143 3.1 15.1 1.0
CG C:HIS121 3.1 12.2 1.0
CG C:ASP229 3.2 12.5 1.0
CG C:ASP147 3.3 20.8 1.0
CB C:HIS121 3.6 11.7 1.0
CB C:ASP229 3.6 14.1 1.0
OD1 C:ASP147 3.8 24.1 1.0
NE2 C:HIS121 4.0 15.8 1.0
CD2 C:HIS121 4.2 12.8 1.0
OD1 C:ASP229 4.3 13.8 1.0
CB C:ASP143 4.4 13.9 1.0
CB C:ASP147 4.5 18.3 1.0
CG C:GLU274 4.7 13.4 1.0
O C:HIS145 4.7 15.5 1.0
NE2 C:GLN141 4.7 21.2 1.0
OD2 C:ASP231 4.9 16.8 1.0
ND1 C:HIS145 4.9 25.5 1.0
OD1 C:ASP231 4.9 11.4 1.0
O C:HOH1611 4.9 33.8 1.0

Manganese binding site 6 out of 12 in 1woi

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Manganese binding site 6 out of 12 in the Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1506

b:32.6
occ:1.00
 OD2 C:ASP229 2.2 14.6 1.0
OD1 C:ASP143 2.3 15.1 1.0
OD2 C:ASP231 2.3 16.8 1.0
ND1 C:HIS145 2.5 25.5 1.0
OD1 C:ASP231 2.5 11.4 1.0
O C:HOH1630 2.7 31.4 1.0
CG C:ASP231 2.7 12.6 1.0
MN C:MN1505 2.9 36.2 1.0
CG C:ASP229 3.0 12.5 1.0
CG C:ASP143 3.2 15.6 1.0
CE1 C:HIS145 3.3 25.6 1.0
OD1 C:ASP229 3.5 13.8 1.0
CG C:HIS145 3.5 24.0 1.0
OD2 C:ASP143 3.6 18.0 1.0
CB C:HIS145 3.9 22.0 1.0
N C:HIS145 3.9 15.4 1.0
CB C:ASP229 4.0 14.1 1.0
N C:ALA144 4.1 14.7 1.0
OD2 C:ASP147 4.2 22.4 1.0
CB C:ASP231 4.3 12.1 1.0
NE2 C:HIS145 4.5 27.5 1.0
CA C:HIS145 4.5 17.5 1.0
CB C:ASP143 4.5 13.9 1.0
CD2 C:HIS145 4.6 26.3 1.0
CA C:ASP143 4.7 14.1 1.0
O C:HOH1517 4.8 12.5 1.0
ND1 C:HIS121 4.8 15.9 1.0
O C:HIS145 4.8 15.5 1.0
CB C:ALA144 4.8 15.4 1.0
C C:ALA144 4.9 15.9 1.0
OD1 C:ASP147 4.9 24.1 1.0
CA C:ALA144 4.9 14.3 1.0
C C:ASP143 4.9 14.1 1.0
CG C:GLU274 5.0 13.4 1.0
CG C:ASP147 5.0 20.8 1.0

Manganese binding site 7 out of 12 in 1woi

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Manganese binding site 7 out of 12 in the Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1507

b:42.7
occ:1.00
 ND1 D:HIS121 2.0 13.7 1.0
OD2 D:ASP147 2.1 25.8 1.0
OD2 D:ASP143 2.2 18.0 1.0
OD2 D:ASP229 2.2 15.3 1.0
O D:HOH1600 2.8 33.6 1.0
CE1 D:HIS121 2.9 13.2 1.0
CG D:ASP143 3.0 16.5 1.0
MN D:MN1508 3.1 28.9 1.0
OD1 D:ASP143 3.1 14.0 1.0
CG D:HIS121 3.1 13.8 1.0
CG D:ASP147 3.2 20.6 1.0
CG D:ASP229 3.3 15.7 1.0
CB D:HIS121 3.6 14.1 1.0
CB D:ASP229 3.7 14.9 1.0
OD1 D:ASP147 3.8 19.0 1.0
NE2 D:HIS121 4.0 13.4 1.0
CD2 D:HIS121 4.1 13.6 1.0
OD1 D:ASP229 4.4 12.9 1.0
CB D:ASP143 4.4 16.0 1.0
CB D:ASP147 4.4 18.7 1.0
O D:ASN159 4.7 14.8 1.0
NE2 D:GLN141 4.7 17.1 1.0
CG D:GLU274 4.7 14.8 1.0
O D:HIS145 4.8 17.6 1.0
OD2 D:ASP231 4.9 18.0 1.0
ND1 D:HIS145 4.9 26.0 1.0
OD1 D:ASP231 4.9 16.3 1.0

Manganese binding site 8 out of 12 in 1woi

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Manganese binding site 8 out of 12 in the Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1508

b:28.9
occ:1.00
 OD2 D:ASP231 2.2 18.0 1.0
OD2 D:ASP229 2.3 15.3 1.0
OD1 D:ASP143 2.3 14.0 1.0
ND1 D:HIS145 2.4 26.0 1.0
OD1 D:ASP231 2.5 16.3 1.0
CG D:ASP231 2.7 13.8 1.0
O D:HOH1600 3.1 33.6 1.0
CG D:ASP229 3.1 15.7 1.0
MN D:MN1507 3.1 42.7 1.0
CE1 D:HIS145 3.2 26.9 1.0
CG D:ASP143 3.3 16.5 1.0
CG D:HIS145 3.5 24.3 1.0
OD1 D:ASP229 3.5 12.9 1.0
OD2 D:ASP143 3.7 18.0 1.0
CB D:HIS145 3.9 20.8 1.0
N D:HIS145 4.0 15.8 1.0
CB D:ASP229 4.1 14.9 1.0
N D:ALA144 4.1 15.2 1.0
CB D:ASP231 4.2 12.9 1.0
OD2 D:ASP147 4.2 25.8 1.0
NE2 D:HIS145 4.4 25.8 1.0
CA D:HIS145 4.5 18.0 1.0
CD2 D:HIS145 4.6 25.1 1.0
CB D:ASP143 4.6 16.0 1.0
O D:HOH1524 4.7 15.5 1.0
CB D:ALA144 4.7 14.6 1.0
CA D:ASP143 4.8 16.3 1.0
C D:ALA144 4.8 16.2 1.0
CA D:ALA144 4.8 15.0 1.0
OD1 D:ASP147 4.9 19.0 1.0
ND1 D:HIS121 4.9 13.7 1.0
C D:ASP143 4.9 16.1 1.0

Manganese binding site 9 out of 12 in 1woi

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Manganese binding site 9 out of 12 in the Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn1509

b:73.8
occ:1.00
 OD2 E:ASP147 2.1 28.9 1.0
ND1 E:HIS121 2.1 17.1 1.0
OD2 E:ASP229 2.2 19.6 1.0
O E:HOH1616 2.4 27.7 1.0
OD2 E:ASP143 2.4 22.1 1.0
MN E:MN1510 3.0 37.5 1.0
CE1 E:HIS121 3.1 12.2 1.0
CG E:HIS121 3.1 16.2 1.0
CG E:ASP147 3.2 25.8 1.0
CG E:ASP143 3.2 20.3 1.0
OD1 E:ASP143 3.3 17.2 1.0
CG E:ASP229 3.4 19.6 1.0
CB E:HIS121 3.5 16.5 1.0
OD1 E:ASP147 3.7 26.3 1.0
CB E:ASP229 3.9 18.5 1.0
NE2 E:HIS121 4.2 17.2 1.0
CD2 E:HIS121 4.2 14.7 1.0
CB E:ASP147 4.3 22.1 1.0
OD1 E:ASP229 4.4 16.6 1.0
CB E:ASP143 4.6 17.2 1.0
O E:ASN159 4.6 16.5 1.0
CG E:GLU274 4.7 18.2 1.0
OD2 E:ASP231 4.8 21.9 1.0
NE2 E:GLN141 4.9 23.4 1.0
O E:HIS145 4.9 23.3 1.0
ND1 E:HIS145 5.0 33.0 1.0
CA E:HIS121 5.0 14.6 1.0

Manganese binding site 10 out of 12 in 1woi

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Manganese binding site 10 out of 12 in the Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn1510

b:37.5
occ:1.00
 OD2 E:ASP231 2.3 21.9 1.0
OD1 E:ASP143 2.4 17.2 1.0
OD2 E:ASP229 2.5 19.6 1.0
ND1 E:HIS145 2.5 33.0 1.0
O E:HOH1616 2.5 27.7 1.0
OD1 E:ASP231 2.6 19.1 1.0
CG E:ASP231 2.8 18.7 1.0
MN E:MN1509 3.0 73.8 1.0
CG E:ASP229 3.2 19.6 1.0
CE1 E:HIS145 3.3 34.3 1.0
CG E:ASP143 3.4 20.3 1.0
CG E:HIS145 3.5 31.1 1.0
OD1 E:ASP229 3.6 16.6 1.0
OD2 E:ASP143 3.7 22.1 1.0
CB E:HIS145 3.9 26.7 1.0
N E:HIS145 4.1 22.0 1.0
OD2 E:ASP147 4.1 28.9 1.0
CB E:ASP229 4.3 18.5 1.0
N E:ALA144 4.3 20.6 1.0
CB E:ASP231 4.3 18.4 1.0
NE2 E:HIS145 4.4 33.7 1.0
CD2 E:HIS145 4.5 32.0 1.0
CA E:HIS145 4.6 23.1 1.0
O E:HOH1582 4.7 20.0 1.0
CB E:ASP143 4.7 17.2 1.0
CB E:ALA144 4.8 20.5 1.0
OD1 E:ASP147 4.8 26.3 1.0
CG E:ASP147 4.9 25.8 1.0
C E:ALA144 4.9 21.3 1.0
ND1 E:HIS121 4.9 17.1 1.0
CA E:ALA144 4.9 20.6 1.0
CG E:GLU274 5.0 18.2 1.0

Reference:

H.J.Ahn, K.H.Kim, J.Lee, J.-Y.Ha, H.H.Lee, D.Kim, H.-J.Yoon, A.-R.Kwon, S.W.Suh. Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily J.Biol.Chem. V. 279 50505 2004.
ISSN: ISSN 0021-9258
PubMed: 15355972
DOI: 10.1074/JBC.M409246200
Page generated: Sat Oct 5 12:56:56 2024

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