Manganese in PDB 4r42: Crystal Structure of Katb, A Manganese Catalase From Anabaena PCC7120

The structure of Crystal Structure of Katb, A Manganese Catalase From Anabaena PCC7120, PDB code: 4r42 was solved by S.C.Bihani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.35 / 1.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.404, 101.404, 136.198, 90.00, 90.00, 90.00
R / Rfree (%)	13.4 / 16

The structure of Crystal Structure of Katb, A Manganese Catalase From Anabaena PCC7120 also contains other interesting chemical elements:

Calcium

(Ca)

5 atoms

The binding sites of Manganese atom in the Crystal Structure of Katb, A Manganese Catalase From Anabaena PCC7120 (pdb code 4r42). 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 Katb, A Manganese Catalase From Anabaena PCC7120, PDB code: 4r42:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Crystal Structure of Katb, A Manganese Catalase From Anabaena PCC7120


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 Katb, A Manganese Catalase From Anabaena PCC7120 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:14.9 occ:1.00 OE2 A:GLU163 2.1 20.4 1.0 OE1 A:GLU65 2.1 16.4 1.0 OE2 A:GLU35 2.2 18.4 1.0 ND1 A:HIS68 2.3 14.4 1.0 OE1 A:GLU35 2.4 14.7 1.0 O A:HOH506 2.5 26.9 1.0 CD A:GLU35 2.6 16.8 1.0 CD A:GLU163 2.9 21.0 1.0 OE1 A:GLU163 2.9 15.3 1.0 CE1 A:HIS68 3.2 16.9 1.0 CD A:GLU65 3.2 15.0 1.0 HE1 A:HIS68 3.3 20.2 1.0 CG A:HIS68 3.3 15.2 1.0 HB2 A:HIS68 3.4 19.2 1.0 HB3 A:HIS68 3.5 19.2 1.0 CB A:HIS68 3.6 16.0 1.0 HA A:GLU65 3.6 19.4 1.0 O A:HOH505 3.7 16.3 1.0 OE2 A:GLU65 3.7 17.8 1.0 MN A:MN302 3.8 15.6 1.0 HE2 A:TYR140 3.9 22.9 1.0 HH A:TYR140 3.9 21.2 1.0 HE1 A:HIS166 4.0 19.9 1.0 CG A:GLU35 4.1 13.3 1.0 O A:HOH496 4.2 24.4 1.0 HB3 A:GLU65 4.3 14.2 1.0 HA A:GLU35 4.3 15.4 1.0 CG A:GLU163 4.3 17.9 1.0 NE2 A:HIS68 4.3 17.7 1.0 CD2 A:HIS68 4.4 16.7 1.0 HD22 A:LEU159 4.5 25.6 1.0 CG A:GLU65 4.5 10.3 1.0 CA A:GLU65 4.5 16.2 1.0 HG3 A:GLU163 4.5 21.4 1.0 HG3 A:GLU35 4.5 16.0 1.0 HG2 A:GLU35 4.6 16.0 1.0 HG2 A:GLU163 4.6 21.4 1.0 CB A:GLU65 4.6 11.8 1.0 HB3 A:ALA38 4.6 17.2 1.0 CE1 A:HIS166 4.7 16.6 1.0 HB3 A:GLU35 4.7 19.4 1.0 OH A:TYR140 4.7 17.6 1.0 CE2 A:TYR140 4.8 19.1 1.0 HB3 A:LEU159 4.8 17.9 1.0 CB A:GLU35 4.9 16.2 1.0 ND1 A:HIS166 4.9 11.9 1.0 HB1 A:ALA136 4.9 15.8 1.0 HG2 A:GLU65 5.0 12.4 1.0

Manganese binding site 2 out of 6 in the Crystal Structure of Katb, A Manganese Catalase From Anabaena PCC7120


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 Katb, A Manganese Catalase From Anabaena PCC7120 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:15.6 occ:1.00 OE2 A:GLU65 2.1 17.8 1.0 OE1 A:GLU163 2.1 15.3 1.0 O A:HOH505 2.2 16.3 1.0 OE2 A:GLU133 2.3 13.4 1.0 ND1 A:HIS166 2.3 11.9 1.0 OE1 A:GLU133 2.3 17.4 1.0 CD A:GLU133 2.6 14.5 1.0 CD A:GLU65 3.0 15.0 1.0 CD A:GLU163 3.1 21.0 1.0 HA A:GLU163 3.1 20.9 1.0 CE1 A:HIS166 3.2 16.6 1.0 HB2 A:HIS166 3.3 17.1 1.0 OE1 A:GLU65 3.3 16.4 1.0 HE1 A:HIS166 3.3 19.9 1.0 CG A:HIS166 3.3 13.6 1.0 HH A:TYR42 3.6 16.9 1.0 CB A:HIS166 3.7 14.3 1.0 HE2 A:TYR42 3.7 12.6 1.0 HB3 A:HIS166 3.7 17.1 1.0 O A:HOH506 3.8 26.9 1.0 OE2 A:GLU163 3.8 20.4 1.0 MN A:MN301 3.8 14.9 1.0 HB3 A:GLU163 3.8 20.4 1.0 CA A:GLU163 4.0 17.4 1.0 CG A:GLU163 4.1 17.9 1.0 CG A:GLU133 4.1 15.9 1.0 CB A:GLU163 4.1 17.0 1.0 HB1 A:ALA38 4.2 17.2 1.0 O A:HOH410 4.3 15.7 1.0 NE2 A:HIS166 4.4 14.1 1.0 OH A:TYR42 4.4 14.1 1.0 CG A:GLU65 4.4 10.3 1.0 HA A:GLU133 4.4 16.8 1.0 HG3 A:GLU163 4.4 21.4 1.0 CD2 A:HIS166 4.4 13.0 1.0 HG2 A:GLU133 4.5 19.1 1.0 HE1 A:HIS68 4.5 20.2 1.0 HG23 A:ILE61 4.5 16.7 1.0 HG3 A:GLU133 4.5 19.1 1.0 HG3 A:GLU65 4.6 12.4 1.0 CE2 A:TYR42 4.6 10.5 1.0 O A:ARG162 4.6 17.3 1.0 HG21 A:ILE61 4.6 16.7 1.0 HG2 A:GLU65 4.7 12.4 1.0 HE2 A:PHE170 4.7 15.4 1.0 HB2 A:ALA38 4.7 17.2 1.0 N A:GLU163 4.7 17.3 1.0 HG22 A:ILE61 4.8 16.7 1.0 HB3 A:GLU133 4.8 16.4 1.0 CB A:ALA38 4.8 14.3 1.0 CG2 A:ILE61 4.9 13.9 1.0 HG2 A:GLU163 4.9 21.4 1.0 CB A:GLU133 4.9 13.7 1.0 HB3 A:ALA136 5.0 15.8 1.0 C A:ARG162 5.0 19.8 1.0

Manganese binding site 3 out of 6 in the Crystal Structure of Katb, A Manganese Catalase From Anabaena PCC7120


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 Katb, A Manganese Catalase From Anabaena PCC7120 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:17.7 occ:1.00 OE2 B:GLU163 2.1 25.1 1.0 OE2 B:GLU65 2.1 18.4 1.0 OE1 B:GLU35 2.2 18.4 1.0 ND1 B:HIS68 2.3 20.2 1.0 OE2 B:GLU35 2.4 18.6 1.0 O B:HOH404 2.5 31.2 1.0 CD B:GLU35 2.6 17.6 1.0 CD B:GLU163 2.8 24.2 1.0 OE1 B:GLU163 2.9 20.7 1.0 CE1 B:HIS68 3.2 19.7 1.0 CD B:GLU65 3.2 18.7 1.0 HE1 B:HIS68 3.3 23.6 1.0 CG B:HIS68 3.3 16.9 1.0 HB2 B:HIS68 3.4 19.5 1.0 HB3 B:HIS68 3.5 19.5 1.0 HA B:GLU65 3.6 19.5 1.0 CB B:HIS68 3.7 16.2 1.0 OE1 B:GLU65 3.7 17.1 1.0 O B:HOH501 3.7 16.3 1.0 MN B:MN302 3.8 17.1 1.0 HE2 B:TYR140 4.0 23.9 1.0 HE1 B:HIS166 4.0 23.8 1.0 HH B:TYR140 4.0 22.9 1.0 CG B:GLU35 4.1 15.7 1.0 HB3 B:GLU65 4.2 18.1 1.0 HA B:GLU35 4.3 18.3 1.0 O B:HOH423 4.3 32.8 1.0 CG B:GLU163 4.3 18.1 1.0 NE2 B:HIS68 4.3 20.9 1.0 CD2 B:HIS68 4.4 22.7 1.0 CG B:GLU65 4.4 17.6 1.0 CA B:GLU65 4.5 16.3 1.0 HD22 B:LEU159 4.5 25.1 1.0 HG3 B:GLU35 4.5 18.8 1.0 HG3 B:GLU163 4.5 21.7 1.0 CB B:GLU65 4.6 15.1 1.0 HG2 B:GLU35 4.6 18.8 1.0 HG2 B:GLU163 4.6 21.7 1.0 HB3 B:ALA38 4.6 17.5 1.0 CE1 B:HIS166 4.7 19.9 1.0 HB3 B:GLU35 4.7 14.1 1.0 CE2 B:TYR140 4.8 19.9 1.0 OH B:TYR140 4.8 19.1 1.0 HB3 B:LEU159 4.9 21.4 1.0 CB B:GLU35 4.9 11.7 1.0 ND1 B:HIS166 4.9 16.0 1.0 HG2 B:GLU65 4.9 21.1 1.0

Manganese binding site 4 out of 6 in the Crystal Structure of Katb, A Manganese Catalase From Anabaena PCC7120


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 Katb, A Manganese Catalase From Anabaena PCC7120 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:17.1 occ:1.00 OE1 B:GLU65 2.1 17.1 1.0 OE1 B:GLU163 2.2 20.7 1.0 O B:HOH501 2.3 16.3 1.0 ND1 B:HIS166 2.3 16.0 1.0 OE2 B:GLU133 2.3 13.8 1.0 OE1 B:GLU133 2.3 18.4 1.0 CD B:GLU133 2.6 16.9 1.0 CD B:GLU65 3.0 18.7 1.0 HA B:GLU163 3.1 24.3 1.0 CD B:GLU163 3.2 24.2 1.0 CE1 B:HIS166 3.2 19.9 1.0 HB2 B:HIS166 3.2 23.4 1.0 OE2 B:GLU65 3.3 18.4 1.0 CG B:HIS166 3.3 19.4 1.0 HE1 B:HIS166 3.3 23.8 1.0 HH B:TYR42 3.5 19.3 1.0 CB B:HIS166 3.6 19.5 1.0 HB3 B:HIS166 3.7 23.4 1.0 HE2 B:TYR42 3.7 21.3 1.0 HB3 B:GLU163 3.7 23.6 1.0 O B:HOH404 3.8 31.2 1.0 MN B:MN301 3.8 17.7 1.0 OE2 B:GLU163 3.9 25.1 1.0 CA B:GLU163 4.0 20.3 1.0 CB B:GLU163 4.1 19.7 1.0 CG B:GLU133 4.1 16.4 1.0 CG B:GLU163 4.2 18.1 1.0 HB1 B:ALA38 4.2 17.5 1.0 O B:HOH411 4.2 19.8 1.0 NE2 B:HIS166 4.3 16.4 1.0 CG B:GLU65 4.4 17.6 1.0 OH B:TYR42 4.4 16.1 1.0 CD2 B:HIS166 4.4 16.6 1.0 HA B:GLU133 4.4 22.0 1.0 HG2 B:GLU133 4.5 19.7 1.0 HG3 B:GLU65 4.5 21.1 1.0 HG23 B:ILE61 4.6 20.2 1.0 HG3 B:GLU133 4.6 19.7 1.0 HE1 B:HIS68 4.6 23.6 1.0 CE2 B:TYR42 4.6 17.7 1.0 O B:ARG162 4.6 20.8 1.0 HG3 B:GLU163 4.6 21.7 1.0 HE2 B:PHE170 4.6 20.4 1.0 HG2 B:GLU65 4.6 21.1 1.0 HB2 B:ALA38 4.7 17.5 1.0 N B:GLU163 4.7 20.2 1.0 HG21 B:ILE61 4.7 20.2 1.0 HG22 B:ILE61 4.7 20.2 1.0 HB3 B:GLU133 4.8 20.4 1.0 CB B:ALA38 4.8 14.6 1.0 CG2 B:ILE61 4.9 16.9 1.0 HG2 B:GLU163 4.9 21.7 1.0 CB B:GLU133 4.9 17.0 1.0 C B:ARG162 4.9 19.8 1.0 O B:GLU163 5.0 16.4 1.0

Manganese binding site 5 out of 6 in the Crystal Structure of Katb, A Manganese Catalase From Anabaena PCC7120


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 Katb, A Manganese Catalase From Anabaena PCC7120 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:19.7 occ:1.00 OE2 C:GLU65 2.1 25.0 1.0 OE2 C:GLU163 2.1 26.1 1.0 OE2 C:GLU35 2.2 19.7 1.0 ND1 C:HIS68 2.3 18.9 1.0 OE1 C:GLU35 2.4 20.2 1.0 O C:HOH404 2.5 30.1 1.0 CD C:GLU35 2.6 15.4 1.0 CD C:GLU163 2.9 27.6 1.0 OE1 C:GLU163 3.0 23.3 1.0 CD C:GLU65 3.2 21.5 1.0 CE1 C:HIS68 3.2 21.5 1.0 HE1 C:HIS68 3.3 25.8 1.0 CG C:HIS68 3.3 17.8 1.0 HB2 C:HIS68 3.4 22.8 1.0 HB3 C:HIS68 3.5 22.8 1.0 CB C:HIS68 3.6 19.0 1.0 HA C:GLU65 3.6 23.3 1.0 OE1 C:GLU65 3.7 19.2 1.0 HE2 C:TYR140 3.9 28.4 1.0 O C:HOH480 3.9 18.3 1.0 HH C:TYR140 3.9 23.7 1.0 MN C:MN302 4.0 19.2 1.0 HE1 C:HIS166 4.1 27.0 1.0 CG C:GLU35 4.1 18.0 1.0 HB3 C:GLU65 4.2 26.1 1.0 HA C:GLU35 4.2 18.1 1.0 O C:HOH406 4.2 24.6 1.0 NE2 C:HIS68 4.3 22.6 1.0 CG C:GLU163 4.4 21.2 1.0 HD22 C:LEU159 4.4 32.1 1.0 CG C:GLU65 4.4 20.2 1.0 CD2 C:HIS68 4.4 21.9 1.0 CA C:GLU65 4.5 19.4 1.0 HG3 C:GLU35 4.5 21.6 1.0 HG3 C:GLU163 4.6 25.4 1.0 HG2 C:GLU35 4.6 21.6 1.0 CB C:GLU65 4.6 21.7 1.0 HG2 C:GLU163 4.6 25.4 1.0 HB3 C:ALA38 4.7 15.2 1.0 HB3 C:GLU35 4.7 18.1 1.0 CE2 C:TYR140 4.7 23.7 1.0 OH C:TYR140 4.7 19.8 1.0 HB3 C:LEU159 4.8 30.3 1.0 CE1 C:HIS166 4.8 22.5 1.0 CB C:GLU35 4.9 15.1 1.0 HG2 C:GLU65 4.9 24.2 1.0 HG3 C:GLU65 5.0 24.2 1.0

Manganese binding site 6 out of 6 in the Crystal Structure of Katb, A Manganese Catalase From Anabaena PCC7120


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 Katb, A Manganese Catalase From Anabaena PCC7120 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn302 b:19.2 occ:1.00 OE1 C:GLU65 2.1 19.2 1.0 OE1 C:GLU163 2.1 23.3 1.0 OE2 C:GLU133 2.2 17.8 1.0 O C:HOH480 2.2 18.3 1.0 OE1 C:GLU133 2.2 21.0 1.0 ND1 C:HIS166 2.3 19.9 1.0 CD C:GLU133 2.5 19.6 1.0 CD C:GLU65 3.1 21.5 1.0 HA C:GLU163 3.1 25.2 1.0 CD C:GLU163 3.2 27.6 1.0 HB2 C:HIS166 3.2 20.8 1.0 CE1 C:HIS166 3.2 22.5 1.0 CG C:HIS166 3.4 22.6 1.0 HE1 C:HIS166 3.4 27.0 1.0 OE2 C:GLU65 3.4 25.0 1.0 HH C:TYR42 3.5 22.4 1.0 CB C:HIS166 3.6 17.4 1.0 HE2 C:TYR42 3.7 17.4 1.0 HB3 C:HIS166 3.7 20.8 1.0 HB3 C:GLU163 3.8 26.4 1.0 O C:HOH404 3.8 30.1 1.0 OE2 C:GLU163 3.9 26.1 1.0 CA C:GLU163 3.9 21.0 1.0 MN C:MN301 4.0 19.7 1.0 CG C:GLU133 4.0 17.6 1.0 CB C:GLU163 4.1 22.0 1.0 CG C:GLU163 4.1 21.2 1.0 HB1 C:ALA38 4.2 15.2 1.0 O C:HOH405 4.3 18.7 1.0 OH C:TYR42 4.4 18.7 1.0 CG C:GLU65 4.4 20.2 1.0 NE2 C:HIS166 4.4 21.2 1.0 HG2 C:GLU133 4.4 21.1 1.0 HA C:GLU133 4.4 20.8 1.0 HG3 C:GLU133 4.4 21.1 1.0 CD2 C:HIS166 4.5 19.1 1.0 HG3 C:GLU65 4.5 24.2 1.0 HG3 C:GLU163 4.5 25.4 1.0 CE2 C:TYR42 4.5 14.5 1.0 HG23 C:ILE61 4.6 26.4 1.0 HG2 C:GLU65 4.6 24.2 1.0 O C:ARG162 4.6 22.9 1.0 HE1 C:HIS68 4.7 25.8 1.0 HG21 C:ILE61 4.7 26.4 1.0 N C:GLU163 4.7 23.3 1.0 HE2 C:PHE170 4.7 17.7 1.0 HB2 C:ALA38 4.7 15.2 1.0 HB3 C:GLU133 4.8 23.0 1.0 HG22 C:ILE61 4.8 26.4 1.0 CB C:ALA38 4.9 12.6 1.0 CB C:GLU133 4.9 19.1 1.0 CG2 C:ILE61 4.9 22.0 1.0 HG2 C:GLU163 4.9 25.4 1.0 O C:GLU163 4.9 18.6 1.0 CZ C:TYR42 5.0 17.3 1.0 HB3 C:ALA136 5.0 18.6 1.0 C C:GLU163 5.0 20.0 1.0 C C:ARG162 5.0 20.4 1.0

S.C.Bihani, D.Chakravarty, A.Ballal. Katb, A Cyanobacterial Mn-Catalase with Unique Active Site Configuration: Implications For Enzyme Function. Free Radic. Biol. Med. V. 93 118 2016.
ISSN: ISSN 1873-4596
PubMed: 26826576
DOI: 10.1016/J.FREERADBIOMED.2016.01.022