Manganese in PDB 2d3b: Crystal Structure of the Maize Glutamine Synthetase Complexed with Amppnp and Methionine Sulfoximine

All present enzymatic activity of Crystal Structure of the Maize Glutamine Synthetase Complexed with Amppnp and Methionine Sulfoximine:
6.3.1.2;

The structure of Crystal Structure of the Maize Glutamine Synthetase Complexed with Amppnp and Methionine Sulfoximine, PDB code: 2d3b 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)	33.50 / 3.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	95.881, 190.943, 117.904, 90.00, 101.23, 90.00
R / Rfree (%)	16.6 / 20.9

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 Amppnp and Methionine Sulfoximine (pdb code 2d3b). 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 Amppnp and Methionine Sulfoximine, PDB code: 2d3b:
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 Amppnp and Methionine Sulfoximine


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 Amppnp and Methionine Sulfoximine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:68.3 occ:1.00 N3B A:ANP6001 2.0 71.0 1.0 OE1 A:GLU199 2.1 65.6 1.0 OE2 A:GLU129 2.1 61.8 1.0 O2A A:ANP6001 2.3 66.3 1.0 O2G A:ANP6001 2.3 80.5 1.0 PG A:ANP6001 2.5 76.7 1.0 O3G A:ANP6001 2.8 76.3 1.0 CD A:GLU199 3.2 64.5 1.0 CD A:GLU129 3.2 63.5 1.0 PB A:ANP6001 3.3 61.8 1.0 PA A:ANP6001 3.4 60.4 1.0 OE2 A:GLU199 3.6 65.0 1.0 O3A A:ANP6001 3.8 60.7 1.0 MN A:MN1003 3.8 57.4 1.0 O2B A:ANP6001 3.9 61.3 1.0 OE1 A:GLN201 4.0 64.3 1.0 O1A A:ANP6001 4.0 61.2 1.0 OE1 A:GLU129 4.0 62.8 1.0 O1G A:ANP6001 4.0 74.1 1.0 CG A:GLU129 4.1 64.4 1.0 ND2 A:ASN190 4.1 62.3 1.0 MN A:MN1002 4.2 62.9 1.0 CB A:GLU129 4.3 64.7 1.0 O1B A:ANP6001 4.4 60.0 1.0 CD A:GLN201 4.4 64.1 1.0 CG A:GLU199 4.4 62.7 1.0 CG A:GLN201 4.4 64.5 1.0 NE C:MSL5001 4.5 51.1 1.0 O5' A:ANP6001 4.8 64.3 1.0

Manganese binding site 2 out of 30 in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Amppnp and Methionine Sulfoximine


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 Amppnp and Methionine Sulfoximine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1002 b:62.9 occ:1.00 OE2 A:GLU330 1.8 77.1 1.0 OE1 A:GLU129 1.9 62.8 1.0 ND1 A:HIS249 2.5 71.2 1.0 CD A:GLU129 2.7 63.5 1.0 OE2 A:GLU129 2.8 61.8 1.0 O1B A:ANP6001 2.9 60.0 1.0 N3B A:ANP6001 2.9 71.0 1.0 O1G A:ANP6001 2.9 74.1 1.0 O2G A:ANP6001 2.9 80.5 1.0 CD A:GLU330 2.9 76.4 1.0 PG A:ANP6001 3.0 76.7 1.0 CE1 A:HIS249 3.4 70.7 1.0 CG A:HIS249 3.4 70.4 1.0 PB A:ANP6001 3.5 61.8 1.0 CB A:HIS249 3.7 69.6 1.0 OE1 A:GLU330 3.8 75.0 1.0 CG A:GLU330 3.8 76.5 1.0 NH2 A:ARG332 3.9 71.0 1.0 NH1 A:ARG316 4.0 76.2 1.0 NE C:MSL5001 4.0 51.1 1.0 CG A:GLU129 4.1 64.4 1.0 MN A:MN1001 4.2 68.3 1.0 NE A:ARG332 4.3 69.9 1.0 O3A A:ANP6001 4.3 60.7 1.0 NE2 A:HIS249 4.5 70.4 1.0 CD2 A:HIS249 4.5 70.4 1.0 O3G A:ANP6001 4.5 76.3 1.0 CZ A:ARG332 4.6 70.4 1.0 O2A A:ANP6001 4.7 66.3 1.0 NH1 A:ARG311 4.7 74.9 1.0 O2B A:ANP6001 4.8 61.3 1.0 O A:HOH6018 4.8 50.3 1.0 MN A:MN1003 4.9 57.4 1.0 CB A:GLU129 4.9 64.7 1.0

Manganese binding site 3 out of 30 in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Amppnp and Methionine Sulfoximine


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 Amppnp and Methionine Sulfoximine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1003 b:57.4 occ:1.00 OE2 A:GLU199 2.0 65.0 1.0 NE C:MSL5001 2.1 51.1 1.0 OE1 A:GLU131 2.2 59.6 1.0 O2G A:ANP6001 2.3 80.5 1.0 OE2 A:GLU192 2.7 60.9 1.0 CD A:GLU199 3.0 64.5 1.0 SD C:MSL5001 3.2 54.8 1.0 O3G A:ANP6001 3.2 76.3 1.0 PG A:ANP6001 3.3 76.7 1.0 CD A:GLU131 3.3 60.0 1.0 OE1 A:GLU199 3.3 65.6 1.0 CD A:GLU192 3.3 61.6 1.0 CG C:MSL5001 3.6 54.5 1.0 CE C:MSL5001 3.6 54.3 1.0 MN A:MN1001 3.8 68.3 1.0 CG A:GLU131 4.0 60.4 1.0 OE1 A:GLU192 4.0 62.6 1.0 OE2 A:GLU129 4.0 61.8 1.0 O1G A:ANP6001 4.0 74.1 1.0 CG A:GLU192 4.1 61.4 1.0 OE2 A:GLU131 4.2 58.9 1.0 CG A:GLU199 4.3 62.7 1.0 CB C:MSL5001 4.3 54.1 1.0 CE1 A:HIS249 4.4 70.7 1.0 N C:MSL5001 4.5 56.0 1.0 OE C:MSL5001 4.5 55.8 1.0 N3B A:ANP6001 4.6 71.0 1.0 ND1 A:HIS249 4.6 71.2 1.0 OD1 A:ASN190 4.7 61.3 1.0 CB A:GLU199 4.8 61.8 1.0 MN A:MN1002 4.9 62.9 1.0

Manganese binding site 4 out of 30 in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Amppnp and Methionine Sulfoximine


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 Amppnp and Methionine Sulfoximine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1011 b:62.6 occ:1.00 N3B B:ANP6002 2.1 57.9 1.0 OE2 B:GLU129 2.2 61.7 1.0 OE1 B:GLU199 2.2 65.7 1.0 O2A B:ANP6002 2.2 45.3 1.0 O2G B:ANP6002 2.3 65.9 1.0 PG B:ANP6002 2.7 62.7 1.0 O3G B:ANP6002 3.1 59.4 1.0 PB B:ANP6002 3.2 50.0 1.0 CD B:GLU199 3.2 64.2 1.0 CD B:GLU129 3.3 63.3 1.0 PA B:ANP6002 3.3 42.6 1.0 O3A B:ANP6002 3.4 48.2 1.0 OE2 B:GLU199 3.6 64.8 1.0 O2B B:ANP6002 3.8 48.7 1.0 O1A B:ANP6002 3.9 42.2 1.0 MN B:MN1013 4.0 56.8 1.0 OE1 B:GLN201 4.0 64.2 1.0 OE1 B:GLU129 4.0 62.7 1.0 ND2 B:ASN190 4.1 62.2 1.0 O1G B:ANP6002 4.1 60.6 1.0 CG B:GLU129 4.1 64.2 1.0 MN B:MN1012 4.3 60.2 1.0 CB B:GLU129 4.4 64.7 1.0 O1B B:ANP6002 4.4 49.9 1.0 CD B:GLN201 4.4 64.1 1.0 CG B:GLU199 4.4 62.5 1.0 CG B:GLN201 4.5 64.6 1.0 O5' B:ANP6002 4.7 44.4 1.0 NE C:MSL5002 4.8 41.8 1.0 CG B:ASN190 4.9 61.4 1.0

Manganese binding site 5 out of 30 in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Amppnp and Methionine Sulfoximine


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 Amppnp and Methionine Sulfoximine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1012 b:60.2 occ:1.00 OE2 B:GLU330 1.7 77.0 1.0 OE1 B:GLU129 2.0 62.7 1.0 ND1 B:HIS249 2.5 70.9 1.0 O1G B:ANP6002 2.5 60.6 1.0 N3B B:ANP6002 2.6 57.9 1.0 O1B B:ANP6002 2.6 49.9 1.0 CD B:GLU129 2.8 63.3 1.0 CD B:GLU330 2.9 76.4 1.0 OE2 B:GLU129 2.9 61.7 1.0 PG B:ANP6002 2.9 62.7 1.0 PB B:ANP6002 3.1 50.0 1.0 CG B:HIS249 3.3 70.3 1.0 O2G B:ANP6002 3.4 65.9 1.0 CE1 B:HIS249 3.4 70.5 1.0 CB B:HIS249 3.5 69.6 1.0 CG B:GLU330 3.7 76.5 1.0 OE1 B:GLU330 3.8 75.1 1.0 NH2 B:ARG332 4.0 70.9 1.0 NH1 B:ARG316 4.0 76.1 1.0 O2B B:ANP6002 4.1 48.7 1.0 CG B:GLU129 4.2 64.2 1.0 NE B:ARG332 4.3 69.7 1.0 MN B:MN1011 4.3 62.6 1.0 O3G B:ANP6002 4.3 59.4 1.0 CD2 B:HIS249 4.4 70.2 1.0 NE2 B:HIS249 4.5 70.0 1.0 O3A B:ANP6002 4.5 48.2 1.0 O2A B:ANP6002 4.6 45.3 1.0 CZ B:ARG332 4.6 70.3 1.0 NE C:MSL5002 4.9 41.8 1.0 OE C:MSL5002 4.9 37.4 1.0 NH1 B:ARG311 4.9 75.0 1.0 CB B:GLU129 4.9 64.7 1.0

Manganese binding site 6 out of 30 in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Amppnp and Methionine Sulfoximine


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 Amppnp and Methionine Sulfoximine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1013 b:56.8 occ:1.00 OE2 B:GLU199 1.9 64.8 1.0 NE C:MSL5002 1.9 41.8 1.0 OE1 B:GLU131 2.1 59.5 1.0 O2G B:ANP6002 2.2 65.9 1.0 OE2 B:GLU192 2.4 60.9 1.0 CD B:GLU199 2.8 64.2 1.0 CD B:GLU192 3.2 61.6 1.0 CD B:GLU131 3.2 60.0 1.0 OE1 B:GLU199 3.2 65.7 1.0 PG B:ANP6002 3.2 62.7 1.0 SD C:MSL5002 3.4 41.0 1.0 O3G B:ANP6002 3.4 59.4 1.0 CG B:GLU131 3.7 60.3 1.0 CG B:GLU192 3.8 61.4 1.0 O1G B:ANP6002 3.8 60.6 1.0 CE C:MSL5002 3.9 41.9 1.0 OE1 B:GLU192 3.9 62.6 1.0 MN B:MN1011 4.0 62.6 1.0 CB C:MSL5002 4.0 40.1 1.0 OE C:MSL5002 4.1 37.4 1.0 CG B:GLU199 4.1 62.5 1.0 OE2 B:GLU129 4.1 61.7 1.0 OE2 B:GLU131 4.2 59.0 1.0 N C:MSL5002 4.3 43.8 1.0 CG C:MSL5002 4.4 38.4 1.0 CE1 B:HIS249 4.5 70.5 1.0 N3B B:ANP6002 4.5 57.9 1.0 CB B:GLU199 4.5 61.9 1.0 OD1 B:ASN190 4.5 61.2 1.0 ND1 B:HIS249 4.7 70.9 1.0 CA C:MSL5002 4.9 44.0 1.0

Manganese binding site 7 out of 30 in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Amppnp and Methionine Sulfoximine


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 Amppnp and Methionine Sulfoximine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1021 b:66.0 occ:1.00 OE1 C:GLU199 2.1 65.7 1.0 OE2 C:GLU129 2.2 61.8 1.0 O2A C:ANP6003 2.2 75.1 1.0 N3B C:ANP6003 2.3 72.8 1.0 O2G C:ANP6003 2.8 76.5 1.0 PG C:ANP6003 3.0 75.1 1.0 CD C:GLU199 3.0 64.4 1.0 O3G C:ANP6003 3.1 73.0 1.0 PA C:ANP6003 3.3 72.4 1.0 PB C:ANP6003 3.3 66.8 1.0 O3A C:ANP6003 3.3 69.1 1.0 OE2 C:GLU199 3.4 64.8 1.0 CD C:GLU129 3.4 63.4 1.0 O2B C:ANP6003 3.6 64.3 1.0 O C:HOH6004 3.6 35.7 1.0 MN C:MN1023 3.7 63.5 1.0 ND2 C:ASN190 3.9 61.9 1.0 O1A C:ANP6003 4.0 68.9 1.0 OE1 C:GLN201 4.1 64.2 1.0 OE1 C:GLU129 4.2 62.8 1.0 CG C:GLU129 4.2 64.3 1.0 MN C:MN1022 4.3 66.1 1.0 CG C:GLU199 4.3 62.8 1.0 O1G C:ANP6003 4.4 72.3 1.0 CB C:GLU129 4.4 64.6 1.0 CD C:GLN201 4.6 64.2 1.0 O1B C:ANP6003 4.6 64.5 1.0 CG C:GLN201 4.6 64.6 1.0 O5' C:ANP6003 4.7 72.9 1.0 CG C:ASN190 4.8 61.4 1.0 NE C:MSL5003 4.8 64.0 1.0 OD1 C:ASN190 4.9 61.2 1.0

Manganese binding site 8 out of 30 in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Amppnp and Methionine Sulfoximine


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 Amppnp and Methionine Sulfoximine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1022 b:66.1 occ:1.00 OE2 C:GLU330 1.8 76.9 1.0 OE1 C:GLU129 2.1 62.8 1.0 ND1 C:HIS249 2.3 71.2 1.0 N3B C:ANP6003 2.6 72.8 1.0 O1B C:ANP6003 2.7 64.5 1.0 CD C:GLU129 2.8 63.4 1.0 O1G C:ANP6003 2.8 72.3 1.0 O2G C:ANP6003 2.9 76.5 1.0 OE2 C:GLU129 2.9 61.8 1.0 PG C:ANP6003 2.9 75.1 1.0 CD C:GLU330 3.0 76.4 1.0 PB C:ANP6003 3.1 66.8 1.0 CG C:HIS249 3.3 70.4 1.0 CE1 C:HIS249 3.3 70.7 1.0 CB C:HIS249 3.5 69.5 1.0 O3A C:ANP6003 3.6 69.1 1.0 OE1 C:GLU330 3.9 75.0 1.0 CG C:GLU330 3.9 76.5 1.0 NH2 C:ARG332 3.9 71.2 1.0 NH1 C:ARG316 4.1 76.2 1.0 CG C:GLU129 4.2 64.3 1.0 MN C:MN1021 4.3 66.0 1.0 NE C:ARG332 4.3 69.7 1.0 NE2 C:HIS249 4.4 70.3 1.0 CD2 C:HIS249 4.4 70.3 1.0 O3G C:ANP6003 4.5 73.0 1.0 O2B C:ANP6003 4.5 64.3 1.0 CZ C:ARG332 4.6 70.4 1.0 NH1 C:ARG311 4.8 75.0 1.0 CB C:GLU129 4.9 64.6 1.0

Manganese binding site 9 out of 30 in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Amppnp and Methionine Sulfoximine


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 Amppnp and Methionine Sulfoximine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1023 b:63.5 occ:1.00 OE2 C:GLU199 1.8 64.8 1.0 NE C:MSL5003 2.1 64.0 1.0 OE1 C:GLU131 2.2 59.9 1.0 O2G C:ANP6003 2.3 76.5 1.0 OE2 C:GLU192 2.5 61.1 1.0 CD C:GLU199 2.8 64.4 1.0 O3G C:ANP6003 3.1 73.0 1.0 CD C:GLU192 3.2 61.9 1.0 CD C:GLU131 3.2 60.1 1.0 OE1 C:GLU199 3.2 65.7 1.0 PG C:ANP6003 3.2 75.1 1.0 SD C:MSL5003 3.6 64.5 1.0 MN C:MN1021 3.7 66.0 1.0 CG C:GLU131 3.7 60.5 1.0 OE1 C:GLU192 3.8 62.9 1.0 CG C:GLU192 3.8 61.6 1.0 CB C:MSL5003 4.0 65.3 1.0 O1G C:ANP6003 4.0 72.3 1.0 CG C:GLU199 4.1 62.8 1.0 OE2 C:GLU129 4.2 61.8 1.0 OE2 C:GLU131 4.2 58.7 1.0 N3B C:ANP6003 4.4 72.8 1.0 CE C:MSL5003 4.4 63.4 1.0 OE C:MSL5003 4.4 65.6 1.0 CG C:MSL5003 4.4 64.8 1.0 CB C:GLU199 4.5 62.0 1.0 OD1 C:ASN190 4.5 61.2 1.0 CE1 C:HIS249 4.6 70.7 1.0 N C:MSL5003 4.6 64.1 1.0 ND1 C:HIS249 4.8 71.2 1.0 ND2 C:ASN190 5.0 61.9 1.0 CA C:MSL5003 5.0 66.8 1.0

Manganese binding site 10 out of 30 in the Crystal Structure of the Maize Glutamine Synthetase Complexed with Amppnp and Methionine Sulfoximine


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 Amppnp and Methionine Sulfoximine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1031 b:65.8 occ:1.00 OE2 D:GLU129 2.0 61.5 1.0 OE1 D:GLU199 2.1 65.6 1.0 N3B D:ANP6004 2.1 93.5 1.0 O2G D:ANP6004 2.3 96.4 1.0 O2A D:ANP6004 2.4 84.8 1.0 PG D:ANP6004 2.8 96.4 1.0 CD D:GLU199 3.1 64.4 1.0 PB D:ANP6004 3.2 88.8 1.0 CD D:GLU129 3.2 63.5 1.0 PA D:ANP6004 3.3 83.7 1.0 O3A D:ANP6004 3.4 85.6 1.0 O3G D:ANP6004 3.4 96.2 1.0 OE2 D:GLU199 3.4 64.8 1.0 MN D:MN1033 3.6 56.7 1.0 CG D:GLU129 4.0 64.1 1.0 O1A D:ANP6004 4.0 84.2 1.0 OE1 D:GLU129 4.1 63.0 1.0 MN D:MN1032 4.1 70.2 1.0 O1G D:ANP6004 4.1 94.9 1.0 OE1 D:GLN201 4.1 64.6 1.0 O1B D:ANP6004 4.1 89.3 1.0 ND2 D:ASN190 4.2 62.0 1.0 O2B D:ANP6004 4.2 88.7 1.0 CB D:GLU129 4.2 64.6 1.0 CG D:GLU199 4.4 62.7 1.0 NE C:MSL5004 4.5 71.8 1.0 CG D:GLN201 4.6 64.6 1.0 CD D:GLN201 4.6 64.3 1.0 O A:HOH6032 4.8 91.8 1.0 O5' D:ANP6004 4.8 85.0 1.0 CG D:ASN190 5.0 61.6 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