Manganese in PDB 6j42: Crystal Structure of Wild Type Katb, A Manganese Catalase From Anabaena

The structure of Crystal Structure of Wild Type Katb, A Manganese Catalase From Anabaena, PDB code: 6j42 was solved by S.C.Bihani, D.Chakravarty, A.Ballal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.59 / 2.49
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	102.070, 102.070, 138.980, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 26.1

The structure of Crystal Structure of Wild Type Katb, A Manganese Catalase From Anabaena also contains other interesting chemical elements:

Calcium

(Ca)

5 atoms

The binding sites of Manganese atom in the Crystal Structure of Wild Type Katb, A Manganese Catalase From Anabaena (pdb code 6j42). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of Wild Type Katb, A Manganese Catalase From Anabaena, PDB code: 6j42:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Crystal Structure of Wild Type Katb, A Manganese Catalase From Anabaena


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 Wild Type Katb, A Manganese Catalase From Anabaena within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:38.1 occ:1.00 OE1 A:GLU65 2.1 39.7 1.0 OE1 A:GLU35 2.2 46.5 1.0 OE2 A:GLU163 2.3 48.0 1.0 O A:HOH412 2.4 39.8 1.0 ND1 A:HIS68 2.5 43.3 1.0 OE2 A:GLU35 2.7 50.1 1.0 CD A:GLU35 2.8 43.1 1.0 CD A:GLU163 3.1 45.3 1.0 OE1 A:GLU163 3.3 46.4 1.0 CD A:GLU65 3.3 41.5 1.0 CG A:HIS68 3.5 45.7 1.0 CE1 A:HIS68 3.5 44.6 1.0 CB A:HIS68 3.7 45.8 1.0 OE2 A:GLU65 3.8 36.5 1.0 MN A:MN302 3.9 39.5 1.0 O A:HOH402 4.0 38.3 1.0 CG A:GLU35 4.3 43.9 1.0 CA A:GLU65 4.5 42.5 1.0 CG A:GLU65 4.6 36.3 1.0 CG A:GLU163 4.6 45.7 1.0 NE2 A:HIS68 4.6 52.5 1.0 CE1 A:HIS166 4.6 38.4 1.0 CD2 A:HIS68 4.6 44.1 1.0 OH A:TYR140 4.7 37.1 1.0 CB A:GLU65 4.7 34.2 1.0 CE2 A:TYR140 4.8 46.3 1.0 ND1 A:HIS166 4.9 43.2 1.0 CB A:GLU35 4.9 42.6 1.0

Manganese binding site 2 out of 6 in the Crystal Structure of Wild Type Katb, A Manganese Catalase From Anabaena


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 Wild Type Katb, A Manganese Catalase From Anabaena within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:39.5 occ:1.00 OE1 A:GLU163 2.0 46.4 1.0 OE2 A:GLU65 2.1 36.5 1.0 ND1 A:HIS166 2.3 43.2 1.0 O A:HOH402 2.3 38.3 1.0 OE1 A:GLU133 2.3 39.3 1.0 OE2 A:GLU133 2.4 36.8 1.0 CD A:GLU133 2.7 38.6 1.0 CD A:GLU65 3.0 41.5 1.0 CE1 A:HIS166 3.2 38.4 1.0 CD A:GLU163 3.2 45.3 1.0 OE1 A:GLU65 3.3 39.7 1.0 CG A:HIS166 3.4 39.9 1.0 O A:HOH412 3.6 39.8 1.0 CB A:HIS166 3.7 38.9 1.0 OE2 A:GLU163 3.9 48.0 1.0 MN A:MN301 3.9 38.1 1.0 CA A:GLU163 4.1 43.2 1.0 CG A:GLU133 4.2 40.2 1.0 OH A:TYR42 4.2 43.0 1.0 CB A:GLU163 4.3 38.7 1.0 CG A:GLU163 4.3 45.7 1.0 NE2 A:HIS166 4.3 38.9 1.0 CG A:GLU65 4.4 36.3 1.0 CD2 A:HIS166 4.4 41.3 1.0 CE2 A:TYR42 4.4 37.3 1.0 O A:ARG162 4.6 47.0 1.0 N A:GLU163 4.8 44.8 1.0 CB A:ALA38 4.8 38.6 1.0 CZ A:TYR42 4.9 36.7 1.0 CG2 A:ILE61 4.9 37.5 1.0 CB A:GLU133 5.0 36.1 1.0 O A:GLU163 5.0 43.2 1.0

Manganese binding site 3 out of 6 in the Crystal Structure of Wild Type Katb, A Manganese Catalase From Anabaena


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 Wild Type Katb, A Manganese Catalase From Anabaena within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:47.5 occ:1.00 OE1 B:GLU65 2.0 46.2 1.0 OE1 B:GLU35 2.1 44.3 1.0 ND1 B:HIS68 2.3 42.4 1.0 O B:HOH411 2.4 44.3 1.0 OE2 B:GLU163 2.4 46.2 1.0 CD B:GLU35 2.8 41.4 1.0 OE2 B:GLU35 2.9 47.1 1.0 CD B:GLU65 3.1 45.8 1.0 OE1 B:GLU163 3.1 49.8 1.0 CD B:GLU163 3.2 50.6 1.0 CG B:HIS68 3.3 47.4 1.0 CE1 B:HIS68 3.3 52.1 1.0 CB B:HIS68 3.5 44.5 1.0 OE2 B:GLU65 3.6 45.4 1.0 MN B:MN302 3.8 48.9 1.0 O B:HOH415 4.2 42.3 1.0 O B:HOH412 4.2 47.9 1.0 CG B:GLU35 4.3 42.7 1.0 CG B:GLU65 4.4 42.7 1.0 NE2 B:HIS68 4.4 57.5 1.0 CD2 B:HIS68 4.4 48.7 1.0 CA B:GLU65 4.5 45.9 1.0 CB B:GLU65 4.6 44.3 1.0 CG B:GLU163 4.6 50.0 1.0 CE1 B:HIS166 4.6 49.6 1.0 CB B:GLU35 4.8 40.7 1.0 ND1 B:HIS166 4.9 45.3 1.0 CE2 B:TYR140 4.9 44.3 1.0 O B:LEU159 5.0 48.3 1.0 OH B:TYR140 5.0 37.5 1.0

Manganese binding site 4 out of 6 in the Crystal Structure of Wild Type Katb, A Manganese Catalase From Anabaena


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 Wild Type Katb, A Manganese Catalase From Anabaena within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:48.9 occ:1.00 OE2 B:GLU133 1.9 43.9 1.0 OE1 B:GLU163 2.0 49.8 1.0 OE2 B:GLU65 2.0 45.4 1.0 O B:HOH412 2.3 47.9 1.0 ND1 B:HIS166 2.3 45.3 1.0 CD B:GLU133 2.9 47.1 1.0 CD B:GLU65 3.1 45.8 1.0 O B:HOH411 3.2 44.3 1.0 CE1 B:HIS166 3.2 49.6 1.0 CD B:GLU163 3.2 50.6 1.0 OE1 B:GLU133 3.4 48.9 1.0 CG B:HIS166 3.4 42.1 1.0 OE1 B:GLU65 3.4 46.2 1.0 CB B:HIS166 3.7 47.8 1.0 MN B:MN301 3.8 47.5 1.0 OE2 B:GLU163 3.9 46.2 1.0 CA B:GLU163 4.0 48.7 1.0 CG B:GLU133 4.2 48.2 1.0 CB B:GLU163 4.3 47.0 1.0 CG B:GLU163 4.3 50.0 1.0 OH B:TYR42 4.4 38.1 1.0 CG B:GLU65 4.4 42.7 1.0 NE2 B:HIS166 4.4 50.5 1.0 CD2 B:HIS166 4.5 45.7 1.0 CE2 B:TYR42 4.5 41.4 1.0 O B:ARG162 4.6 50.4 1.0 N B:GLU163 4.7 49.0 1.0 CB B:ALA38 4.7 38.7 1.0 C B:ARG162 4.9 51.3 1.0 CG2 B:ILE61 4.9 38.7 1.0 CZ B:TYR42 5.0 38.0 1.0

Manganese binding site 5 out of 6 in the Crystal Structure of Wild Type Katb, A Manganese Catalase From Anabaena


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 Wild Type Katb, A Manganese Catalase From Anabaena within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:50.5 occ:1.00 OE2 C:GLU163 2.1 53.4 1.0 OE2 C:GLU65 2.1 45.1 1.0 OE1 C:GLU35 2.4 46.4 1.0 ND1 C:HIS68 2.4 57.0 1.0 OE2 C:GLU35 2.6 59.2 1.0 CD C:GLU163 2.8 55.8 1.0 CD C:GLU35 2.8 51.6 1.0 O C:HOH403 2.8 48.4 1.0 OE1 C:GLU163 2.9 54.7 1.0 CD C:GLU65 3.1 51.8 1.0 CE1 C:HIS68 3.4 55.6 1.0 CG C:HIS68 3.4 56.7 1.0 OE1 C:GLU65 3.5 44.5 1.0 CB C:HIS68 3.6 49.2 1.0 MN C:MN302 3.8 50.3 1.0 CG C:GLU163 4.2 56.5 1.0 CG C:GLU35 4.3 49.7 1.0 NE2 C:HIS68 4.4 59.9 1.0 CG C:GLU65 4.5 50.0 1.0 CD2 C:HIS68 4.5 56.5 1.0 CE1 C:HIS166 4.6 56.9 1.0 CA C:GLU65 4.7 59.3 1.0 OH C:TYR140 4.7 53.6 1.0 CE2 C:TYR140 4.7 53.4 1.0 CB C:GLU65 4.8 54.5 1.0 ND1 C:HIS166 4.8 55.1 1.0 O C:LEU159 5.0 53.3 1.0

Manganese binding site 6 out of 6 in the Crystal Structure of Wild Type Katb, A Manganese Catalase From Anabaena


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 Wild Type Katb, A Manganese Catalase From Anabaena within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn302 b:50.3 occ:1.00 OE1 C:GLU163 1.9 54.7 1.0 OE1 C:GLU65 2.0 44.5 1.0 OE2 C:GLU133 2.2 49.4 1.0 OE1 C:GLU133 2.4 50.1 1.0 ND1 C:HIS166 2.5 55.1 1.0 CD C:GLU133 2.6 48.3 1.0 CD C:GLU163 3.0 55.8 1.0 CD C:GLU65 3.1 51.8 1.0 O C:HOH403 3.3 48.4 1.0 CE1 C:HIS166 3.4 56.9 1.0 CG C:HIS166 3.5 56.2 1.0 OE2 C:GLU65 3.5 45.1 1.0 OE2 C:GLU163 3.7 53.4 1.0 CB C:HIS166 3.7 56.3 1.0 MN C:MN301 3.8 50.5 1.0 CA C:GLU163 4.0 58.5 1.0 OH C:TYR42 4.0 45.2 1.0 CG C:GLU133 4.1 45.0 1.0 CB C:GLU163 4.1 57.6 1.0 CG C:GLU163 4.1 56.5 1.0 CG C:GLU65 4.4 50.0 1.0 CE2 C:TYR42 4.4 48.1 1.0 NE2 C:HIS166 4.5 60.4 1.0 CD2 C:HIS166 4.6 57.9 1.0 CB C:ALA38 4.7 49.3 1.0 O C:ARG162 4.7 64.5 1.0 CZ C:TYR42 4.7 43.6 1.0 N C:GLU163 4.8 61.3 1.0 CB C:GLU133 4.9 47.2 1.0 O C:GLU163 5.0 60.3 1.0

D.Chakravarty, S.C.Bihani, M.Banerjee, A.Ballal. Molecular Basis of the Unique Role Played By An N-Terminal Non-Active Site Residue of Cyanobacterial Mn-Catalase in Structure-Function Maintenance To Be Published.