Calcium 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:

Manganese

(Mn)

6 atoms

The binding sites of Calcium 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 Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Katb, A Manganese Catalase From Anabaena PCC7120, PDB code: 4r42:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of Katb, A Manganese Catalase From Anabaena PCC7120


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca303 b:22.3 occ:1.00 OD2 A:ASP60 2.4 16.3 1.0 OD1 A:ASP56 2.5 25.7 1.0 O A:HOH421 2.5 25.9 1.0 O A:HOH507 2.5 23.0 1.0 OD1 A:ASP60 2.6 19.5 1.0 OD2 A:ASP56 2.6 23.2 1.0 CG A:ASP60 2.9 22.8 1.0 CG A:ASP56 2.9 24.4 1.0 HZ1 B:LYS6 4.2 93.1 1.0 HE2 B:LYS6 4.4 91.8 1.0 CB A:ASP60 4.4 17.3 1.0 CB A:ASP56 4.4 18.6 1.0 O A:ASP56 4.4 19.7 1.0 HE3 B:LYS6 4.5 91.8 1.0 HB2 A:ASP60 4.7 20.8 1.0 CE B:LYS6 4.8 76.5 1.0 HB3 A:ASP60 4.8 20.8 1.0 HB2 A:ASP56 4.8 22.3 1.0 HB3 A:ASP56 4.8 22.3 1.0 C A:ASP56 4.8 18.8 1.0 NZ B:LYS6 4.9 77.5 1.0 H A:ASP60 4.9 16.5 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of Katb, A Manganese Catalase From Anabaena PCC7120


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca304 b:14.6 occ:1.00 O A:GLN107 2.4 13.8 1.0 O C:GLN107 2.4 13.5 1.0 O A:HOH404 2.4 15.3 1.0 O A:HOH407 2.5 15.0 1.0 O C:HOH481 2.5 14.2 1.0 O C:HOH483 2.5 14.4 1.0 HB3 A:GLN107 3.2 13.7 1.0 HB3 C:GLN107 3.2 17.1 1.0 C A:GLN107 3.5 11.7 1.0 C C:GLN107 3.5 10.1 1.0 HA A:GLN107 3.8 14.3 1.0 HA C:GLN107 3.9 17.3 1.0 CB A:GLN107 4.0 11.4 1.0 CA A:GLN107 4.0 11.9 1.0 CB C:GLN107 4.0 14.2 1.0 CA C:GLN107 4.1 14.4 1.0 HB2 A:GLN107 4.3 13.7 1.0 HB2 C:GLN107 4.4 17.1 1.0 HA3 A:GLY108 4.4 15.7 1.0 HA3 C:GLY108 4.4 14.9 1.0 O C:HOH435 4.4 19.9 1.0 O A:HOH466 4.5 21.4 1.0 N C:GLY108 4.6 13.3 1.0 N A:GLY108 4.6 12.8 1.0 OE1 A:GLN107 4.8 17.4 1.0 OE1 C:GLN107 4.8 19.2 1.0 CA C:GLY108 4.9 12.4 1.0 CA A:GLY108 5.0 13.1 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of Katb, A Manganese Catalase From Anabaena PCC7120


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca303 b:15.3 occ:1.00 OD1 B:ASN109 2.3 13.2 1.0 O A:HOH508 2.4 24.1 1.0 O B:HOH484 2.4 27.1 1.0 O B:HOH502 2.4 25.9 1.0 CG B:ASN109 3.4 16.3 1.0 HA B:ASN109 3.5 21.8 1.0 HB3 B:ASN109 3.8 20.0 1.0 CB B:ASN109 4.0 16.7 1.0 O B:HOH434 4.0 27.5 1.0 O B:HOH503 4.1 32.1 1.0 CA B:ASN109 4.2 18.2 1.0 ND2 B:ASN109 4.5 16.1 1.0 O B:HOH428 4.5 24.1 1.0 HD21 B:ASN109 4.6 19.3 1.0 H B:ALA110 4.6 16.2 1.0 O A:HOH422 4.7 24.4 1.0 HB2 B:ASN109 5.0 20.0 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of Katb, A Manganese Catalase From Anabaena PCC7120


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca304 b:22.4 occ:1.00 OD1 C:ASN199 2.3 30.8 1.0 O C:HOH417 2.4 26.5 1.0 OD2 B:ASP60 2.4 18.6 1.0 OD1 B:ASP56 2.4 21.0 1.0 O C:SER201 2.5 29.7 1.0 O C:HOH419 2.6 26.1 1.0 OD1 B:ASP60 2.6 19.6 1.0 OD2 B:ASP56 2.6 24.6 1.0 CG B:ASP60 2.9 19.5 1.0 CG B:ASP56 2.9 23.0 1.0 CG C:ASN199 3.5 31.1 1.0 C C:SER201 3.7 34.0 1.0 HA C:ASN199 3.8 31.6 1.0 H C:SER201 3.8 36.7 1.0 HH C:TYR197 3.9 28.9 1.0 HB3 C:SER201 3.9 34.6 1.0 HZ2 A:LYS6 4.0 83.5 1.0 HA C:SER202 4.0 60.6 1.0 HE2 A:LYS6 4.2 82.9 1.0 HE1 C:TYR197 4.2 35.6 1.0 HD21 C:ASN199 4.3 39.7 1.0 HE3 A:LYS6 4.4 82.9 1.0 CB B:ASP56 4.4 23.9 1.0 CB B:ASP60 4.4 18.7 1.0 ND2 C:ASN199 4.4 33.1 1.0 N C:SER201 4.4 30.6 1.0 CA C:ASN199 4.4 26.3 1.0 O B:ASP56 4.4 19.1 1.0 CA C:SER201 4.5 29.6 1.0 CB C:ASN199 4.5 30.4 1.0 H C:GLU209 4.5 52.3 1.0 CE A:LYS6 4.6 69.1 1.0 N C:SER202 4.6 44.6 1.0 CB C:SER201 4.6 28.9 1.0 HB2 C:ASN199 4.7 36.5 1.0 OH C:TYR221 4.7 29.6 1.0 OD1 C:ASP208 4.7 65.6 1.0 NZ A:LYS6 4.7 69.6 1.0 HB2 B:ASP60 4.7 22.4 1.0 C C:ASN199 4.7 30.1 1.0 OH C:TYR197 4.7 24.1 1.0 HB2 C:GLU209 4.7 46.4 1.0 CA C:SER202 4.7 50.5 1.0 HB2 B:ASP56 4.8 28.7 1.0 HB3 B:ASP56 4.8 28.7 1.0 HB3 B:ASP60 4.8 22.4 1.0 C B:ASP56 4.8 22.8 1.0 O C:GLU209 4.8 23.6 1.0 H C:LEU200 4.9 33.1 1.0 HB3 C:SER202 4.9 63.2 1.0 N C:LEU200 5.0 27.6 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca303 b:46.4 occ:1.00 OD1 B:ASN199 2.3 61.3 1.0 OD2 C:ASP60 2.4 32.8 1.0 O B:SER201 2.4 49.9 1.0 OD2 C:ASP56 2.5 37.8 1.0 OD1 C:ASP56 2.5 37.4 1.0 O B:HOH530 2.6 46.9 1.0 O B:HOH527 2.6 40.4 1.0 OD1 C:ASP60 2.7 30.5 1.0 CG C:ASP56 2.8 37.3 1.0 CG C:ASP60 2.9 31.4 1.0 CG B:ASN199 3.5 66.9 1.0 C B:SER201 3.6 61.4 1.0 HH B:TYR197 3.7 49.2 1.0 H B:SER201 3.7 74.4 1.0 HA B:ASN199 3.8 64.4 1.0 HB3 B:SER201 3.9 65.3 1.0 HE1 B:TYR197 4.1 48.7 1.0 HD21 B:ASN199 4.2 90.0 1.0 OD1 B:ASP208 4.2 0.2 1.0 ND2 B:ASN199 4.3 75.0 1.0 CB C:ASP56 4.3 37.7 1.0 N B:SER201 4.4 62.0 1.0 CB C:ASP60 4.4 27.0 1.0 CA B:SER201 4.4 61.4 1.0 CB B:ASN199 4.5 60.2 1.0 CA B:ASN199 4.5 53.7 1.0 O C:ASP56 4.5 26.9 1.0 H B:GLU209 4.5 0.8 1.0 OH B:TYR221 4.6 56.6 1.0 OH B:TYR197 4.6 41.0 1.0 CB B:SER201 4.6 54.4 1.0 HB2 B:ASN199 4.6 72.2 1.0 HB2 C:ASP60 4.7 32.4 1.0 HB3 C:ASP56 4.7 45.3 1.0 O B:GLU209 4.7 53.5 1.0 HB2 C:ASP56 4.8 45.3 1.0 C B:ASN199 4.8 50.1 1.0 C C:ASP56 4.8 31.8 1.0 HB2 B:GLU209 4.8 67.9 1.0 HB3 C:ASP60 4.9 32.4 1.0 HE1 B:TYR221 4.9 62.9 1.0 HA B:ASP208 5.0 0.7 1.0 CE1 B:TYR197 5.0 40.6 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