Manganese in PDB 1lt1: Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein

The structure of Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein, PDB code: 1lt1 was solved by L.Di Costanzo, S.Geremia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.91
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.225, 89.270, 146.288, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Manganese atom in the Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein (pdb code 1lt1). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein, PDB code: 1lt1:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in the Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1101 b:11.6 occ:1.00 OE2 B:GLU36 2.1 13.3 1.0 OE1 A:GLU36 2.2 13.0 1.0 ND1 A:HIS39 2.2 9.0 1.0 OE1 A:GLU10 2.3 13.7 1.0 OE2 A:GLU10 2.3 14.0 1.0 O A:HOH1111 2.5 13.0 1.0 CD A:GLU10 2.6 15.5 1.0 CD B:GLU36 3.0 11.9 1.0 CE1 A:HIS39 3.1 4.4 1.0 OE1 B:GLU36 3.2 14.8 1.0 CD A:GLU36 3.2 12.2 1.0 CG A:HIS39 3.3 10.6 1.0 MN B:MN1102 3.6 11.8 1.0 OE2 A:GLU36 3.7 11.9 1.0 CB A:HIS39 3.7 11.5 1.0 O B:HOH1136 4.1 34.9 1.0 CG A:GLU10 4.2 13.0 1.0 NE2 A:HIS39 4.3 8.7 1.0 O A:HOH1118 4.3 16.1 1.0 CG2 B:ILE32 4.3 9.8 1.0 CA A:GLU36 4.3 12.5 1.0 CG B:GLU36 4.4 10.5 1.0 CD2 A:HIS39 4.4 11.0 1.0 CG A:GLU36 4.4 10.9 1.0 CB A:GLU36 4.5 11.9 1.0 OH B:TYR17 4.6 11.8 1.0 CE1 B:HIS39 4.8 5.3 1.0 ND1 B:HIS39 4.9 8.7 1.0 CE1 B:TYR17 4.9 5.0 1.0 CB A:GLU10 5.0 10.3 1.0

Manganese binding site 2 out of 12 in the Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1110 b:35.0 occ:1.00 O A:HOH1116 2.0 35.0 1.0 O A:HOH1113 2.0 28.6 1.0 O A:HOH1114 2.1 27.7 1.0 O A:HOH1112 2.1 29.1 1.0 O A:HOH1115 2.2 34.4 1.0 OE1 A:GLU19 2.4 32.9 1.0 CD A:GLU19 3.4 32.4 1.0 OE2 A:GLU19 3.6 35.6 1.0 O B:HOH1157 4.3 30.6 1.0 OE1 A:GLN16 4.4 22.7 1.0 CG A:GLU19 4.7 25.6 1.0

Manganese binding site 3 out of 12 in the Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1102 b:11.8 occ:1.00 OE2 A:GLU36 2.0 11.9 1.0 OE1 B:GLU36 2.1 14.8 1.0 ND1 B:HIS39 2.2 8.7 1.0 OE2 B:GLU10 2.3 13.0 1.0 OE1 B:GLU10 2.3 14.6 1.0 O A:HOH1111 2.4 13.0 1.0 CD B:GLU10 2.7 13.3 1.0 CD A:GLU36 2.9 12.2 1.0 OE1 A:GLU36 3.1 13.0 1.0 CE1 B:HIS39 3.1 5.3 1.0 CD B:GLU36 3.2 11.9 1.0 CG B:HIS39 3.3 9.4 1.0 MN A:MN1101 3.6 11.6 1.0 OE2 B:GLU36 3.7 13.3 1.0 CB B:HIS39 3.7 9.9 1.0 CG B:GLU10 4.2 8.6 1.0 NE2 B:HIS39 4.3 9.8 1.0 CA B:GLU36 4.4 11.3 1.0 CG A:GLU36 4.4 10.9 1.0 O B:HOH1119 4.4 14.8 1.0 CG2 A:ILE32 4.4 13.4 1.0 CG B:GLU36 4.4 10.5 1.0 CD2 B:HIS39 4.4 12.4 1.0 O B:HOH1136 4.5 34.9 1.0 CB B:GLU36 4.5 12.9 1.0 OH A:TYR17 4.6 15.4 1.0 CE1 A:HIS39 4.8 4.4 1.0 ND1 A:HIS39 4.9 9.0 1.0 CE1 A:TYR17 5.0 9.3 1.0

Manganese binding site 4 out of 12 in the Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1112 b:42.5 occ:1.00 O H:HOH1111 2.0 43.2 1.0 O B:HOH1117 2.1 44.1 1.0 O H:HOH1110 2.2 36.9 1.0 O H:HOH1112 2.2 40.3 1.0 O B:HOH1116 2.3 27.8 1.0 OE1 B:GLU19 2.4 38.6 1.0 CD B:GLU19 3.6 34.3 1.0 OE2 B:GLU19 4.1 37.5 1.0 OE1 H:GLU22 4.2 26.1 1.0 OH H:TYR23 4.2 13.2 1.0 OE2 H:GLU22 4.3 26.6 1.0 O B:HOH1135 4.5 32.8 1.0 OE1 B:GLN16 4.6 30.2 1.0 CD H:GLU22 4.7 28.0 1.0 OE2 H:GLU19 4.7 33.9 1.0 CG B:GLU19 4.8 26.1 1.0 O B:HOH1118 5.0 37.3 1.0

Manganese binding site 5 out of 12 in the Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1103 b:15.2 occ:1.00 OE2 D:GLU36 2.1 20.0 1.0 ND1 C:HIS39 2.1 10.7 1.0 OE1 C:GLU36 2.1 14.9 1.0 OE1 C:GLU10 2.2 17.6 1.0 O D:HOH1112 2.3 16.9 1.0 OE2 C:GLU10 2.4 19.8 1.0 CD C:GLU10 2.6 19.2 1.0 CE1 C:HIS39 3.0 13.6 1.0 CD D:GLU36 3.0 18.5 1.0 CD C:GLU36 3.1 20.5 1.0 OE1 D:GLU36 3.2 23.2 1.0 CG C:HIS39 3.3 8.6 1.0 OE2 C:GLU36 3.5 17.4 1.0 MN D:MN1104 3.6 16.0 1.0 CB C:HIS39 3.7 11.1 1.0 O C:HOH1128 3.8 20.7 1.0 CG C:GLU10 4.1 17.8 1.0 NE2 C:HIS39 4.2 14.5 1.0 O C:HOH1120 4.2 17.9 1.0 O C:HOH1123 4.3 19.8 1.0 CD2 C:HIS39 4.3 11.5 1.0 CG D:GLU36 4.4 13.4 1.0 CG C:GLU36 4.5 13.3 1.0 CG2 D:ILE32 4.6 12.8 1.0 OH D:TYR17 4.6 22.3 1.0 CA C:GLU36 4.6 15.5 1.0 CB C:GLU36 4.8 14.3 1.0 CE1 D:TYR17 4.9 20.0 1.0 CB C:GLU10 5.0 21.5 1.0 CE1 D:HIS39 5.0 14.3 1.0

Manganese binding site 6 out of 12 in the Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1109 b:18.0 occ:1.00 O B:HOH1114 2.0 17.4 1.0 O C:HOH1111 2.1 18.5 1.0 O B:HOH1113 2.1 19.9 1.0 OD1 C:ASP1 2.1 20.1 1.0 OD1 B:ASP35 2.2 10.8 1.0 O C:HOH1110 2.2 20.1 1.0 CG C:ASP1 3.2 19.1 1.0 CG B:ASP35 3.2 15.4 1.0 OD2 B:ASP35 3.4 12.3 1.0 OD2 C:ASP1 3.4 15.8 1.0 O C:HOH1114 3.9 24.4 1.0 OE1 B:GLU34 4.1 19.6 1.0 O C:HOH1140 4.4 39.7 1.0 CE B:LYS31 4.4 30.4 1.0 O B:LYS31 4.5 12.8 1.0 CG B:GLU34 4.5 15.8 1.0 CB C:ASP1 4.5 18.5 1.0 CB B:ASP35 4.5 8.3 1.0 CD B:GLU34 4.5 21.8 1.0 O A:HOH1123 4.6 42.1 1.0 CA B:ASP35 4.8 9.8 1.0 N B:ASP35 4.9 10.7 1.0 NZ B:LYS31 4.9 27.8 1.0 O A:HOH1124 4.9 46.5 1.0 NZ B:LYS38 4.9 28.4 1.0

Manganese binding site 7 out of 12 in the Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1104 b:16.0 occ:1.00 OE2 C:GLU36 2.1 17.4 1.0 OE2 D:GLU10 2.2 14.9 1.0 OE1 D:GLU36 2.2 23.2 1.0 ND1 D:HIS39 2.3 16.3 1.0 OE1 D:GLU10 2.4 20.7 1.0 O D:HOH1112 2.4 16.9 1.0 CD D:GLU10 2.6 20.8 1.0 CD C:GLU36 3.1 20.5 1.0 CE1 D:HIS39 3.1 14.3 1.0 CD D:GLU36 3.1 18.5 1.0 CG D:HIS39 3.4 10.2 1.0 OE1 C:GLU36 3.5 14.9 1.0 OE2 D:GLU36 3.5 20.0 1.0 MN C:MN1103 3.6 15.2 1.0 CB D:HIS39 3.8 13.8 1.0 O C:HOH1123 4.1 19.8 1.0 CG D:GLU10 4.1 16.4 1.0 CA D:GLU36 4.3 15.9 1.0 NE2 D:HIS39 4.3 15.5 1.0 CG D:GLU36 4.3 13.4 1.0 O D:HOH1120 4.4 17.1 1.0 CG C:GLU36 4.4 13.3 1.0 OH C:TYR17 4.4 13.0 1.0 CD2 D:HIS39 4.4 13.7 1.0 CE1 C:HIS39 4.5 13.6 1.0 CG2 C:ILE32 4.5 18.4 1.0 CB D:GLU36 4.6 16.3 1.0 O C:HOH1128 4.6 20.7 1.0 ND1 C:HIS39 4.7 10.7 1.0 CE1 C:TYR17 4.7 12.2 1.0 N D:GLU36 4.9 16.0 1.0 CZ C:TYR17 5.0 10.6 1.0 CB D:GLU10 5.0 12.0 1.0

Manganese binding site 8 out of 12 in the Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1111 b:34.7 occ:1.00 O D:HOH1114 1.8 30.2 1.0 O D:HOH1113 2.0 34.7 1.0 O D:HOH1115 2.1 37.3 1.0 OE1 D:GLU19 2.1 34.0 1.0 OE1 D:GLN16 2.2 23.8 1.0 O B:HOH1115 2.3 31.4 1.0 CD D:GLN16 3.2 25.7 1.0 CD D:GLU19 3.3 33.0 1.0 NE2 D:GLN16 3.6 24.7 1.0 OE2 D:GLU19 4.0 33.4 1.0 OE1 B:GLU41 4.0 38.4 1.0 OE2 B:GLU41 4.1 35.9 1.0 O D:HOH1116 4.2 21.9 1.0 CG D:GLU19 4.5 28.5 1.0 CD B:GLU41 4.5 31.8 1.0 CB D:GLU19 4.5 23.4 1.0 CG D:GLN16 4.6 18.9 1.0 OE1 C:GLU5 4.7 41.9 1.0 CA D:GLN16 4.9 17.1 1.0

Manganese binding site 9 out of 12 in the Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn1105 b:16.1 occ:1.00 OE1 E:GLU36 2.1 13.4 1.0 ND1 E:HIS39 2.1 11.0 1.0 OE2 F:GLU36 2.1 14.9 1.0 OE1 E:GLU10 2.2 21.8 1.0 OE2 E:GLU10 2.2 21.6 1.0 O F:HOH1107 2.4 15.6 1.0 CD E:GLU10 2.6 21.0 1.0 CE1 E:HIS39 2.9 10.8 1.0 CD F:GLU36 2.9 13.5 1.0 OE1 F:GLU36 3.1 14.6 1.0 CD E:GLU36 3.1 19.0 1.0 CG E:HIS39 3.2 11.2 1.0 OE2 E:GLU36 3.6 18.8 1.0 MN F:MN1106 3.6 14.9 1.0 O F:HOH1128 3.6 31.0 1.0 CB E:HIS39 3.7 15.3 1.0 NE2 E:HIS39 4.1 12.2 1.0 CG E:GLU10 4.1 18.4 1.0 O E:HOH1115 4.3 21.7 1.0 CD2 E:HIS39 4.3 8.0 1.0 O E:HOH1111 4.3 19.4 1.0 CG F:GLU36 4.4 13.5 1.0 CG E:GLU36 4.5 12.4 1.0 CG2 F:ILE32 4.5 12.4 1.0 OH F:TYR17 4.5 23.9 1.0 CE1 F:TYR17 4.6 21.7 1.0 CA E:GLU36 4.6 14.9 1.0 CB E:GLU36 4.8 13.8 1.0 CB E:GLU10 4.9 18.8 1.0 CE1 F:HIS39 4.9 15.8 1.0

Manganese binding site 10 out of 12 in the Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Sliding Helix Induced Change of Coordination Geometry in A Model Di-Mn(II) Protein within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn1106 b:14.9 occ:1.00 OE2 E:GLU36 2.0 18.8 1.0 ND1 F:HIS39 2.2 16.7 1.0 OE2 F:GLU10 2.2 11.7 1.0 OE1 F:GLU36 2.2 14.6 1.0 O F:HOH1107 2.3 15.6 1.0 OE1 F:GLU10 2.3 14.9 1.0 CD F:GLU10 2.6 17.5 1.0 CE1 F:HIS39 3.0 15.8 1.0 CD E:GLU36 3.0 19.0 1.0 CD F:GLU36 3.1 13.5 1.0 CG F:HIS39 3.3 11.8 1.0 OE1 E:GLU36 3.3 13.4 1.0 OE2 F:GLU36 3.6 14.9 1.0 MN E:MN1105 3.6 16.1 1.0 CB F:HIS39 3.8 14.7 1.0 O E:HOH1115 4.0 21.7 1.0 CG F:GLU10 4.1 14.0 1.0 NE2 F:HIS39 4.2 11.3 1.0 CA F:GLU36 4.3 15.7 1.0 O F:HOH1125 4.3 23.5 1.0 CG F:GLU36 4.3 13.5 1.0 O F:HOH1128 4.4 31.0 1.0 CD2 F:HIS39 4.4 14.4 1.0 CG E:GLU36 4.4 12.4 1.0 CB F:GLU36 4.5 16.1 1.0 CE1 E:HIS39 4.5 10.8 1.0 OH E:TYR17 4.5 14.6 1.0 CG2 E:ILE32 4.5 14.1 1.0 ND1 E:HIS39 4.7 11.0 1.0 CE1 E:TYR17 4.8 13.2 1.0 N F:GLU36 5.0 15.2 1.0 CB F:GLU10 5.0 16.7 1.0

W.F.Degrado, L.Di Costanzo, S.Geremia, A.Lombardi, V.Pavone, L.Randaccio. Sliding Helix and Change of Coordination Geometry in A Model Di-Mnii Protein Angew.Chem.Int.Ed.Engl. V. 42 417 2003.
ISSN: ISSN 1433-7851
PubMed: 12569505
DOI: 10.1002/ANIE.200390127