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Manganese in PDB 1m6v: Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase

Enzymatic activity of Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase

All present enzymatic activity of Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase:
6.3.5.5;

Protein crystallography data

The structure of Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase, PDB code: 1m6v was solved by J.B.Thoden, X.Huang, F.M.Raushel, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.500, 164.200, 331.500, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 24.5

Other elements in 1m6v:

The structure of Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase also contains other interesting chemical elements:

Potassium (K) 26 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 Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase (pdb code 1m6v). 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 the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase, PDB code: 1m6v:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 1m6v

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Manganese binding site 1 out of 12 in the Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn4002

b:21.7
occ:1.00
 O3B A:ADP4001 2.0 18.1 1.0
O1 A:PO44006 2.0 16.9 1.0
OD1 A:ASN301 2.1 24.9 1.0
O A:HOH4111 2.2 21.7 1.0
OE2 A:GLU299 2.2 21.5 1.0
OE1 A:GLU299 2.4 17.2 1.0
CD A:GLU299 2.6 25.1 1.0
CG A:ASN301 2.9 25.3 1.0
PB A:ADP4001 3.2 23.4 1.0
ND2 A:ASN301 3.2 17.2 1.0
P A:PO44006 3.2 30.3 1.0
O1B A:ADP4001 3.4 14.4 1.0
O3 A:PO44006 3.5 23.6 1.0
MN A:MN4003 3.7 21.8 1.0
K A:K4005 3.8 25.0 1.0
CB A:MET174 3.9 13.5 1.0
CG A:GLU299 4.0 15.2 1.0
O4 A:PO44006 4.1 22.3 1.0
O2B A:ADP4001 4.1 18.4 1.0
O2 A:PO44006 4.1 28.4 1.0
NH2 A:ARG129 4.1 41.7 1.0
O A:HOH4092 4.2 23.7 1.0
O3A A:ADP4001 4.2 21.7 1.0
NH2 A:ARG303 4.3 18.7 1.0
CB A:ASN301 4.4 24.9 1.0
O A:THR173 4.4 21.4 1.0
CA A:MET174 4.4 9.3 1.0
O1A A:ADP4001 4.5 18.3 1.0
OE1 A:GLN285 4.6 16.4 1.0
O A:HOH4112 4.8 50.9 1.0
PA A:ADP4001 4.8 23.7 1.0
CB A:GLU299 4.9 14.4 1.0
O A:MET300 4.9 24.7 1.0
OE1 A:GLU127 4.9 26.9 1.0
CZ A:ARG129 5.0 29.5 1.0
NH1 A:ARG129 5.0 14.3 1.0

Manganese binding site 2 out of 12 in 1m6v

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Manganese binding site 2 out of 12 in the Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn4003

b:21.8
occ:1.00
 OE1 A:GLN285 1.9 16.4 1.0
O1B A:ADP4001 2.0 14.4 1.0
O1A A:ADP4001 2.1 18.3 1.0
O3 A:PO44006 2.1 23.6 1.0
O A:HOH4537 2.2 22.0 1.0
OE2 A:GLU299 2.2 21.5 1.0
CD A:GLN285 2.9 19.2 1.0
PB A:ADP4001 3.1 23.4 1.0
P A:PO44006 3.2 30.3 1.0
PA A:ADP4001 3.3 23.7 1.0
NE2 A:GLN285 3.3 19.7 1.0
CD A:GLU299 3.3 25.1 1.0
O3A A:ADP4001 3.5 21.7 1.0
O4 A:PO44006 3.5 22.3 1.0
O3B A:ADP4001 3.6 18.1 1.0
O1 A:PO44006 3.6 16.9 1.0
MN A:MN4002 3.7 21.7 1.0
NE2 A:HIS243 3.7 20.9 1.0
O A:HOH4214 3.8 6.0 1.0
CG A:GLU299 3.9 15.2 1.0
CE1 A:HIS243 4.1 19.0 1.0
ND2 A:ASN301 4.2 17.2 1.0
C5' A:ADP4001 4.2 29.2 1.0
OE1 A:GLU299 4.2 17.2 1.0
O5' A:ADP4001 4.3 26.1 1.0
CG A:GLN285 4.3 24.9 1.0
OG1 A:THR244 4.4 17.8 1.0
O2A A:ADP4001 4.4 21.9 1.0
O2B A:ADP4001 4.4 18.4 1.0
O2 A:PO44006 4.4 28.4 1.0
O3' A:ADP4001 4.5 20.1 1.0
CD2 A:HIS243 4.6 17.6 1.0

Manganese binding site 3 out of 12 in 1m6v

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Manganese binding site 3 out of 12 in the Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn4008

b:28.4
occ:1.00
 O2A A:ADP4007 1.9 32.7 1.0
OE2 A:GLU841 2.2 36.6 1.0
OE1 A:GLN829 2.2 23.6 1.0
O3B A:ADP4007 2.2 25.9 1.0
O A:HOH4638 2.3 30.9 1.0
O A:HOH4590 2.4 24.0 1.0
CD A:GLU841 3.2 43.9 1.0
PA A:ADP4007 3.2 33.9 1.0
CD A:GLN829 3.2 56.2 1.0
PB A:ADP4007 3.4 28.4 1.0
O3A A:ADP4007 3.6 37.4 1.0
NE2 A:GLN829 3.6 34.8 1.0
CG A:GLU841 3.8 26.6 1.0
O A:HOH4432 3.8 27.4 1.0
O A:HOH4434 3.8 18.3 1.0
OE1 A:GLU841 4.0 40.6 1.0
K A:K4009 4.1 80.8 1.0
O1A A:ADP4007 4.1 77.0 1.0
O5' A:ADP4007 4.2 21.7 1.0
O2B A:ADP4007 4.2 47.5 1.0
C5' A:ADP4007 4.4 18.8 1.0
O3' A:ADP4007 4.4 27.3 1.0
OG A:SER789 4.4 33.8 1.0
ND2 A:ASN843 4.4 37.6 1.0
O1B A:ADP4007 4.5 48.3 1.0
NE2 A:HIS788 4.5 25.8 1.0
CG A:GLN829 4.5 20.0 1.0
CE1 A:HIS788 4.6 16.1 1.0
C3' A:ADP4007 4.8 17.0 1.0
CB A:GLN829 5.0 19.2 1.0
CB A:GLU841 5.0 25.0 1.0

Manganese binding site 4 out of 12 in 1m6v

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Manganese binding site 4 out of 12 in the Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn4022

b:21.4
occ:1.00
 O3B C:ADP4021 1.9 16.5 1.0
O1 C:PO44026 2.1 19.1 1.0
OD1 C:ASN301 2.1 22.5 1.0
O C:HOH4133 2.1 19.4 1.0
OE2 C:GLU299 2.2 16.1 1.0
OE1 C:GLU299 2.3 19.0 1.0
CD C:GLU299 2.6 38.8 1.0
CG C:ASN301 3.1 12.5 1.0
PB C:ADP4021 3.1 24.1 1.0
P C:PO44026 3.3 24.6 1.0
O1B C:ADP4021 3.4 19.4 1.0
O3 C:PO44026 3.4 14.9 1.0
ND2 C:ASN301 3.4 15.8 1.0
MN C:MN4023 3.6 24.1 1.0
K C:K4025 3.7 25.2 1.0
CB C:MET174 3.9 20.7 1.0
CG C:GLU299 4.1 8.5 1.0
O3A C:ADP4021 4.1 14.6 1.0
O4 C:PO44026 4.2 19.2 1.0
NH2 C:ARG303 4.2 15.3 1.0
O2B C:ADP4021 4.2 22.1 1.0
O2 C:PO44026 4.2 15.9 1.0
O C:THR173 4.2 32.8 1.0
O C:HOH4114 4.2 28.9 1.0
CA C:MET174 4.3 32.3 1.0
NH2 C:ARG129 4.3 23.0 1.0
CB C:ASN301 4.4 15.6 1.0
O1A C:ADP4021 4.6 19.9 1.0
OE1 C:GLN285 4.8 19.9 1.0
PA C:ADP4021 4.9 21.3 1.0
NH1 C:ARG129 4.9 19.3 1.0
O C:HOH4134 4.9 33.1 1.0
CB C:GLU299 4.9 19.5 1.0
OE1 C:GLU127 5.0 25.2 1.0

Manganese binding site 5 out of 12 in 1m6v

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Manganese binding site 5 out of 12 in the Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn4023

b:24.1
occ:1.00
 O3 C:PO44026 2.1 14.9 1.0
O C:HOH4628 2.1 31.7 1.0
O1A C:ADP4021 2.2 19.9 1.0
OE1 C:GLN285 2.3 19.9 1.0
O1B C:ADP4021 2.3 19.4 1.0
OE2 C:GLU299 2.3 16.1 1.0
CD C:GLN285 3.1 18.6 1.0
NE2 C:GLN285 3.2 13.4 1.0
PB C:ADP4021 3.2 24.1 1.0
P C:PO44026 3.3 24.6 1.0
CD C:GLU299 3.3 38.8 1.0
PA C:ADP4021 3.3 21.3 1.0
O3A C:ADP4021 3.5 14.6 1.0
O3B C:ADP4021 3.6 16.5 1.0
MN C:MN4022 3.6 21.4 1.0
O1 C:PO44026 3.7 19.1 1.0
O4 C:PO44026 3.7 19.2 1.0
O C:HOH4231 3.8 6.0 1.0
CG C:GLU299 3.8 8.5 1.0
NE2 C:HIS243 3.9 15.8 1.0
OE1 C:GLU299 4.2 19.0 1.0
ND2 C:ASN301 4.2 15.8 1.0
CE1 C:HIS243 4.3 11.4 1.0
O5' C:ADP4021 4.3 18.5 1.0
C5' C:ADP4021 4.3 45.0 1.0
O3' C:ADP4021 4.3 16.4 1.0
O2 C:PO44026 4.4 15.9 1.0
O2A C:ADP4021 4.4 19.9 1.0
O2B C:ADP4021 4.5 22.1 1.0
CG C:GLN285 4.5 11.1 1.0
OG1 C:THR244 4.6 17.4 1.0
CD2 C:HIS243 4.7 12.0 1.0
OD1 C:ASN301 4.9 22.5 1.0

Manganese binding site 6 out of 12 in 1m6v

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Manganese binding site 6 out of 12 in the Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn4028

b:39.6
occ:1.00
 O3B C:ADP4027 2.0 33.8 1.0
OE2 C:GLU841 2.2 25.9 1.0
O C:HOH4630 2.2 52.1 1.0
OE1 C:GLN829 2.2 46.6 1.0
O C:HOH4631 2.2 51.0 1.0
O2A C:ADP4027 2.2 32.7 1.0
CD C:GLU841 3.0 26.8 1.0
CD C:GLN829 3.1 51.3 1.0
NE2 C:GLN829 3.3 0.0 1.0
PA C:ADP4027 3.3 36.9 1.0
PB C:ADP4027 3.4 38.3 1.0
O3A C:ADP4027 3.6 45.0 1.0
O C:HOH4440 3.7 33.1 1.0
OE1 C:GLU841 3.8 50.2 1.0
CG C:GLU841 3.8 46.1 1.0
O C:HOH4438 4.1 33.7 1.0
O2B C:ADP4027 4.2 83.5 1.0
C5' C:ADP4027 4.3 27.5 1.0
O1A C:ADP4027 4.3 62.6 1.0
O5' C:ADP4027 4.4 42.4 1.0
O1B C:ADP4027 4.4 81.5 1.0
O3' C:ADP4027 4.4 31.8 1.0
ND2 C:ASN843 4.5 33.9 1.0
CG C:GLN829 4.5 37.2 1.0
OG C:SER789 4.5 26.0 1.0
NE2 C:HIS788 4.6 32.2 1.0
CE1 C:HIS788 4.7 31.9 1.0
C3' C:ADP4027 4.8 23.3 1.0
K C:K4029 4.9 76.2 1.0
CB C:GLN829 5.0 38.9 1.0
CB C:GLU841 5.0 53.4 1.0

Manganese binding site 7 out of 12 in 1m6v

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Manganese binding site 7 out of 12 in the Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn4045

b:24.3
occ:1.00
 O3B E:ADP4044 1.9 25.2 1.0
O1 E:PO44049 2.0 18.0 1.0
OD1 E:ASN301 2.1 38.5 1.0
O E:HOH1271 2.1 17.7 1.0
OE1 E:GLU299 2.2 23.9 1.0
OE2 E:GLU299 2.3 27.0 1.0
CD E:GLU299 2.5 21.3 1.0
CG E:ASN301 3.0 19.3 1.0
PB E:ADP4044 3.2 21.6 1.0
ND2 E:ASN301 3.3 17.7 1.0
P E:PO44049 3.3 25.7 1.0
O1B E:ADP4044 3.3 18.1 1.0
MN E:MN4046 3.6 21.9 1.0
O3 E:PO44049 3.6 21.5 1.0
CB E:MET174 3.7 17.1 1.0
K E:K4048 3.8 23.9 1.0
NH2 E:ARG303 4.0 31.5 1.0
CG E:GLU299 4.0 18.4 1.0
O E:HOH1251 4.1 18.9 1.0
O4 E:PO44049 4.2 21.5 1.0
O3A E:ADP4044 4.2 25.1 1.0
O2 E:PO44049 4.2 17.5 1.0
NH2 E:ARG129 4.2 29.1 1.0
O2B E:ADP4044 4.2 13.0 1.0
CA E:MET174 4.3 14.9 1.0
O E:THR173 4.4 25.6 1.0
CB E:ASN301 4.5 15.4 1.0
O1A E:ADP4044 4.5 20.3 1.0
OE1 E:GLN285 4.8 19.6 1.0
PA E:ADP4044 4.9 22.8 1.0
O E:HOH1272 4.9 48.5 1.0
OE1 E:GLU127 4.9 30.1 1.0
CB E:GLU299 5.0 16.6 1.0

Manganese binding site 8 out of 12 in 1m6v

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Manganese binding site 8 out of 12 in the Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn4046

b:21.9
occ:1.00
 O E:HOH2516 2.0 27.1 1.0
O1A E:ADP4044 2.0 20.3 1.0
O1B E:ADP4044 2.0 18.1 1.0
OE1 E:GLN285 2.1 19.6 1.0
OE2 E:GLU299 2.2 27.0 1.0
O3 E:PO44049 2.2 21.5 1.0
CD E:GLN285 3.1 33.0 1.0
PB E:ADP4044 3.1 21.6 1.0
PA E:ADP4044 3.3 22.8 1.0
P E:PO44049 3.3 25.7 1.0
CD E:GLU299 3.3 21.3 1.0
NE2 E:GLN285 3.4 25.4 1.0
O3A E:ADP4044 3.4 25.1 1.0
O3B E:ADP4044 3.5 25.2 1.0
O1 E:PO44049 3.5 18.0 1.0
MN E:MN4045 3.6 24.3 1.0
O E:HOH1371 3.7 5.4 1.0
NE2 E:HIS243 3.7 23.5 1.0
O4 E:PO44049 3.8 21.5 1.0
CG E:GLU299 3.9 18.4 1.0
OE1 E:GLU299 4.2 23.9 1.0
ND2 E:ASN301 4.2 17.7 1.0
CE1 E:HIS243 4.2 17.1 1.0
O5' E:ADP4044 4.2 22.6 1.0
O2A E:ADP4044 4.3 18.4 1.0
C5' E:ADP4044 4.3 13.8 1.0
O2B E:ADP4044 4.4 13.0 1.0
OG1 E:THR244 4.4 25.9 1.0
O2 E:PO44049 4.5 17.5 1.0
CG E:GLN285 4.5 11.1 1.0
O3' E:ADP4044 4.5 21.7 1.0
CD2 E:HIS243 4.5 18.5 1.0
OD1 E:ASN301 5.0 38.5 1.0

Manganese binding site 9 out of 12 in 1m6v

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Manganese binding site 9 out of 12 in the Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn4051

b:36.0
occ:1.00
 O2A E:ADP4050 1.9 35.4 1.0
OE2 E:GLU841 2.0 42.4 1.0
O3B E:ADP4050 2.0 27.2 1.0
OE1 E:GLN829 2.3 28.8 1.0
O E:HOH2518 2.3 43.8 1.0
O E:HOH2519 2.4 24.1 1.0
CD E:GLU841 3.1 66.0 1.0
PA E:ADP4050 3.2 31.6 1.0
CD E:GLN829 3.3 53.0 1.0
PB E:ADP4050 3.4 31.4 1.0
O3A E:ADP4050 3.6 31.5 1.0
CG E:GLU841 3.6 22.3 1.0
NE2 E:GLN829 3.8 35.5 1.0
O E:HOH1604 3.9 22.8 1.0
OE1 E:GLU841 4.0 55.6 1.0
O E:HOH1602 4.1 49.5 1.0
O5' E:ADP4050 4.2 33.2 1.0
O2B E:ADP4050 4.2 58.4 1.0
C5' E:ADP4050 4.2 19.8 1.0
O1A E:ADP4050 4.2 50.4 1.0
O3' E:ADP4050 4.3 37.4 1.0
O1B E:ADP4050 4.4 33.4 1.0
OG E:SER789 4.4 41.6 1.0
ND2 E:ASN843 4.5 41.7 1.0
NE2 E:HIS788 4.6 25.8 1.0
CG E:GLN829 4.6 23.0 1.0
C3' E:ADP4050 4.8 28.0 1.0
CE1 E:HIS788 4.8 26.8 1.0
K E:K4052 4.9 61.8 1.0

Manganese binding site 10 out of 12 in 1m6v

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Manganese binding site 10 out of 12 in the Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of the G359F (Small Subunit) Point Mutant of Carbamoyl Phosphate Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn4067

b:25.4
occ:1.00
 O1 G:PO44071 2.0 15.2 1.0
OD1 G:ASN301 2.1 43.6 1.0
O3B G:ADP4066 2.1 38.4 1.0
OE1 G:GLU299 2.3 20.8 1.0
OE2 G:GLU299 2.3 26.0 1.0
O G:HOH4181 2.3 30.2 1.0
CD G:GLU299 2.6 23.7 1.0
CG G:ASN301 3.1 22.1 1.0
PB G:ADP4066 3.2 27.8 1.0
O1B G:ADP4066 3.3 18.6 1.0
P G:PO44071 3.3 32.5 1.0
ND2 G:ASN301 3.5 21.0 1.0
O3 G:PO44071 3.5 17.1 1.0
MN G:MN4068 3.6 22.6 1.0
K G:K4070 3.8 30.3 1.0
CB G:MET174 3.8 15.9 1.0
CG G:GLU299 4.0 14.0 1.0
NH2 G:ARG303 4.1 19.1 1.0
O3A G:ADP4066 4.1 22.3 1.0
O2B G:ADP4066 4.2 21.1 1.0
O4 G:PO44071 4.2 16.2 1.0
O2 G:PO44071 4.2 16.4 1.0
O G:HOH4160 4.3 26.7 1.0
CA G:MET174 4.3 25.8 1.0
NH2 G:ARG129 4.3 23.4 1.0
O G:THR173 4.3 22.1 1.0
O1A G:ADP4066 4.3 26.1 1.0
CB G:ASN301 4.5 33.1 1.0
OE1 G:GLN285 4.7 28.5 1.0
PA G:ADP4066 4.8 25.3 1.0
NH1 G:ARG129 4.8 32.6 1.0
CB G:GLU299 4.9 21.0 1.0
N G:GLY175 4.9 22.4 1.0

Reference:

J.B.Thoden, X.Huang, F.M.Raushel, H.M.Holden. Carbamoyl-Phosphate Synthetase. Creation of An Escape Route For Ammonia J.Biol.Chem. V. 277 39722 2002.
ISSN: ISSN 0021-9258
PubMed: 12130656
DOI: 10.1074/JBC.M206915200
Page generated: Sat Oct 5 11:41:44 2024

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