Manganese in PDB 2glf: Crystal Structure of Aminipeptidase (M18 Family) From Thermotoga Maritima

The structure of Crystal Structure of Aminipeptidase (M18 Family) From Thermotoga Maritima, PDB code: 2glf was solved by T.Min, L.Shapiro, S.K.Burley, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.83 / 2.80
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	191.225, 191.225, 191.225, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 23.9

The binding sites of Manganese atom in the Crystal Structure of Aminipeptidase (M18 Family) From Thermotoga Maritima (pdb code 2glf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Aminipeptidase (M18 Family) From Thermotoga Maritima, PDB code: 2glf:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in the Crystal Structure of Aminipeptidase (M18 Family) From Thermotoga Maritima


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 Aminipeptidase (M18 Family) From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn5001 b:17.5 occ:1.00 OD1 A:ASP251 2.3 19.5 1.0 O A:HOH5079 2.4 24.1 1.0 OD2 A:ASP328 2.4 16.2 1.0 NE2 A:HIS94 2.4 15.7 1.0 OD1 A:ASP328 2.6 16.6 1.0 CG A:ASP328 2.8 14.2 1.0 CG A:ASP251 3.3 16.8 1.0 MN A:MN5002 3.3 19.7 1.0 CE1 A:HIS94 3.4 16.4 1.0 CD2 A:HIS94 3.4 14.9 1.0 OD2 A:ASP251 3.6 16.8 1.0 OE1 A:GLU280 3.6 35.0 1.0 OE2 A:GLU281 3.9 13.0 1.0 CB A:ASP252 4.3 29.0 1.0 CB A:ASP328 4.3 12.9 1.0 CG A:ASP252 4.4 30.9 1.0 CD A:GLU280 4.4 32.1 1.0 OD1 A:ASP252 4.5 29.6 1.0 ND1 A:HIS94 4.5 16.6 1.0 CG A:HIS94 4.6 14.3 1.0 CE A:MSE426 4.6 34.1 1.0 CG2 A:VAL329 4.6 15.8 1.0 CB A:ASP251 4.7 17.4 1.0 C A:ASP251 4.7 24.6 1.0 CG A:GLU280 4.8 27.6 1.0 O A:ASP251 4.8 24.2 1.0 CD A:GLU281 4.8 10.7 1.0 N A:ASP252 4.9 55.6 1.0 N A:VAL329 4.9 13.8 1.0 OD2 A:ASP252 5.0 31.0 1.0

Manganese binding site 2 out of 8 in the Crystal Structure of Aminipeptidase (M18 Family) From Thermotoga Maritima


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 Aminipeptidase (M18 Family) From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn5002 b:19.7 occ:1.00 OE2 A:GLU281 2.0 13.0 1.0 OD2 A:ASP251 2.4 16.8 1.0 NE2 A:HIS427 2.4 4.8 1.0 OE1 A:GLU281 2.6 10.7 1.0 CD A:GLU281 2.7 10.7 1.0 CG A:ASP251 3.2 16.8 1.0 MN A:MN5001 3.3 17.5 1.0 CE A:MSE426 3.4 34.1 1.0 CD2 A:HIS427 3.4 4.8 1.0 OD1 A:ASP251 3.4 19.5 1.0 CE1 A:HIS427 3.4 4.8 1.0 O A:HOH5079 3.9 24.1 1.0 OE1 A:GLU280 4.0 35.0 1.0 CG A:GLU281 4.2 10.8 1.0 CB A:ASP251 4.4 17.4 1.0 NE2 A:HIS94 4.4 15.7 1.0 CE1 A:HIS94 4.5 16.4 1.0 ND1 A:HIS427 4.5 4.8 1.0 CG A:HIS427 4.5 4.8 1.0 CE1 D:HIS169 4.6 18.9 1.0 NE2 D:HIS169 4.7 19.1 1.0 O A:HOH5072 4.9 11.4 1.0 CD A:PRO98 4.9 17.6 1.0 SE A:MSE426 5.0 40.8 1.0

Manganese binding site 3 out of 8 in the Crystal Structure of Aminipeptidase (M18 Family) From Thermotoga Maritima


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 Aminipeptidase (M18 Family) From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn5003 b:18.1 occ:1.00 OE2 B:GLU281 2.2 21.7 1.0 O B:HOH5072 2.2 28.7 1.0 NE2 B:HIS427 2.2 5.8 1.0 OD2 B:ASP251 2.3 18.6 1.0 OE1 B:GLU281 2.6 22.9 1.0 CD B:GLU281 2.7 22.0 1.0 CG B:ASP251 3.1 19.9 1.0 CE1 B:HIS427 3.2 5.8 1.0 CD2 B:HIS427 3.2 5.8 1.0 CE B:MSE426 3.4 34.5 1.0 MN B:MN5004 3.5 17.9 1.0 OD1 B:ASP251 3.5 19.6 1.0 OE1 B:GLU280 4.2 44.8 1.0 CG B:GLU281 4.2 17.9 1.0 ND1 B:HIS427 4.3 5.8 1.0 CG B:HIS427 4.4 5.8 1.0 CB B:ASP251 4.4 20.2 1.0 CE1 B:HIS94 4.4 9.2 1.0 NE2 B:HIS94 4.5 9.2 1.0 CD B:PRO98 4.7 1.8 1.0 CG B:PRO98 4.7 1.8 1.0

Manganese binding site 4 out of 8 in the Crystal Structure of Aminipeptidase (M18 Family) From Thermotoga Maritima


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 Aminipeptidase (M18 Family) From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn5004 b:17.9 occ:1.00 OD2 B:ASP328 2.0 19.6 1.0 OD1 B:ASP251 2.3 19.6 1.0 NE2 B:HIS94 2.3 9.2 1.0 CG B:ASP328 2.7 23.0 1.0 OD1 B:ASP328 2.7 27.4 1.0 O B:HOH5072 2.8 28.7 1.0 CG B:ASP251 3.2 19.9 1.0 CE1 B:HIS94 3.3 9.2 1.0 CD2 B:HIS94 3.3 9.2 1.0 MN B:MN5003 3.5 18.1 1.0 OD2 B:ASP251 3.5 18.6 1.0 OE1 B:GLU280 3.6 44.8 1.0 CB B:ASP328 4.2 22.0 1.0 CE B:MSE426 4.2 34.5 1.0 O B:HOH5064 4.3 33.6 1.0 ND1 B:HIS94 4.4 9.2 1.0 OE2 B:GLU281 4.4 21.7 1.0 CG B:HIS94 4.4 9.2 1.0 CG B:ASP252 4.5 24.5 1.0 CB B:ASP252 4.5 23.6 1.0 CD B:GLU280 4.5 43.3 1.0 CB B:ASP251 4.6 20.2 1.0 CA B:ASP328 4.7 23.8 1.0 C B:ASP251 4.7 12.2 1.0 OD1 B:ASP252 4.7 21.1 1.0 O B:ASP251 4.8 12.2 1.0 N B:VAL329 4.8 21.1 1.0 OD2 B:ASP252 4.8 28.7 1.0 CG2 B:VAL329 4.9 8.4 1.0 CG B:GLU280 4.9 39.0 1.0

Manganese binding site 5 out of 8 in the Crystal Structure of Aminipeptidase (M18 Family) From Thermotoga Maritima


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 Aminipeptidase (M18 Family) From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn5006 b:15.1 occ:1.00 OD2 C:ASP328 2.3 19.6 1.0 OD1 C:ASP251 2.3 28.1 1.0 NE2 C:HIS94 2.3 7.4 1.0 OD1 C:ASP328 2.6 24.4 1.0 CG C:ASP328 2.8 22.0 1.0 CE1 C:HIS94 3.0 7.4 1.0 OE1 C:GLU280 3.2 35.1 1.0 CG C:ASP251 3.3 26.0 1.0 MN C:MN5007 3.3 17.6 1.0 CD2 C:HIS94 3.5 7.4 1.0 OD2 C:ASP251 3.6 26.9 1.0 O C:HOH5058 3.9 18.3 1.0 OE1 C:GLU281 4.0 11.0 1.0 CD C:GLU280 4.2 35.0 1.0 OD1 C:ASP252 4.2 30.4 1.0 ND1 C:HIS94 4.2 7.4 1.0 CB C:ASP328 4.3 20.8 1.0 CG C:ASP252 4.4 30.6 1.0 CG C:HIS94 4.5 7.4 1.0 CB C:ASP252 4.5 28.1 1.0 O C:HOH5019 4.6 11.4 1.0 CB C:ASP251 4.6 24.5 1.0 CD C:GLU281 4.8 11.8 1.0 CG2 C:VAL329 4.8 9.9 1.0 CE C:MSE426 4.8 40.8 1.0 C C:ASP251 4.8 20.2 1.0 CG C:GLU280 4.8 29.8 1.0 N C:VAL329 4.8 11.2 1.0 O C:ASP251 4.9 20.6 1.0 OE2 C:GLU280 5.0 35.2 1.0 N C:ASP252 5.0 39.0 1.0 CA C:ASP328 5.0 16.4 1.0

Manganese binding site 6 out of 8 in the Crystal Structure of Aminipeptidase (M18 Family) From Thermotoga Maritima


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 Aminipeptidase (M18 Family) From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn5007 b:17.6 occ:1.00 OE1 C:GLU281 2.1 11.0 1.0 NE2 C:HIS427 2.4 6.0 1.0 OD2 C:ASP251 2.6 26.9 1.0 OE2 C:GLU281 2.6 11.0 1.0 CD C:GLU281 2.7 11.8 1.0 CG C:ASP251 3.3 26.0 1.0 MN C:MN5006 3.3 15.1 1.0 CE1 C:HIS427 3.3 6.0 1.0 CD2 C:HIS427 3.4 6.0 1.0 OD1 C:ASP251 3.5 28.1 1.0 CE C:MSE426 3.6 40.8 1.0 OE1 C:GLU280 3.7 35.1 1.0 O C:HOH5058 3.7 18.3 1.0 CG C:GLU281 4.2 13.4 1.0 ND1 C:HIS427 4.5 6.0 1.0 CE1 C:HIS94 4.5 7.4 1.0 CG C:HIS427 4.5 6.0 1.0 O C:HOH5009 4.5 11.4 1.0 CB C:ASP251 4.6 24.5 1.0 NE2 C:HIS94 4.6 7.4 1.0 CD C:GLU280 4.9 35.0 1.0 CG C:PRO98 5.0 16.7 1.0 CD C:PRO98 5.0 16.6 1.0

Manganese binding site 7 out of 8 in the Crystal Structure of Aminipeptidase (M18 Family) From Thermotoga Maritima


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 Aminipeptidase (M18 Family) From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn5008 b:16.2 occ:1.00 O D:HOH5083 2.1 34.6 1.0 OD2 D:ASP328 2.2 11.2 1.0 OD1 D:ASP251 2.2 25.2 1.0 NE2 D:HIS94 2.3 9.2 1.0 OD1 D:ASP328 2.7 14.1 1.0 CG D:ASP328 2.8 13.7 1.0 CE1 D:HIS94 3.3 9.4 1.0 CD2 D:HIS94 3.3 9.2 1.0 CG D:ASP251 3.3 24.9 1.0 OE1 D:GLU280 3.5 33.8 1.0 O D:HOH5096 3.5 44.5 1.0 MN D:MN5009 3.6 18.1 1.0 OD2 D:ASP251 3.8 24.9 1.0 OE1 D:GLU281 4.1 17.3 1.0 OD1 D:ASP252 4.2 24.8 1.0 CG2 D:VAL329 4.2 9.2 1.0 CG D:ASP252 4.2 25.3 1.0 CB D:ASP328 4.3 14.9 1.0 CB D:ASP252 4.4 24.9 1.0 ND1 D:HIS94 4.4 9.2 1.0 CD D:GLU280 4.4 31.1 1.0 CG D:HIS94 4.4 10.4 1.0 N D:VAL329 4.6 12.8 1.0 CB D:ASP251 4.6 23.7 1.0 O D:HOH5026 4.7 23.8 1.0 C D:ASP251 4.7 45.1 1.0 CE D:MSE426 4.7 38.4 1.0 OD2 D:ASP252 4.8 22.1 1.0 N D:ASP252 4.8 59.6 1.0 O D:ASP251 4.9 44.5 1.0 CG D:GLU280 4.9 26.5 1.0 CA D:ASP328 4.9 29.0 1.0 CA D:ASP251 4.9 45.3 1.0

Manganese binding site 8 out of 8 in the Crystal Structure of Aminipeptidase (M18 Family) From Thermotoga Maritima


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 Aminipeptidase (M18 Family) From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn5009 b:18.1 occ:1.00 OE1 D:GLU281 2.1 17.3 1.0 O D:HOH5096 2.3 44.5 1.0 NE2 D:HIS427 2.3 12.8 1.0 OD2 D:ASP251 2.5 24.9 1.0 OE2 D:GLU281 2.8 14.6 1.0 CD D:GLU281 2.8 15.3 1.0 CG D:ASP251 3.1 24.9 1.0 CD2 D:HIS427 3.2 14.4 1.0 OD1 D:ASP251 3.3 25.2 1.0 O D:HOH5083 3.3 34.6 1.0 CE D:MSE426 3.4 38.4 1.0 CE1 D:HIS427 3.4 14.2 1.0 MN D:MN5008 3.6 16.2 1.0 OE1 D:GLU280 4.0 33.8 1.0 CG D:GLU281 4.3 14.7 1.0 CB D:ASP251 4.3 23.7 1.0 CG D:HIS427 4.4 12.9 1.0 ND1 D:HIS427 4.5 13.9 1.0 CE1 A:HIS169 4.5 25.0 1.0 CE1 D:HIS94 4.6 9.4 1.0 NE2 D:HIS94 4.6 9.2 1.0 O D:HOH5032 4.6 11.4 1.0 O D:HOH5026 4.7 23.8 1.0 NE2 A:HIS169 4.7 24.8 1.0 CD D:PRO98 4.8 8.7 1.0 CG D:PRO98 5.0 8.6 1.0

T.Min, L.Shapiro. Crystal Structure of Aminipeptidase (M18 Family) From Thermotoga Maritima To Be Published.