Manganese in PDB 2d3c: Crystal Structure of the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate

All present enzymatic activity of Crystal Structure of the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate:
6.3.1.2;

The structure of Crystal Structure of the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate, PDB code: 2d3c was solved by H.Unno, T.Uchida, H.Sugawara, G.Kurisu, T.Sugiyama, T.Yamaya, H.Sakakibara, T.Hase, M.Kusunoki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.36 / 3.81
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	95.958, 191.012, 118.124, 90.00, 101.23, 90.00
R / Rfree (%)	18.5 / 22.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate (pdb code 2d3c). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 30 binding sites of Manganese where determined in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate, PDB code: 2d3c:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 30 in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate


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 the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:52.5 occ:1.00 OE2 A:GLU129 1.9 58.9 1.0 O3B A:ADP6001 2.2 55.8 1.0 OE1 A:GLU199 2.3 57.9 1.0 O2A A:ADP6001 2.3 61.8 1.0 O15 A:P3P5001 2.4 50.8 1.0 CD A:GLU129 3.0 59.0 1.0 CD A:GLU199 3.2 55.8 1.0 O3A A:ADP6001 3.3 58.2 1.0 PA A:ADP6001 3.3 62.1 1.0 PB A:ADP6001 3.3 57.9 1.0 O14 A:P3P5001 3.4 50.9 1.0 P12 A:P3P5001 3.4 52.9 1.0 OE2 A:GLU199 3.4 56.2 1.0 MN A:MN1002 3.6 62.6 1.0 MN A:MN1003 3.7 40.7 1.0 OE1 A:GLU129 3.8 59.0 1.0 CG A:GLU129 3.8 59.2 1.0 O1B A:ADP6001 4.1 55.7 1.0 OE1 A:GLN201 4.2 59.2 1.0 ND2 A:ASN190 4.3 54.4 1.0 O13 A:P3P5001 4.3 50.8 1.0 O5' A:ADP6001 4.3 67.6 1.0 O2B A:ADP6001 4.5 55.3 1.0 CB A:GLU129 4.5 58.6 1.0 OEB A:P3P5001 4.5 53.0 1.0 O1A A:ADP6001 4.5 62.8 1.0 CG A:GLU199 4.6 55.6 1.0 CD A:GLN201 4.8 58.1 1.0 CG A:GLN201 4.8 57.7 1.0 ND1 A:HIS249 5.0 62.0 1.0

Manganese binding site 2 out of 30 in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate


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 the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1002 b:62.6 occ:1.00 OE2 A:GLU330 2.0 70.4 1.0 OE1 A:GLU129 2.2 59.0 1.0 ND1 A:HIS249 2.4 62.0 1.0 OE2 A:GLU129 2.5 58.9 1.0 CD A:GLU129 2.7 59.0 1.0 O14 A:P3P5001 2.7 50.9 1.0 O1B A:ADP6001 2.7 55.7 1.0 CE1 A:HIS249 3.1 61.1 1.0 O3B A:ADP6001 3.2 55.8 1.0 CD A:GLU330 3.2 69.1 1.0 PB A:ADP6001 3.4 57.9 1.0 CG A:HIS249 3.5 62.0 1.0 P12 A:P3P5001 3.5 52.9 1.0 O15 A:P3P5001 3.6 50.8 1.0 MN A:MN1001 3.6 52.5 1.0 OEB A:P3P5001 3.6 53.0 1.0 NH2 A:ARG332 3.6 65.8 1.0 OE1 A:GLU330 3.9 68.4 1.0 NH1 A:ARG316 3.9 65.2 1.0 CB A:HIS249 3.9 62.3 1.0 O3A A:ADP6001 4.0 58.2 1.0 CG A:GLU129 4.2 59.2 1.0 CG A:GLU330 4.3 69.1 1.0 NE2 A:HIS249 4.3 60.1 1.0 NH1 A:ARG311 4.4 67.0 1.0 CD2 A:HIS249 4.5 60.7 1.0 NE A:ARG332 4.5 63.8 1.0 CZ A:ARG332 4.5 64.6 1.0 MN A:MN1003 4.7 40.7 1.0 CB A:GLU129 4.9 58.6 1.0 O2B A:ADP6001 4.9 55.3 1.0

Manganese binding site 3 out of 30 in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate


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 the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1003 b:40.7 occ:1.00 O15 A:P3P5001 1.7 50.8 1.0 OE2 A:GLU199 1.9 56.2 1.0 OE1 A:GLU131 2.0 53.0 1.0 OE2 A:GLU192 2.2 55.3 1.0 P12 A:P3P5001 2.8 52.9 1.0 OEB A:P3P5001 2.9 53.0 1.0 CD A:GLU199 2.9 55.8 1.0 CD A:GLU192 3.0 55.5 1.0 CD A:GLU131 3.1 53.6 1.0 O13 A:P3P5001 3.4 50.8 1.0 OE1 A:GLU199 3.4 57.9 1.0 CG A:GLU131 3.6 53.8 1.0 CGP A:P3P5001 3.6 57.9 1.0 MN A:MN1001 3.7 52.5 1.0 CG A:GLU192 3.7 54.4 1.0 PDP A:P3P5001 3.8 56.0 1.0 OE2 A:GLU129 3.9 58.9 1.0 OE1 A:GLU192 3.9 55.8 1.0 CBP A:P3P5001 3.9 59.9 1.0 O14 A:P3P5001 4.1 50.9 1.0 CG A:GLU199 4.1 55.6 1.0 OE2 A:GLU131 4.2 53.7 1.0 CE1 A:HIS249 4.3 61.1 1.0 CEP A:P3P5001 4.5 51.2 1.0 CB A:GLU199 4.5 54.8 1.0 ND1 A:HIS249 4.6 62.0 1.0 OD1 A:ASN190 4.6 56.5 1.0 MN A:MN1002 4.7 62.6 1.0 CD A:GLU129 5.0 59.0 1.0

Manganese binding site 4 out of 30 in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate


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 the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1011 b:61.8 occ:1.00 OE2 B:GLU129 1.9 58.8 1.0 O2A B:ADP6002 2.0 40.1 1.0 O3B B:ADP6002 2.1 43.7 1.0 OE1 B:GLU199 2.1 57.8 1.0 O15 B:P3P5002 2.4 41.4 1.0 CD B:GLU129 3.0 59.0 1.0 O13 B:P3P5002 3.1 33.2 1.0 CD B:GLU199 3.1 55.7 1.0 P12 B:P3P5002 3.1 40.8 1.0 PB B:ADP6002 3.3 43.2 1.0 OE2 B:GLU199 3.3 56.0 1.0 PA B:ADP6002 3.4 39.5 1.0 O3A B:ADP6002 3.7 40.8 1.0 CG B:GLU129 3.8 59.2 1.0 MN B:MN1013 3.8 54.9 1.0 O1B B:ADP6002 3.9 37.5 1.0 OE1 B:GLU129 3.9 59.0 1.0 MN B:MN1012 4.0 32.7 1.0 OE1 B:GLN201 4.0 59.3 1.0 ND2 B:ASN190 4.1 54.4 1.0 O14 B:P3P5002 4.2 32.9 1.0 OEB B:P3P5002 4.3 39.1 1.0 O5' B:ADP6002 4.4 40.3 1.0 O1A B:ADP6002 4.4 38.4 1.0 CB B:GLU129 4.4 58.6 1.0 CG B:GLU199 4.5 55.6 1.0 O2B B:ADP6002 4.5 39.5 1.0 CD B:GLN201 4.6 58.1 1.0 CG B:GLN201 4.7 57.8 1.0

Manganese binding site 5 out of 30 in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate


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 the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1012 b:32.7 occ:1.00 OE2 B:GLU330 1.7 70.4 1.0 OE1 B:GLU129 1.9 59.0 1.0 O1B B:ADP6002 2.2 37.5 1.0 ND1 B:HIS249 2.3 62.0 1.0 O15 B:P3P5002 2.5 41.4 1.0 CD B:GLU129 2.5 59.0 1.0 OE2 B:GLU129 2.6 58.8 1.0 CD B:GLU330 2.8 69.0 1.0 O14 B:P3P5002 3.0 32.9 1.0 CE1 B:HIS249 3.2 61.0 1.0 CG B:HIS249 3.2 62.0 1.0 PB B:ADP6002 3.4 43.2 1.0 P12 B:P3P5002 3.4 40.8 1.0 CB B:HIS249 3.5 62.3 1.0 OE1 B:GLU330 3.6 68.4 1.0 O3B B:ADP6002 3.8 43.7 1.0 CG B:GLU330 3.8 69.2 1.0 NH2 B:ARG332 3.9 65.9 1.0 NH1 B:ARG316 3.9 65.2 1.0 MN B:MN1011 4.0 61.8 1.0 CG B:GLU129 4.0 59.2 1.0 O3A B:ADP6002 4.2 40.8 1.0 O B:HOH6019 4.3 51.4 1.0 NE2 B:HIS249 4.3 60.0 1.0 CD2 B:HIS249 4.3 60.7 1.0 NE B:ARG332 4.5 63.8 1.0 OEB B:P3P5002 4.6 39.1 1.0 O2A B:ADP6002 4.6 40.1 1.0 O13 B:P3P5002 4.6 33.2 1.0 CZ B:ARG332 4.6 64.6 1.0 O2B B:ADP6002 4.6 39.5 1.0 CB B:GLU129 4.8 58.6 1.0 NH1 B:ARG311 4.8 67.1 1.0

Manganese binding site 6 out of 30 in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate


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 the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1013 b:54.9 occ:1.00 OE2 B:GLU199 1.9 56.0 1.0 OE1 B:GLU131 2.0 52.9 1.0 OE2 B:GLU192 2.2 55.2 1.0 OEB B:P3P5002 2.3 39.1 1.0 O15 B:P3P5002 2.8 41.4 1.0 CD B:GLU199 2.9 55.7 1.0 P12 B:P3P5002 3.0 40.8 1.0 CD B:GLU192 3.0 55.4 1.0 CD B:GLU131 3.0 53.5 1.0 OE1 B:GLU199 3.4 57.8 1.0 CG B:GLU131 3.5 53.7 1.0 O13 B:P3P5002 3.7 33.2 1.0 CG B:GLU192 3.7 54.4 1.0 PDP B:P3P5002 3.7 33.8 1.0 MN B:MN1011 3.8 61.8 1.0 OE1 B:GLU192 3.8 55.8 1.0 OE2 B:GLU129 3.9 58.8 1.0 CG B:GLU199 4.0 55.6 1.0 CBP B:P3P5002 4.0 32.8 1.0 OE2 B:GLU131 4.1 53.6 1.0 O14 B:P3P5002 4.2 32.9 1.0 CEP B:P3P5002 4.3 30.9 1.0 CB B:GLU199 4.4 54.8 1.0 CE1 B:HIS249 4.4 61.0 1.0 CGP B:P3P5002 4.4 32.6 1.0 OD1 B:ASN190 4.6 56.6 1.0 ND1 B:HIS249 4.7 62.0 1.0 NP B:P3P5002 4.8 32.1 1.0 OEA B:P3P5002 4.9 36.3 1.0

Manganese binding site 7 out of 30 in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate


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 the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1021 b:88.1 occ:1.00 OE2 C:GLU129 1.8 58.9 1.0 O15 C:P3P5003 2.1 59.2 1.0 O3B C:ADP6003 2.2 65.0 1.0 O2A C:ADP6003 2.3 50.0 1.0 OE1 C:GLU199 2.3 57.8 1.0 CD C:GLU129 2.9 59.0 1.0 P12 C:P3P5003 3.0 58.8 1.0 CD C:GLU199 3.1 55.8 1.0 OE2 C:GLU199 3.2 56.1 1.0 O13 C:P3P5003 3.4 52.6 1.0 PB C:ADP6003 3.4 61.9 1.0 O3A C:ADP6003 3.5 57.5 1.0 MN C:MN1023 3.5 56.7 1.0 PA C:ADP6003 3.5 52.4 1.0 MN C:MN1022 3.5 51.9 1.0 O14 C:P3P5003 3.6 53.2 1.0 OE1 C:GLU129 3.8 59.0 1.0 CG C:GLU129 3.8 59.2 1.0 O2B C:ADP6003 4.1 59.5 1.0 ND2 C:ASN190 4.3 54.4 1.0 OEB C:P3P5003 4.3 57.1 1.0 OE1 C:GLN201 4.4 59.2 1.0 CB C:GLU129 4.4 58.6 1.0 CG C:GLU199 4.6 55.6 1.0 O5' C:ADP6003 4.6 55.6 1.0 O1A C:ADP6003 4.6 45.4 1.0 O1B C:ADP6003 4.6 60.0 1.0 O C:HOH6005 4.8 52.9 1.0 ND1 C:HIS249 4.8 61.9 1.0 O C:HOH6004 4.8 35.0 1.0 CD C:GLN201 5.0 58.1 1.0 OE2 C:GLU192 5.0 55.3 1.0 CG C:GLN201 5.0 57.8 1.0

Manganese binding site 8 out of 30 in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate


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 the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1022 b:51.9 occ:1.00 OE2 C:GLU330 1.9 70.4 1.0 O14 C:P3P5003 2.2 53.2 1.0 OE1 C:GLU129 2.2 59.0 1.0 O3B C:ADP6003 2.2 65.0 1.0 ND1 C:HIS249 2.6 61.9 1.0 OE2 C:GLU129 2.6 58.9 1.0 CD C:GLU129 2.8 59.0 1.0 O1B C:ADP6003 3.0 60.0 1.0 CD C:GLU330 3.0 69.1 1.0 PB C:ADP6003 3.2 61.9 1.0 P12 C:P3P5003 3.3 58.8 1.0 CE1 C:HIS249 3.4 61.0 1.0 MN C:MN1021 3.5 88.1 1.0 CG C:HIS249 3.6 62.0 1.0 NH1 C:ARG316 3.7 65.2 1.0 NH2 C:ARG332 3.7 65.9 1.0 OE1 C:GLU330 3.7 68.4 1.0 O15 C:P3P5003 3.8 59.2 1.0 O3A C:ADP6003 3.9 57.5 1.0 CB C:HIS249 4.0 62.3 1.0 CG C:GLU330 4.1 69.1 1.0 O13 C:P3P5003 4.1 52.6 1.0 CG C:GLU129 4.3 59.2 1.0 NH1 C:ARG311 4.3 67.1 1.0 OEB C:P3P5003 4.5 57.1 1.0 NE C:ARG332 4.5 63.8 1.0 O2B C:ADP6003 4.5 59.5 1.0 NE2 C:HIS249 4.5 60.0 1.0 CZ C:ARG332 4.6 64.6 1.0 CD2 C:HIS249 4.7 60.7 1.0 O2A C:ADP6003 4.8 50.0 1.0 O C:HOH6005 4.8 52.9 1.0 CZ C:ARG316 4.9 66.5 1.0 MN C:MN1023 5.0 56.7 1.0

Manganese binding site 9 out of 30 in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate


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 the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1023 b:56.7 occ:1.00 O15 C:P3P5003 1.8 59.2 1.0 OE2 C:GLU199 1.9 56.1 1.0 OE1 C:GLU131 2.1 52.8 1.0 OE2 C:GLU192 2.2 55.3 1.0 OEB C:P3P5003 2.5 57.1 1.0 P12 C:P3P5003 2.8 58.8 1.0 CD C:GLU199 2.9 55.8 1.0 CD C:GLU192 3.1 55.4 1.0 CD C:GLU131 3.1 53.5 1.0 O C:HOH6005 3.4 52.9 1.0 OE1 C:GLU199 3.4 57.8 1.0 MN C:MN1021 3.5 88.1 1.0 CG C:GLU131 3.5 53.8 1.0 O14 C:P3P5003 3.7 53.2 1.0 CG C:GLU192 3.7 54.4 1.0 OE2 C:GLU129 3.9 58.9 1.0 OE1 C:GLU192 3.9 55.8 1.0 O13 C:P3P5003 3.9 52.6 1.0 PDP C:P3P5003 3.9 54.3 1.0 CG C:GLU199 4.0 55.6 1.0 CBP C:P3P5003 4.0 52.8 1.0 OE2 C:GLU131 4.2 53.6 1.0 CE1 C:HIS249 4.3 61.0 1.0 CEP C:P3P5003 4.4 53.7 1.0 CB C:GLU199 4.4 54.8 1.0 NP C:P3P5003 4.5 49.0 1.0 CGP C:P3P5003 4.5 53.2 1.0 OD1 C:ASN190 4.6 56.5 1.0 ND1 C:HIS249 4.6 61.9 1.0 O3B C:ADP6003 4.9 65.0 1.0 CD C:GLU129 4.9 59.0 1.0 CAP C:P3P5003 5.0 52.6 1.0 MN C:MN1022 5.0 51.9 1.0

Manganese binding site 10 out of 30 in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate


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 the Maize Glutamine Synthetase Complexed with Adp and Phosphinothricin Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1031 b:57.5 occ:1.00 OE2 D:GLU129 1.8 58.8 1.0 O3B D:ADP6005 2.1 67.6 1.0 O15 D:P3P5004 2.1 64.5 1.0 OE1 D:GLU199 2.3 57.9 1.0 O2A D:ADP6005 2.4 69.9 1.0 CD D:GLU129 2.9 59.1 1.0 CD D:GLU199 3.1 55.8 1.0 PB D:ADP6005 3.2 71.4 1.0 OE2 D:GLU199 3.3 56.1 1.0 P12 D:P3P5004 3.3 67.9 1.0 O3A D:ADP6005 3.3 70.4 1.0 PA D:ADP6005 3.4 69.9 1.0 MN D:MN1032 3.5 83.3 1.0 MN D:MN1033 3.5 51.2 1.0 CG D:GLU129 3.8 59.2 1.0 OE1 D:GLU129 3.8 59.1 1.0 O13 D:P3P5004 3.8 71.6 1.0 O1B D:ADP6005 4.0 67.5 1.0 O14 D:P3P5004 4.0 65.1 1.0 O A:HOH6003 4.1 50.8 1.0 ND2 D:ASN190 4.3 54.4 1.0 OE1 D:GLN201 4.3 59.2 1.0 OEB D:P3P5004 4.4 65.4 1.0 CB D:GLU129 4.4 58.5 1.0 O1A D:ADP6005 4.4 70.6 1.0 O2B D:ADP6005 4.5 71.1 1.0 O5' D:ADP6005 4.5 69.1 1.0 CG D:GLU199 4.5 55.5 1.0 O D:HOH6017 4.8 86.3 1.0 ND1 D:HIS249 4.9 62.0 1.0 CD D:GLN201 4.9 58.1 1.0 CG D:GLN201 4.9 57.7 1.0 OE2 D:GLU192 5.0 55.1 1.0

H.Unno, T.Uchida, H.Sugawara, G.Kurisu, T.Sugiyama, T.Yamaya, H.Sakakibara, T.Hase, M.Kusunoki. Atomic Structure of Plant Glutamine Synthetase: A Key Enzyme For Plant Productivity J.Biol.Chem. V. 281 29287 2006.
ISSN: ISSN 0021-9258
PubMed: 16829528
DOI: 10.1074/JBC.M601497200