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Potassium in PDB 1jdb: Carbamoyl Phosphate Synthetase From Escherichia Coli

Enzymatic activity of Carbamoyl Phosphate Synthetase From Escherichia Coli

All present enzymatic activity of Carbamoyl Phosphate Synthetase From Escherichia Coli:
6.3.5.5;

Protein crystallography data

The structure of Carbamoyl Phosphate Synthetase From Escherichia Coli, PDB code: 1jdb was solved by J.B.Thoden, H.M.Holden, G.Wesenberg, F.M.Raushel, I.Rayment, 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 (°) 143.800, 167.700, 323.000, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / n/a

Other elements in 1jdb:

The structure of Carbamoyl Phosphate Synthetase From Escherichia Coli also contains other interesting chemical elements:

Manganese (Mn) 16 atoms
Chlorine (Cl) 29 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 29;

Binding sites:

The binding sites of Potassium atom in the Carbamoyl Phosphate Synthetase From Escherichia Coli (pdb code 1jdb). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 29 binding sites of Potassium where determined in the Carbamoyl Phosphate Synthetase From Escherichia Coli, PDB code: 1jdb:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 29 in 1jdb

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Potassium binding site 1 out of 29 in the Carbamoyl Phosphate Synthetase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Carbamoyl Phosphate Synthetase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1075

b:11.3
occ:1.00
 OE1 B:GLU214 2.5 10.9 1.0
OD1 B:ASN235 2.6 20.4 1.0
O B:ILE241 2.6 14.7 1.0
O B:ALA238 2.8 18.5 1.0
O B:ASP237 2.8 11.5 1.0
OG B:SER246 2.8 10.9 1.0
C B:ALA238 3.5 14.8 1.0
CG B:ASN235 3.5 18.5 1.0
C B:ASP237 3.6 9.6 1.0
CD B:GLU214 3.6 25.1 1.0
CB B:ASN235 3.8 16.8 1.0
C B:ILE241 3.8 16.5 1.0
CB B:SER246 3.8 5.6 1.0
CB B:GLU214 4.0 7.3 1.0
CG B:GLU214 4.2 6.8 1.0
N B:ALA238 4.2 3.9 1.0
O2' B:ADP1093 4.2 11.5 1.0
CA B:ALA238 4.3 6.0 1.0
N B:MET239 4.3 17.9 1.0
O B:HIS242 4.3 17.4 1.0
C B:HIS242 4.4 11.6 1.0
CB B:ASP237 4.4 17.0 1.0
N B:ILE241 4.4 15.6 1.0
CB B:ILE241 4.4 20.2 1.0
N B:THR243 4.4 13.8 1.0
CA B:ILE241 4.4 14.6 1.0
CA B:THR243 4.5 5.5 1.0
CA B:ASP237 4.5 9.8 1.0
CA B:MET239 4.5 8.4 1.0
OE2 B:GLU214 4.5 18.1 1.0
CG2 B:THR243 4.7 10.8 1.0
ND2 B:ASN235 4.7 12.2 1.0
N B:HIS242 4.8 12.5 1.0
CG2 B:ILE241 4.9 4.6 1.0
N B:GLY240 5.0 23.7 1.0
N B:ASP237 5.0 13.0 1.0

Potassium binding site 2 out of 29 in 1jdb

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Potassium binding site 2 out of 29 in the Carbamoyl Phosphate Synthetase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Carbamoyl Phosphate Synthetase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1076

b:17.1
occ:1.00
 OE1 B:GLU298 2.7 12.7 1.0
O B:MET299 2.8 16.9 1.0
O B:HOH1100 2.8 20.3 1.0
O B:HOH1105 2.8 38.8 1.0
O B:HOH1097 2.8 23.5 1.0
OE2 B:GLU126 3.2 30.9 1.0
O B:ALA125 3.3 21.7 1.0
OD1 B:ASN300 3.4 15.3 1.0
O B:HOH1162 3.5 23.5 1.0
MN B:MN1073 3.8 15.8 1.0
CD B:GLU298 3.8 23.6 1.0
C B:MET299 3.8 17.1 1.0
CD B:GLU126 3.8 47.3 1.0
C B:ALA125 4.1 18.1 1.0
OE1 B:GLU126 4.2 20.4 1.0
N B:MET299 4.2 8.8 1.0
CB B:GLU298 4.3 7.0 1.0
NH1 B:ARG128 4.3 15.0 1.0
CA B:GLU126 4.4 7.7 1.0
CG B:ASN300 4.4 27.9 1.0
NH2 B:ARG128 4.5 17.2 1.0
CZ B:ARG128 4.5 21.0 1.0
N B:ASN300 4.5 12.0 1.0
CA B:ASN300 4.5 12.7 1.0
N B:GLU126 4.6 23.0 1.0
O B:HOH1256 4.6 9.8 1.0
CG B:GLU298 4.6 5.1 1.0
OE2 B:GLU298 4.7 13.8 1.0
O3B B:ADP1093 4.7 10.7 1.0
CA B:MET299 4.7 15.2 1.0
O B:HOH1254 4.8 12.8 1.0
CB B:ALA125 4.8 13.7 1.0
CG B:GLU126 4.9 10.7 1.0
CD B:PRO301 4.9 14.7 1.0

Potassium binding site 3 out of 29 in 1jdb

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Potassium binding site 3 out of 29 in the Carbamoyl Phosphate Synthetase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Carbamoyl Phosphate Synthetase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1077

b:28.2
occ:1.00
 OE1 B:GLN284 2.6 13.8 1.0
OE1 B:GLU216 2.8 18.4 1.0
O3 B:PO41078 2.8 6.5 1.0
O B:HOH1099 3.1 2.3 1.0
OG1 B:THR243 3.2 10.8 1.0
CD B:GLN284 3.4 13.3 1.0
OD1 B:ASN282 3.5 42.7 1.0
O B:HOH1101 3.5 9.4 1.0
MN B:MN1074 3.6 14.2 1.0
CD B:GLU216 3.7 43.0 1.0
O B:HOH1098 3.8 16.2 1.0
ND2 B:ASN282 3.9 45.0 1.0
CG B:GLN284 3.9 12.1 1.0
P B:PO41078 4.0 14.6 1.0
O2 B:PO41078 4.0 15.8 1.0
CG B:ASN282 4.1 24.9 1.0
OG B:SER306 4.2 20.8 1.0
CB B:THR243 4.2 10.7 1.0
ND2 B:ASN300 4.2 13.3 1.0
CG2 B:THR243 4.4 10.8 1.0
NE2 B:GLN284 4.4 9.8 1.0
OE2 B:GLU216 4.5 18.9 1.0
NH1 B:ARG305 4.5 8.1 1.0
CG B:GLU216 4.6 35.0 1.0
OE2 B:GLU298 4.7 13.8 1.0
O4 B:PO41078 4.7 14.4 1.0
CB B:SER306 4.8 9.1 1.0

Potassium binding site 4 out of 29 in 1jdb

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Potassium binding site 4 out of 29 in the Carbamoyl Phosphate Synthetase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Carbamoyl Phosphate Synthetase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1081

b:22.9
occ:1.00
 OE1 B:GLU760 2.7 24.6 1.0
O B:VAL786 2.7 17.5 1.0
O B:GLU782 2.8 18.0 1.0
ND1 B:HIS780 2.9 21.2 1.0
O B:GLN783 2.9 29.2 1.0
OG B:SER791 2.9 17.5 1.0
C B:GLN783 3.4 28.1 1.0
CB B:GLU760 3.6 15.0 1.0
C B:GLU782 3.6 23.7 1.0
CD B:GLU760 3.6 19.6 1.0
CG B:HIS780 3.8 33.0 1.0
C B:VAL786 3.8 29.1 1.0
CB B:HIS780 3.9 20.2 1.0
CE1 B:HIS780 3.9 17.3 1.0
CB B:SER791 4.0 17.1 1.0
N B:ALA784 4.1 18.7 1.0
CG B:GLU760 4.1 37.6 1.0
CB B:VAL786 4.2 42.4 1.0
CA B:GLN783 4.2 34.5 1.0
N B:GLN783 4.2 22.6 1.0
O2' B:ADP1094 4.2 21.5 1.0
CA B:ALA784 4.2 19.2 1.0
N B:VAL786 4.3 28.3 1.0
CB B:GLU782 4.4 13.3 1.0
CA B:VAL786 4.4 14.2 1.0
O B:HIS787 4.5 18.1 1.0
OE2 B:GLU760 4.5 28.6 1.0
CA B:GLU782 4.5 8.5 1.0
C B:HIS787 4.6 13.7 1.0
N B:SER788 4.6 15.0 1.0
CA B:SER788 4.7 10.5 1.0
O B:HOH1666 4.7 15.7 1.0
CG1 B:VAL786 4.8 23.4 1.0
CA B:GLU760 4.9 17.2 1.0
C B:ALA784 4.9 23.0 1.0
N B:HIS787 4.9 20.7 1.0
N B:GLY785 4.9 23.9 1.0

Potassium binding site 5 out of 29 in 1jdb

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Potassium binding site 5 out of 29 in the Carbamoyl Phosphate Synthetase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Carbamoyl Phosphate Synthetase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1083

b:35.9
occ:1.00
 O B:HOH1275 2.6 52.9 1.0
OG1 B:THR142 2.8 16.6 1.0
O B:HOH1272 2.8 29.6 1.0
O B:ALA143 2.9 23.8 1.0
O B:THR142 3.1 16.8 1.0
O B:HOH1274 3.1 19.1 1.0
C B:ALA143 3.6 20.9 1.0
C B:THR142 3.6 9.9 1.0
O B:HOH1273 3.7 37.8 1.0
CB B:THR142 4.0 21.3 1.0
N B:ARG144 4.1 15.1 1.0
CA B:ARG144 4.1 17.6 1.0
CA B:THR142 4.2 30.3 1.0
N B:THR142 4.3 18.3 1.0
N B:ALA143 4.4 17.1 1.0
OD1 B:ASP132 4.5 51.5 1.0
CA B:ALA143 4.5 6.7 1.0
O B:HOH1266 4.7 41.1 1.0
O B:HOH1276 4.7 28.4 1.0
N B:SER145 4.8 22.0 1.0
O B:HOH1334 4.8 15.0 1.0
OD2 B:ASP132 4.9 55.4 1.0
C B:ARG144 4.9 30.0 1.0
OG B:SER145 5.0 24.9 1.0

Potassium binding site 6 out of 29 in 1jdb

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Potassium binding site 6 out of 29 in the Carbamoyl Phosphate Synthetase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Carbamoyl Phosphate Synthetase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1084

b:49.0
occ:1.00
 O B:GLY111 2.8 43.3 1.0
OG1 B:THR113 2.9 61.2 1.0
O B:ASP83 2.9 23.7 1.0
C B:GLY111 3.7 31.2 1.0
C B:ASP83 3.8 13.5 1.0
N B:THR113 3.8 21.8 1.0
CB B:THR113 4.0 39.4 1.0
CA B:ASP83 4.0 10.8 1.0
CB B:ASP83 4.4 27.3 1.0
OD1 B:ASP83 4.4 40.7 1.0
C B:VAL112 4.4 45.8 1.0
CA B:VAL112 4.4 30.1 1.0
N B:VAL112 4.4 48.8 1.0
CA B:THR113 4.5 58.7 1.0
O B:HOH1220 4.5 40.1 1.0
CA B:GLY111 4.7 41.6 1.0
CG B:ASP83 5.0 52.1 1.0

Potassium binding site 7 out of 29 in 1jdb

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Potassium binding site 7 out of 29 in the Carbamoyl Phosphate Synthetase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Carbamoyl Phosphate Synthetase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K383

b:23.6
occ:1.00
 O C:HOH435 2.6 22.9 1.0
O C:HOH434 2.6 22.9 1.0
O C:ASP112 2.7 14.9 1.0
O C:HIS16 2.8 20.0 1.0
O C:HOH433 3.0 35.8 1.0
O B:HOH1649 3.1 22.1 1.0
O C:HOH438 3.9 39.6 1.0
C C:ASP112 3.9 11.8 1.0
C C:HIS16 4.0 15.2 1.0
NH2 B:ARG493 4.2 9.2 1.0
O B:HOH1925 4.3 33.8 1.0
CL C:CL384 4.4 24.4 1.0
O B:HOH1488 4.4 13.2 1.0
CA C:GLY17 4.4 14.4 1.0
O C:HOH432 4.4 15.8 1.0
CB C:ASP112 4.5 17.0 1.0
CA C:ILE113 4.5 12.3 1.0
CZ B:ARG493 4.6 21.7 1.0
O C:HOH437 4.6 42.3 1.0
N C:GLY17 4.7 13.8 1.0
N C:ILE113 4.8 22.4 1.0
NH1 B:ARG493 4.8 17.1 1.0
CA C:ASP112 4.9 13.0 1.0
CG2 C:ILE113 4.9 8.6 1.0
O B:HOH1654 4.9 44.8 1.0

Potassium binding site 8 out of 29 in 1jdb

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Potassium binding site 8 out of 29 in the Carbamoyl Phosphate Synthetase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Carbamoyl Phosphate Synthetase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K1075

b:15.1
occ:1.00
 OE1 E:GLU214 2.6 19.0 1.0
OG E:SER246 2.6 13.3 1.0
O E:ILE241 2.7 12.5 1.0
OD1 E:ASN235 2.7 16.5 1.0
O E:ASP237 2.9 16.2 1.0
O E:ALA238 2.9 13.9 1.0
C E:ASP237 3.6 13.7 1.0
C E:ALA238 3.6 18.7 1.0
CG E:ASN235 3.7 16.4 1.0
CB E:SER246 3.7 4.1 1.0
CD E:GLU214 3.7 44.9 1.0
C E:ILE241 3.8 29.4 1.0
CB E:ASN235 3.9 10.9 1.0
CB E:GLU214 4.1 7.8 1.0
N E:ALA238 4.2 12.1 1.0
CG E:GLU214 4.3 19.4 1.0
CA E:ALA238 4.3 9.1 1.0
O E:HIS242 4.3 14.3 1.0
CB E:ASP237 4.3 9.6 1.0
O2' E:ADP1095 4.4 15.3 1.0
N E:MET239 4.4 11.5 1.0
C E:HIS242 4.4 6.4 1.0
CB E:ILE241 4.4 8.0 1.0
CA E:ASP237 4.4 8.8 1.0
N E:THR243 4.4 18.5 1.0
N E:ILE241 4.5 11.0 1.0
CA E:ILE241 4.5 20.9 1.0
CA E:THR243 4.5 21.2 1.0
CA E:MET239 4.5 20.0 1.0
OE2 E:GLU214 4.7 28.3 1.0
N E:HIS242 4.8 17.6 1.0
CG2 E:THR243 4.9 14.4 1.0
ND2 E:ASN235 4.9 14.7 1.0
N E:ASP237 4.9 16.2 1.0
CG2 E:ILE241 4.9 4.0 1.0

Potassium binding site 9 out of 29 in 1jdb

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Potassium binding site 9 out of 29 in the Carbamoyl Phosphate Synthetase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Carbamoyl Phosphate Synthetase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K1076

b:18.7
occ:1.00
 O E:HOH1223 2.6 37.6 1.0
O E:MET299 2.8 18.3 1.0
OE1 E:GLU298 2.9 12.8 1.0
O E:HOH1218 2.9 20.6 1.0
OE2 E:GLU126 3.0 25.4 1.0
O E:ALA125 3.1 15.1 1.0
O E:HOH1215 3.2 21.8 1.0
OD1 E:ASN300 3.4 14.8 1.0
O E:HOH1281 3.5 20.5 1.0
CD E:GLU126 3.7 32.4 1.0
CD E:GLU298 3.8 11.5 1.0
C E:MET299 3.9 8.6 1.0
C E:ALA125 3.9 16.7 1.0
MN E:MN1073 3.9 15.7 1.0
OE1 E:GLU126 4.3 23.5 1.0
N E:MET299 4.3 19.6 1.0
NH1 E:ARG128 4.3 14.7 1.0
CG E:ASN300 4.4 19.4 1.0
CA E:GLU126 4.4 10.3 1.0
N E:GLU126 4.4 17.5 1.0
O E:HOH1372 4.4 13.9 1.0
CB E:GLU298 4.5 8.1 1.0
CA E:ASN300 4.6 27.2 1.0
CG E:GLU298 4.6 10.6 1.0
N E:ASN300 4.6 19.0 1.0
CZ E:ARG128 4.7 14.3 1.0
OE2 E:GLU298 4.7 8.0 1.0
CG E:GLU126 4.7 15.9 1.0
CB E:ALA125 4.7 8.7 1.0
NH2 E:ARG128 4.8 20.1 1.0
CA E:MET299 4.8 9.0 1.0
O3B E:ADP1095 4.8 17.8 1.0
CA E:ALA125 4.8 12.2 1.0
CD E:PRO301 4.9 25.8 1.0

Potassium binding site 10 out of 29 in 1jdb

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Potassium binding site 10 out of 29 in the Carbamoyl Phosphate Synthetase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Carbamoyl Phosphate Synthetase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K1077

b:28.2
occ:1.00
 OE1 E:GLN284 2.7 26.6 1.0
O3 E:PO41078 2.7 7.5 1.0
OE1 E:GLU216 2.9 30.7 1.0
O E:HOH1217 2.9 1.7 1.0
OG1 E:THR243 3.2 14.0 1.0
CD E:GLN284 3.5 30.6 1.0
OD1 E:ASN282 3.6 41.1 1.0
O E:HOH1219 3.6 13.2 1.0
CD E:GLU216 3.6 57.3 1.0
O E:HOH1216 3.6 13.9 1.0
MN E:MN1074 3.6 14.8 1.0
ND2 E:ASN282 3.8 47.4 1.0
P E:PO41078 3.9 16.7 1.0
CG E:GLN284 3.9 15.7 1.0
O2 E:PO41078 3.9 9.5 1.0
CG E:ASN282 4.0 20.6 1.0
CB E:THR243 4.2 14.1 1.0
ND2 E:ASN300 4.2 18.2 1.0
OG E:SER306 4.2 25.5 1.0
CG E:GLU216 4.3 48.5 1.0
CG2 E:THR243 4.4 14.4 1.0
OE2 E:GLU216 4.4 39.2 1.0
NH1 E:ARG305 4.6 14.3 1.0
NE2 E:GLN284 4.6 12.8 1.0
O4 E:PO41078 4.6 12.9 1.0
OE2 E:GLU298 4.7 8.0 1.0
CB E:SER306 4.7 19.5 1.0
O1 E:PO41078 4.9 9.6 1.0

Reference:

J.B.Thoden, F.M.Raushel, M.M.Benning, I.Rayment, H.M.Holden. The Structure of Carbamoyl Phosphate Synthetase Determined to 2.1 A Resolution. Acta Crystallogr.,Sect.D V. 55 8 1999.
ISSN: ISSN 0907-4449
PubMed: 10089390
DOI: 10.1107/S0907444998006234
Page generated: Mon Aug 12 04:38:16 2024

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