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Manganese in PDB 1f52: Crystal Structure of Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp

Enzymatic activity of Crystal Structure of Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp

All present enzymatic activity of Crystal Structure of Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp:
6.3.1.2;

Protein crystallography data

The structure of Crystal Structure of Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp, PDB code: 1f52 was solved by H.S.Gill, G.M.U.Pfluegl, D.Eisenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.90 / 2.49
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 230.600, 132.500, 195.900, 90.00, 102.40, 90.00
R / Rfree (%) 24.3 / 25.7

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp (pdb code 1f52). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 24 binding sites of Manganese where determined in the Crystal Structure of Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp, PDB code: 1f52:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 24 in 1f52

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Manganese binding site 1 out of 24 in the Crystal Structure of Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp


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 Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn469

b:47.4
occ:1.00
 OE2 A:GLU212 2.0 49.0 1.0
O A:HOH5729 2.0 40.0 1.0
OE1 A:GLU220 2.1 43.4 1.0
OE1 A:GLU131 2.1 41.1 1.0
O A:HOH5732 2.1 51.8 1.0
O A:HOH5734 3.1 63.5 1.0
CD A:GLU212 3.1 52.0 1.0
CD A:GLU220 3.1 45.2 1.0
CD A:GLU131 3.2 47.1 1.0
OE2 A:GLU220 3.5 61.2 1.0
CG A:GLU131 3.7 34.3 1.0
O A:HOH5727 3.7 53.1 1.0
CG A:GLU212 3.9 37.9 1.0
OE1 A:GLU212 4.0 45.1 1.0
O A:HOH5512 4.1 47.3 1.0
CE1 A:HIS210 4.2 34.4 1.0
OH A:TYR179 4.3 0.0 1.0
OE2 A:GLU131 4.3 37.3 1.0
CG A:GLU220 4.5 41.1 1.0
NE2 A:HIS210 4.6 47.0 1.0
O A:HOH5492 4.6 43.1 1.0
O A:HOH5672 4.6 63.3 1.0
CB A:GLU220 4.7 45.3 1.0
O A:HOH5728 4.7 57.9 1.0
O A:HOH5740 4.8 81.0 1.0
O3B A:ADP4471 4.8 0.0 0.7

Manganese binding site 2 out of 24 in 1f52

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Manganese binding site 2 out of 24 in the Crystal Structure of Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp


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 Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn470

b:46.8
occ:1.00
 OE2 A:GLU129 2.0 45.4 1.0
O A:HOH5741 2.1 73.8 1.0
OE2 A:GLU357 2.2 53.1 1.0
ND1 A:HIS269 2.3 43.4 1.0
O2B A:ADP4471 2.4 99.6 0.7
O3B A:ADP4471 2.5 0.0 0.7
O A:HOH5734 2.7 63.5 1.0
PB A:ADP4471 2.9 0.0 0.7
CD A:GLU129 3.1 48.1 1.0
CE1 A:HIS269 3.1 62.0 1.0
CD A:GLU357 3.3 49.8 1.0
CG A:HIS269 3.4 51.7 1.0
OE1 A:GLU129 3.4 70.6 1.0
CB A:HIS269 3.7 38.7 1.0
OE1 A:GLU357 3.7 62.8 1.0
NH1 A:ARG359 3.8 0.0 1.0
NE2 A:HIS271 4.0 53.1 1.0
O1B A:ADP4471 4.0 0.0 0.7
O A:HOH5728 4.2 57.9 1.0
O3A A:ADP4471 4.2 0.0 0.7
O A:HOH5732 4.3 51.8 1.0
NE2 A:HIS269 4.3 56.9 1.0
NH2 A:ARG344 4.4 91.0 1.0
CG A:GLU129 4.4 44.6 1.0
CD2 A:HIS269 4.5 45.6 1.0
CG A:GLU357 4.5 39.9 1.0
CZ A:ARG359 4.7 99.8 1.0
CD2 A:HIS271 4.8 60.6 1.0
CB A:GLU129 4.8 46.6 1.0
O A:HOH5492 4.9 43.1 1.0
CE1 A:HIS271 4.9 53.5 1.0

Manganese binding site 3 out of 24 in 1f52

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Manganese binding site 3 out of 24 in the Crystal Structure of Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp


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 Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn469

b:47.4
occ:1.00
 OE2 B:GLU212 2.0 49.0 1.0
O B:HOH5730 2.0 40.0 1.0
OE1 B:GLU220 2.1 43.4 1.0
OE1 B:GLU131 2.1 41.1 1.0
O B:HOH5733 2.1 51.8 1.0
O B:HOH5735 3.1 63.5 1.0
CD B:GLU212 3.1 52.0 1.0
CD B:GLU220 3.1 45.2 1.0
CD B:GLU131 3.2 47.1 1.0
OE2 B:GLU220 3.5 61.2 1.0
CG B:GLU131 3.7 34.3 1.0
O B:HOH5728 3.7 53.1 1.0
CG B:GLU212 3.9 37.9 1.0
OE1 B:GLU212 4.0 45.1 1.0
O B:HOH5515 4.1 47.3 1.0
CE1 B:HIS210 4.2 34.4 1.0
OH B:TYR179 4.3 0.0 1.0
OE2 B:GLU131 4.3 37.3 1.0
CG B:GLU220 4.5 41.1 1.0
NE2 B:HIS210 4.6 47.0 1.0
O B:HOH5494 4.6 43.1 1.0
O B:HOH5674 4.6 63.3 1.0
CB B:GLU220 4.7 45.3 1.0
O B:HOH5729 4.7 57.9 1.0
O B:HOH5741 4.8 81.0 1.0
O3B B:ADP4472 4.8 0.0 0.7

Manganese binding site 4 out of 24 in 1f52

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Manganese binding site 4 out of 24 in the Crystal Structure of Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp


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 Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn470

b:46.8
occ:1.00
 OE2 B:GLU129 2.0 45.4 1.0
O B:HOH5742 2.1 73.8 1.0
OE2 B:GLU357 2.2 53.1 1.0
ND1 B:HIS269 2.3 43.4 1.0
O2B B:ADP4472 2.4 99.6 0.7
O3B B:ADP4472 2.5 0.0 0.7
O B:HOH5735 2.7 63.5 1.0
PB B:ADP4472 2.9 0.0 0.7
CD B:GLU129 3.1 48.1 1.0
CE1 B:HIS269 3.1 62.0 1.0
CD B:GLU357 3.3 49.8 1.0
CG B:HIS269 3.4 51.7 1.0
OE1 B:GLU129 3.4 70.6 1.0
CB B:HIS269 3.7 38.7 1.0
OE1 B:GLU357 3.7 62.8 1.0
NH1 B:ARG359 3.8 0.0 1.0
NE2 B:HIS271 4.0 53.1 1.0
O1B B:ADP4472 4.0 0.0 0.7
O B:HOH5729 4.2 57.9 1.0
O3A B:ADP4472 4.2 0.0 0.7
O B:HOH5733 4.3 51.8 1.0
NE2 B:HIS269 4.3 56.9 1.0
NH2 B:ARG344 4.4 91.0 1.0
CG B:GLU129 4.4 44.6 1.0
CD2 B:HIS269 4.5 45.6 1.0
CG B:GLU357 4.5 39.9 1.0
CZ B:ARG359 4.7 99.8 1.0
CD2 B:HIS271 4.8 60.6 1.0
CB B:GLU129 4.8 46.6 1.0
O B:HOH5494 4.9 43.1 1.0
CE1 B:HIS271 4.9 53.5 1.0

Manganese binding site 5 out of 24 in 1f52

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Manganese binding site 5 out of 24 in the Crystal Structure of Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp


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 Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn469

b:47.4
occ:1.00
 OE2 C:GLU212 2.0 49.0 1.0
O C:HOH5730 2.0 40.0 1.0
OE1 C:GLU220 2.1 43.4 1.0
OE1 C:GLU131 2.1 41.1 1.0
O C:HOH5733 2.1 51.8 1.0
O C:HOH5735 3.1 63.5 1.0
CD C:GLU212 3.1 52.0 1.0
CD C:GLU220 3.1 45.2 1.0
CD C:GLU131 3.2 47.1 1.0
OE2 C:GLU220 3.5 61.2 1.0
CG C:GLU131 3.7 34.3 1.0
O C:HOH5728 3.7 53.1 1.0
CG C:GLU212 3.9 37.9 1.0
OE1 C:GLU212 4.0 45.1 1.0
O C:HOH5515 4.1 47.3 1.0
CE1 C:HIS210 4.2 34.4 1.0
OH C:TYR179 4.3 0.0 1.0
OE2 C:GLU131 4.3 37.3 1.0
CG C:GLU220 4.5 41.1 1.0
NE2 C:HIS210 4.6 47.0 1.0
O C:HOH5495 4.6 43.1 1.0
O C:HOH5674 4.6 63.3 1.0
CB C:GLU220 4.7 45.3 1.0
O C:HOH5729 4.7 57.9 1.0
O C:HOH5741 4.8 81.0 1.0
O3B C:ADP4473 4.8 0.0 0.7

Manganese binding site 6 out of 24 in 1f52

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Manganese binding site 6 out of 24 in the Crystal Structure of Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp


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 Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn470

b:46.8
occ:1.00
 OE2 C:GLU129 2.0 45.4 1.0
O C:HOH5742 2.1 73.8 1.0
OE2 C:GLU357 2.2 53.1 1.0
ND1 C:HIS269 2.3 43.4 1.0
O2B C:ADP4473 2.4 99.6 0.7
O3B C:ADP4473 2.5 0.0 0.7
O C:HOH5735 2.7 63.5 1.0
PB C:ADP4473 2.9 0.0 0.7
CD C:GLU129 3.1 48.1 1.0
CE1 C:HIS269 3.1 62.0 1.0
CD C:GLU357 3.3 49.8 1.0
CG C:HIS269 3.4 51.7 1.0
OE1 C:GLU129 3.4 70.6 1.0
CB C:HIS269 3.7 38.7 1.0
OE1 C:GLU357 3.7 62.8 1.0
NH1 C:ARG359 3.8 0.0 1.0
NE2 C:HIS271 4.0 53.1 1.0
O1B C:ADP4473 4.0 0.0 0.7
O C:HOH5729 4.2 57.9 1.0
O3A C:ADP4473 4.2 0.0 0.7
O C:HOH5733 4.3 51.8 1.0
NE2 C:HIS269 4.3 56.9 1.0
NH2 C:ARG344 4.4 91.0 1.0
CG C:GLU129 4.4 44.6 1.0
CD2 C:HIS269 4.5 45.6 1.0
CG C:GLU357 4.5 39.9 1.0
CZ C:ARG359 4.7 99.8 1.0
CD2 C:HIS271 4.8 60.6 1.0
CB C:GLU129 4.8 46.6 1.0
O C:HOH5495 4.9 43.1 1.0
CE1 C:HIS271 4.9 53.5 1.0

Manganese binding site 7 out of 24 in 1f52

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Manganese binding site 7 out of 24 in the Crystal Structure of Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp


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 Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn469

b:47.4
occ:1.00
 OE2 D:GLU212 2.0 49.0 1.0
O D:HOH1148 2.0 40.0 1.0
OE1 D:GLU220 2.1 43.4 1.0
OE1 D:GLU131 2.1 41.1 1.0
O D:HOH1151 2.1 51.8 1.0
O D:HOH1153 3.1 63.5 1.0
CD D:GLU212 3.1 52.0 1.0
CD D:GLU220 3.1 45.2 1.0
CD D:GLU131 3.2 47.1 1.0
OE2 D:GLU220 3.5 61.2 1.0
CG D:GLU131 3.7 34.3 1.0
O D:HOH1146 3.7 53.1 1.0
CG D:GLU212 3.9 37.9 1.0
OE1 D:GLU212 4.0 45.1 1.0
O D:HOH914 4.1 47.3 1.0
CE1 D:HIS210 4.2 34.4 1.0
OH D:TYR179 4.3 0.0 1.0
OE2 D:GLU131 4.3 37.3 1.0
CG D:GLU220 4.5 41.1 1.0
NE2 D:HIS210 4.6 47.0 1.0
O D:HOH890 4.6 43.1 1.0
O D:HOH1089 4.6 63.3 1.0
CB D:GLU220 4.7 45.3 1.0
O D:HOH1147 4.7 57.9 1.0
O D:HOH1159 4.8 81.0 1.0
O3B D:ADP4474 4.8 0.0 0.7

Manganese binding site 8 out of 24 in 1f52

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Manganese binding site 8 out of 24 in the Crystal Structure of Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp


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 Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn470

b:46.8
occ:1.00
 OE2 D:GLU129 2.0 45.4 1.0
O D:HOH1160 2.1 73.8 1.0
OE2 D:GLU357 2.2 53.1 1.0
ND1 D:HIS269 2.3 43.4 1.0
O2B D:ADP4474 2.4 99.6 0.7
O3B D:ADP4474 2.5 0.0 0.7
O D:HOH1153 2.7 63.5 1.0
PB D:ADP4474 2.9 0.0 0.7
CD D:GLU129 3.1 48.1 1.0
CE1 D:HIS269 3.1 62.0 1.0
CD D:GLU357 3.3 49.8 1.0
CG D:HIS269 3.4 51.7 1.0
OE1 D:GLU129 3.4 70.6 1.0
CB D:HIS269 3.7 38.7 1.0
OE1 D:GLU357 3.7 62.8 1.0
NH1 D:ARG359 3.8 0.0 1.0
NE2 D:HIS271 4.0 53.1 1.0
O1B D:ADP4474 4.0 0.0 0.7
O D:HOH1147 4.2 57.9 1.0
O3A D:ADP4474 4.2 0.0 0.7
O D:HOH1151 4.3 51.8 1.0
NE2 D:HIS269 4.3 56.9 1.0
NH2 D:ARG344 4.4 91.0 1.0
CG D:GLU129 4.4 44.6 1.0
CD2 D:HIS269 4.5 45.6 1.0
CG D:GLU357 4.5 39.9 1.0
CZ D:ARG359 4.7 99.8 1.0
CD2 D:HIS271 4.8 60.6 1.0
CB D:GLU129 4.8 46.6 1.0
O D:HOH890 4.9 43.1 1.0
CE1 D:HIS271 4.9 53.5 1.0

Manganese binding site 9 out of 24 in 1f52

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Manganese binding site 9 out of 24 in the Crystal Structure of Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp


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 Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn469

b:47.4
occ:1.00
 OE2 E:GLU212 2.0 49.0 1.0
O E:HOH1440 2.0 40.0 1.0
OE1 E:GLU220 2.1 43.4 1.0
OE1 E:GLU131 2.1 41.1 1.0
O E:HOH1443 2.1 51.8 1.0
O E:HOH1445 3.1 63.5 1.0
CD E:GLU212 3.1 52.0 1.0
CD E:GLU220 3.1 45.2 1.0
CD E:GLU131 3.2 47.1 1.0
OE2 E:GLU220 3.5 61.2 1.0
CG E:GLU131 3.7 34.3 1.0
O E:HOH1438 3.7 53.1 1.0
CG E:GLU212 3.9 37.9 1.0
OE1 E:GLU212 4.0 45.1 1.0
O E:HOH1206 4.1 47.3 1.0
CE1 E:HIS210 4.2 34.4 1.0
OH E:TYR179 4.3 0.0 1.0
OE2 E:GLU131 4.3 37.3 1.0
CG E:GLU220 4.5 41.1 1.0
NE2 E:HIS210 4.6 47.0 1.0
O E:HOH1182 4.6 43.1 1.0
O E:HOH1381 4.6 63.3 1.0
CB E:GLU220 4.7 45.3 1.0
O E:HOH1439 4.7 57.9 1.0
O E:HOH1451 4.8 81.0 1.0
O3B E:ADP4475 4.8 0.0 0.7

Manganese binding site 10 out of 24 in 1f52

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Manganese binding site 10 out of 24 in the Crystal Structure of Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp


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 Glutamine Synthetase From Salmonella Typhimurium Co-Crystallized with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn470

b:46.8
occ:1.00
 OE2 E:GLU129 2.0 45.4 1.0
O E:HOH1452 2.1 73.8 1.0
OE2 E:GLU357 2.2 53.1 1.0
ND1 E:HIS269 2.3 43.4 1.0
O2B E:ADP4475 2.4 99.6 0.7
O3B E:ADP4475 2.5 0.0 0.7
O E:HOH1445 2.7 63.5 1.0
PB E:ADP4475 2.9 0.0 0.7
CD E:GLU129 3.1 48.1 1.0
CE1 E:HIS269 3.1 62.0 1.0
CD E:GLU357 3.3 49.8 1.0
CG E:HIS269 3.4 51.7 1.0
OE1 E:GLU129 3.4 70.6 1.0
CB E:HIS269 3.7 38.7 1.0
OE1 E:GLU357 3.7 62.8 1.0
NH1 E:ARG359 3.8 0.0 1.0
NE2 E:HIS271 4.0 53.1 1.0
O1B E:ADP4475 4.0 0.0 0.7
O E:HOH1439 4.2 57.9 1.0
O3A E:ADP4475 4.2 0.0 0.7
O E:HOH1443 4.3 51.8 1.0
NE2 E:HIS269 4.3 56.9 1.0
NH2 E:ARG344 4.4 91.0 1.0
CG E:GLU129 4.4 44.6 1.0
CD2 E:HIS269 4.5 45.6 1.0
CG E:GLU357 4.5 39.9 1.0
CZ E:ARG359 4.7 99.8 1.0
CD2 E:HIS271 4.8 60.6 1.0
CB E:GLU129 4.8 46.6 1.0
O E:HOH1182 4.9 43.1 1.0
CE1 E:HIS271 4.9 53.5 1.0

Reference:

H.S.Gill, D.Eisenberg. The Crystal Structure of Phosphinothricin in the Active Site of Glutamine Synthetase Illuminates the Mechanism of Enzymatic Inhibition. Biochemistry V. 40 1903 2001.
ISSN: ISSN 0006-2960
PubMed: 11329256
DOI: 10.1021/BI002438H
Page generated: Sat Oct 5 10:15:36 2024

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