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Manganese in PDB 1a9x: Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis

Protein crystallography data

The structure of Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis, PDB code: 1a9x was solved by J.Thoden, H.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 152.100, 164.400, 332.300, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / n/a

Other elements in 1a9x:

The structure of Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis also contains other interesting chemical elements:

Potassium (K) 32 atoms
Chlorine (Cl) 28 atoms

Manganese Binding Sites:

Pages:

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

Binding sites:

The binding sites of Manganese atom in the Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis (pdb code 1a9x). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis, PDB code: 1a9x:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 1a9x

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Manganese binding site 1 out of 12 in the Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1901

b:24.4
occ:1.00
O1 A:PO41906 2.1 20.2 1.0
OD1 A:ASN301 2.1 16.8 1.0
O3B A:ADP1900 2.2 18.4 1.0
O A:HOH2674 2.2 25.8 1.0
OE1 A:GLU299 2.4 21.7 1.0
OE2 A:GLU299 2.4 16.0 1.0
CD A:GLU299 2.7 31.9 1.0
CG A:ASN301 3.0 42.0 1.0
ND2 A:ASN301 3.3 15.5 1.0
P A:PO41906 3.4 29.5 1.0
PB A:ADP1900 3.4 20.8 1.0
O1B A:ADP1900 3.5 17.8 1.0
O2 A:PO41906 3.6 18.7 1.0
K A:K1904 3.8 28.1 1.0
MN A:MN1902 3.8 20.8 1.0
CB A:MET174 3.8 16.3 1.0
O3 A:PO41906 4.1 19.5 1.0
O A:HOH2128 4.2 21.9 1.0
NH2 A:ARG303 4.2 15.6 1.0
CG A:GLU299 4.2 19.2 1.0
CA A:MET174 4.3 20.5 1.0
O4 A:PO41906 4.3 17.4 1.0
O A:THR173 4.4 25.8 1.0
O3A A:ADP1900 4.4 23.0 1.0
CB A:ASN301 4.5 20.2 1.0
O2B A:ADP1900 4.5 16.9 1.0
NH2 A:ARG129 4.6 23.4 1.0
O1A A:ADP1900 4.6 16.5 1.0
NH1 A:ARG129 4.7 34.5 1.0
OE1 A:GLN285 4.8 30.5 1.0
OE2 A:GLU127 4.9 27.3 1.0
O A:MET300 4.9 18.0 1.0
O A:HOH2085 5.0 36.1 1.0

Manganese binding site 2 out of 12 in 1a9x

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Manganese binding site 2 out of 12 in the Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1902

b:20.8
occ:1.00
O1A A:ADP1900 2.0 16.5 1.0
OE1 A:GLN285 2.1 30.5 1.0
O2 A:PO41906 2.1 18.7 1.0
O1B A:ADP1900 2.2 17.8 1.0
OE2 A:GLU299 2.2 16.0 1.0
CD A:GLN285 3.1 53.0 1.0
PB A:ADP1900 3.2 20.8 1.0
P A:PO41906 3.3 29.5 1.0
PA A:ADP1900 3.3 23.0 1.0
CD A:GLU299 3.4 31.9 1.0
NE2 A:GLN285 3.4 21.8 1.0
O3A A:ADP1900 3.6 23.0 1.0
O3B A:ADP1900 3.6 18.4 1.0
O1 A:PO41906 3.6 20.2 1.0
O3 A:PO41906 3.7 19.5 1.0
MN A:MN1901 3.8 24.4 1.0
NE2 A:HIS243 3.8 19.0 1.0
K A:K1942 4.0 35.6 1.0
CG A:GLU299 4.0 19.2 1.0
ND2 A:ASN301 4.2 15.5 1.0
CE1 A:HIS243 4.3 16.2 1.0
OE1 A:GLU299 4.3 21.7 1.0
O2A A:ADP1900 4.3 23.6 1.0
O5' A:ADP1900 4.3 17.9 1.0
C5' A:ADP1900 4.3 20.9 1.0
O4 A:PO41906 4.5 17.4 1.0
O3' A:ADP1900 4.5 22.8 1.0
CG A:GLN285 4.5 22.0 1.0
O2B A:ADP1900 4.5 16.9 1.0
OG1 A:THR244 4.6 24.4 1.0
CD2 A:HIS243 4.7 13.8 1.0
OD1 A:ASN301 5.0 16.8 1.0

Manganese binding site 3 out of 12 in 1a9x

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Manganese binding site 3 out of 12 in the Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1911

b:34.4
occ:1.00
OE2 A:GLU841 2.0 37.9 1.0
O2A A:ADP1910 2.1 30.6 1.0
O3B A:ADP1910 2.2 26.2 1.0
OE1 A:GLN829 2.4 25.0 1.0
CD A:GLU841 3.2 23.5 1.0
PB A:ADP1910 3.3 28.5 1.0
CD A:GLN829 3.3 46.3 1.0
PA A:ADP1910 3.4 29.1 1.0
O3A A:ADP1910 3.7 37.0 1.0
NE2 A:GLN829 3.8 43.4 1.0
O A:HOH2561 3.8 36.5 1.0
O2B A:ADP1910 3.9 33.8 1.0
K A:K1912 3.9 43.1 1.0
CG A:GLU841 4.0 32.6 1.0
OE1 A:GLU841 4.0 47.8 1.0
C5' A:ADP1910 4.2 20.9 1.0
O5' A:ADP1910 4.3 20.9 1.0
O3' A:ADP1910 4.3 21.4 1.0
O1A A:ADP1910 4.4 50.3 1.0
NE2 A:HIS788 4.4 23.7 1.0
ND2 A:ASN843 4.5 38.2 1.0
OG A:SER789 4.5 28.9 1.0
O1B A:ADP1910 4.5 49.1 1.0
CE1 A:HIS788 4.6 19.9 1.0
CG A:GLN829 4.6 18.0 1.0
C3' A:ADP1910 4.9 25.3 1.0

Manganese binding site 4 out of 12 in 1a9x

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Manganese binding site 4 out of 12 in the Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn3901

b:19.6
occ:1.00
O3B C:ADP3900 2.1 15.1 1.0
O1 C:PO43906 2.2 27.5 1.0
O C:HOH4447 2.2 21.1 1.0
OE1 C:GLU2299 2.2 15.8 1.0
OD1 C:ASN2301 2.2 12.5 1.0
OE2 C:GLU2299 2.5 15.1 1.0
CD C:GLU2299 2.6 41.5 1.0
CG C:ASN2301 3.2 23.2 1.0
PB C:ADP3900 3.3 18.1 1.0
P C:PO43906 3.4 20.5 1.0
O1B C:ADP3900 3.5 20.1 1.0
O2 C:PO43906 3.5 9.4 1.0
ND2 C:ASN2301 3.6 13.8 1.0
K C:K3904 3.7 21.3 1.0
MN C:MN3902 3.8 18.4 1.0
CB C:MET2174 3.8 23.3 1.0
NH2 C:ARG2303 4.1 15.8 1.0
CG C:GLU2299 4.1 9.7 1.0
O C:HOH4126 4.1 17.8 1.0
O4 C:PO43906 4.2 15.1 1.0
O C:THR2173 4.3 19.6 1.0
O3A C:ADP3900 4.3 16.3 1.0
NH2 C:ARG2129 4.3 18.6 1.0
O3 C:PO43906 4.3 13.8 1.0
O2B C:ADP3900 4.4 14.1 1.0
CA C:MET2174 4.4 27.6 1.0
CB C:ASN2301 4.5 6.5 1.0
O1A C:ADP3900 4.5 15.3 1.0
O C:HOH4083 4.7 23.0 1.0
OE1 C:GLN2285 4.8 17.2 1.0
PA C:ADP3900 4.9 17.9 1.0
CB C:GLU2299 5.0 12.3 1.0
NH1 C:ARG2129 5.0 16.0 1.0
OE2 C:GLU2127 5.0 27.4 1.0

Manganese binding site 5 out of 12 in 1a9x

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Manganese binding site 5 out of 12 in the Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn3902

b:18.4
occ:1.00
O1A C:ADP3900 2.0 15.3 1.0
O2 C:PO43906 2.1 9.4 1.0
OE1 C:GLN2285 2.2 17.2 1.0
O C:HOH4661 2.2 23.9 1.0
OE2 C:GLU2299 2.3 15.1 1.0
O1B C:ADP3900 2.4 20.1 1.0
CD C:GLN2285 3.1 24.7 1.0
NE2 C:GLN2285 3.2 22.6 1.0
PB C:ADP3900 3.3 18.1 1.0
PA C:ADP3900 3.4 17.9 1.0
P C:PO43906 3.4 20.5 1.0
CD C:GLU2299 3.4 41.5 1.0
O3A C:ADP3900 3.6 16.3 1.0
O3B C:ADP3900 3.7 15.1 1.0
O1 C:PO43906 3.8 27.5 1.0
MN C:MN3901 3.8 19.6 1.0
K C:K3942 3.8 46.0 1.0
O3 C:PO43906 3.9 13.8 1.0
NE2 C:HIS2243 3.9 14.0 1.0
CG C:GLU2299 3.9 9.7 1.0
OE1 C:GLU2299 4.2 15.8 1.0
O2A C:ADP3900 4.3 19.2 1.0
CE1 C:HIS2243 4.3 16.4 1.0
O5' C:ADP3900 4.3 21.5 1.0
ND2 C:ASN2301 4.4 13.8 1.0
O3' C:ADP3900 4.4 15.3 1.0
C5' C:ADP3900 4.4 14.9 1.0
OG1 C:THR2244 4.4 16.9 1.0
O4 C:PO43906 4.5 15.1 1.0
CG C:GLN2285 4.5 20.7 1.0
O2B C:ADP3900 4.6 14.1 1.0
CD2 C:HIS2243 4.8 13.0 1.0

Manganese binding site 6 out of 12 in 1a9x

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Manganese binding site 6 out of 12 in the Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn3911

b:40.4
occ:1.00
OE2 C:GLU2841 1.9 46.2 1.0
O3B C:ADP3910 2.1 37.1 1.0
O2A C:ADP3910 2.2 34.2 1.0
OE1 C:GLN2829 2.4 0.0 1.0
O C:HOH4825 2.4 33.1 1.0
NE2 C:GLN2829 2.8 0.0 1.0
CD C:GLN2829 2.9 39.7 1.0
CD C:GLU2841 3.1 46.6 1.0
PB C:ADP3910 3.4 38.1 1.0
PA C:ADP3910 3.4 40.4 1.0
O3A C:ADP3910 3.7 44.5 1.0
OE1 C:GLU2841 3.7 40.4 1.0
CG C:GLU2841 4.0 56.3 1.0
K C:K3912 4.1 50.2 1.0
O2B C:ADP3910 4.2 62.0 1.0
O C:HOH4556 4.2 34.5 1.0
C5' C:ADP3910 4.3 20.3 1.0
O3' C:ADP3910 4.4 27.6 1.0
O5' C:ADP3910 4.4 35.2 1.0
NE2 C:HIS2788 4.4 25.7 1.0
O1B C:ADP3910 4.4 54.5 1.0
CG C:GLN2829 4.4 49.1 1.0
O1A C:ADP3910 4.4 60.4 1.0
ND2 C:ASN2843 4.5 48.3 1.0
OG C:SER2789 4.6 38.4 1.0
CE1 C:HIS2788 4.7 27.1 1.0
C3' C:ADP3910 4.9 17.1 1.0

Manganese binding site 7 out of 12 in 1a9x

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Manganese binding site 7 out of 12 in the Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn5901

b:28.4
occ:1.00
O1 E:PO45906 1.9 23.6 1.0
OD1 E:ASN4301 2.1 27.7 1.0
O E:HOH6698 2.2 32.4 1.0
O3B E:ADP5900 2.2 26.8 1.0
OE1 E:GLU4299 2.4 21.6 1.0
OE2 E:GLU4299 2.4 21.2 1.0
CD E:GLU4299 2.7 11.9 1.0
CG E:ASN4301 3.1 13.6 1.0
P E:PO45906 3.2 28.7 1.0
PB E:ADP5900 3.3 22.3 1.0
O1B E:ADP5900 3.4 19.8 1.0
ND2 E:ASN4301 3.5 22.4 1.0
O2 E:PO45906 3.5 22.8 1.0
MN E:MN5902 3.7 24.2 1.0
K E:K5904 3.8 26.1 1.0
CB E:MET4174 3.9 16.8 1.0
NH2 E:ARG4303 4.0 19.0 1.0
O4 E:PO45906 4.1 19.4 1.0
O3 E:PO45906 4.1 23.3 1.0
NH2 E:ARG4129 4.2 18.6 1.0
O3A E:ADP5900 4.2 20.2 1.0
CG E:GLU4299 4.2 8.3 1.0
O2B E:ADP5900 4.3 22.4 1.0
CA E:MET4174 4.3 29.5 1.0
O E:HOH6132 4.4 26.1 1.0
O E:THR4173 4.4 29.8 1.0
CB E:ASN4301 4.5 25.2 1.0
O1A E:ADP5900 4.6 18.1 1.0
OE1 E:GLN4285 4.7 21.7 1.0
N E:GLY4175 4.9 29.6 1.0
O E:MET4300 4.9 20.8 1.0
OE2 E:GLU4127 4.9 27.9 1.0
PA E:ADP5900 4.9 21.8 1.0

Manganese binding site 8 out of 12 in 1a9x

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Manganese binding site 8 out of 12 in the Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn5902

b:24.2
occ:1.00
O1A E:ADP5900 2.1 18.1 1.0
O1B E:ADP5900 2.1 19.8 1.0
O2 E:PO45906 2.1 22.8 1.0
OE2 E:GLU4299 2.2 21.2 1.0
OE1 E:GLN4285 2.2 21.7 1.0
O E:HOH6707 2.2 31.0 1.0
CD E:GLN4285 3.0 31.1 1.0
PB E:ADP5900 3.2 22.3 1.0
NE2 E:GLN4285 3.3 21.3 1.0
CD E:GLU4299 3.3 11.9 1.0
P E:PO45906 3.3 28.7 1.0
PA E:ADP5900 3.3 21.8 1.0
O3A E:ADP5900 3.5 20.2 1.0
O1 E:PO45906 3.6 23.6 1.0
O3B E:ADP5900 3.6 26.8 1.0
MN E:MN5901 3.7 28.4 1.0
K E:K5942 3.7 41.9 1.0
O3 E:PO45906 3.9 23.3 1.0
CG E:GLU4299 3.9 8.3 1.0
NE2 E:HIS4243 4.0 27.1 1.0
OE1 E:GLU4299 4.2 21.6 1.0
CE1 E:HIS4243 4.2 26.3 1.0
C5' E:ADP5900 4.3 17.5 1.0
O5' E:ADP5900 4.3 25.7 1.0
ND2 E:ASN4301 4.4 22.4 1.0
O2A E:ADP5900 4.4 17.7 1.0
OG1 E:THR4244 4.4 20.6 1.0
O3' E:ADP5900 4.4 18.1 1.0
CG E:GLN4285 4.4 16.8 1.0
O4 E:PO45906 4.5 19.4 1.0
O2B E:ADP5900 4.5 22.4 1.0
OD1 E:ASN4301 4.9 27.7 1.0
CD2 E:HIS4243 4.9 30.5 1.0
C3' E:ADP5900 5.0 11.9 1.0

Manganese binding site 9 out of 12 in 1a9x

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Manganese binding site 9 out of 12 in the Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn5911

b:38.7
occ:1.00
OE2 E:GLU4841 1.9 31.5 1.0
O2A E:ADP5910 2.1 67.0 1.0
O3B E:ADP5910 2.2 34.7 1.0
OE1 E:GLN4829 2.3 31.5 1.0
CD E:GLU4841 3.0 48.1 1.0
PA E:ADP5910 3.2 34.5 1.0
CD E:GLN4829 3.3 68.0 1.0
PB E:ADP5910 3.4 30.0 1.0
O3A E:ADP5910 3.5 26.6 1.0
NE2 E:GLN4829 3.6 57.5 1.0
CG E:GLU4841 3.6 26.6 1.0
OE1 E:GLU4841 4.0 30.7 1.0
O E:HOH6569 4.1 34.1 1.0
O1A E:ADP5910 4.2 61.0 1.0
O2B E:ADP5910 4.2 56.5 1.0
O3' E:ADP5910 4.2 31.2 1.0
K E:K5912 4.3 49.2 1.0
O5' E:ADP5910 4.3 28.0 1.0
C5' E:ADP5910 4.3 15.6 1.0
OG E:SER4789 4.4 48.6 1.0
ND2 E:ASN4843 4.4 29.0 1.0
NE2 E:HIS4788 4.5 31.1 1.0
O1B E:ADP5910 4.5 29.5 1.0
O E:HOH6824 4.6 52.1 1.0
CG E:GLN4829 4.7 29.6 1.0
CE1 E:HIS4788 4.7 18.0 1.0
C3' E:ADP5910 4.8 27.1 1.0
CB E:GLU4841 5.0 21.2 1.0

Manganese binding site 10 out of 12 in 1a9x

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Manganese binding site 10 out of 12 in the Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn7901

b:26.6
occ:1.00
O1 G:PO47906 1.8 21.6 1.0
OD1 G:ASN6301 2.2 30.7 1.0
OE1 G:GLU6299 2.3 18.6 1.0
OE2 G:GLU6299 2.4 21.1 1.0
O3B G:ADP7900 2.4 22.7 1.0
O G:HOH851 2.5 31.0 1.0
CD G:GLU6299 2.7 19.4 1.0
P G:PO47906 3.2 38.1 1.0
CG G:ASN6301 3.2 29.9 1.0
O1B G:ADP7900 3.3 10.9 1.0
PB G:ADP7900 3.4 21.2 1.0
CB G:MET6174 3.5 18.4 1.0
ND2 G:ASN6301 3.6 29.4 1.0
O2 G:PO47906 3.6 23.9 1.0
MN G:MN7902 3.7 22.3 1.0
K G:K7904 3.8 29.7 1.0
CA G:MET6174 4.0 35.5 1.0
O4 G:PO47906 4.1 23.4 1.0
NH2 G:ARG6129 4.1 23.4 1.0
O3 G:PO47906 4.1 23.1 1.0
O G:HOH147 4.1 27.6 1.0
CG G:GLU6299 4.2 4.2 1.0
NH2 G:ARG6303 4.2 20.0 1.0
O G:THR6173 4.2 54.5 1.0
O2B G:ADP7900 4.3 21.8 1.0
O3A G:ADP7900 4.4 26.5 1.0
O1A G:ADP7900 4.6 22.4 1.0
CB G:ASN6301 4.6 15.8 1.0
O G:HOH100 4.8 41.0 1.0
N G:GLY6175 4.9 21.4 1.0
PA G:ADP7900 4.9 21.2 1.0
CG G:MET6174 4.9 33.7 1.0
NH1 G:ARG6129 4.9 24.3 1.0
CZ G:ARG6129 5.0 59.3 1.0
OE1 G:GLN6285 5.0 24.3 1.0
C G:MET6174 5.0 40.4 1.0
N G:MET6174 5.0 23.3 1.0

Reference:

J.B.Thoden, S.G.Miran, J.C.Phillips, A.J.Howard, F.M.Raushel, H.M.Holden. Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis. Biochemistry V. 37 8825 1998.
ISSN: ISSN 0006-2960
PubMed: 9636022
DOI: 10.1021/BI9807761
Page generated: Tue Dec 15 03:46:10 2020

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