Manganese in PDB 6kk8: Xn Joint Refinement of Manganese Catalase From Thermus Thermophilus HB27

All present enzymatic activity of Xn Joint Refinement of Manganese Catalase From Thermus Thermophilus HB27:
1.11.1.6;

The structure of Xn Joint Refinement of Manganese Catalase From Thermus Thermophilus HB27, PDB code: 6kk8 was solved by T.Yamada, N.Yano, K.Kusaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.37
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	133.396, 133.396, 133.396, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 19.1

The binding sites of Manganese atom in the Xn Joint Refinement of Manganese Catalase From Thermus Thermophilus HB27 (pdb code 6kk8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Xn Joint Refinement of Manganese Catalase From Thermus Thermophilus HB27, PDB code: 6kk8:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Xn Joint Refinement of Manganese Catalase From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Xn Joint Refinement of Manganese Catalase From Thermus Thermophilus HB27 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:7.3 occ:1.00 OE2 A:GLU70 2.1 8.3 1.0 O A:O1003 2.1 9.8 1.0 O A:O1004 2.1 6.8 0.4 OE2 A:GLU155 2.1 7.4 1.0 ND1 A:HIS188 2.2 6.2 1.0 OE1 A:GLU155 2.6 8.8 1.0 O A:O1004 2.6 9.4 0.6 CD A:GLU155 2.7 8.2 1.0 CE1 A:HIS188 3.1 7.5 1.0 CD A:GLU70 3.1 7.2 1.0 MN A:MN31002 3.1 7.3 1.0 HE1 A:HIS188 3.2 6.7 1.0 CG A:HIS188 3.3 5.2 1.0 HE2 A:TYR43 3.4 9.4 1.0 OE1 A:GLU70 3.4 9.1 1.0 HB2 A:HIS188 3.4 8.1 1.0 HA2 A:GLY185 3.6 10.2 1.0 O A:O1005 3.6 8.8 0.3 HB A:THR39 3.6 8.6 1.0 HH A:TYR43 3.7 7.9 0.2 DH A:TYR43 3.7 7.9 0.8 DG1 A:THR39 3.7 10.3 0.8 HG1 A:THR39 3.7 10.1 0.2 CB A:HIS188 3.7 5.9 1.0 HB3 A:HIS188 3.8 8.4 1.0 HG21 A:THR39 4.0 11.7 1.0 O A:O1005 4.1 10.5 0.7 HE1 A:HIS73 4.2 6.7 1.0 CG A:GLU155 4.2 7.0 1.0 HG22 A:THR39 4.3 9.6 1.0 NE2 A:HIS188 4.3 7.6 1.0 CB A:THR39 4.3 6.7 1.0 CE2 A:TYR43 4.4 6.5 1.0 CD2 A:HIS188 4.4 7.4 1.0 CG A:GLU70 4.4 6.5 1.0 CG2 A:THR39 4.4 8.1 1.0 OG1 A:THR39 4.4 7.8 1.0 HG3 A:GLU155 4.5 9.5 1.0 HG23 A:ILE66 4.5 6.9 1.0 HG2 A:GLU155 4.6 7.2 1.0 OH A:TYR43 4.6 8.2 1.0 HG3 A:GLU70 4.6 8.2 1.0 ND1 A:HIS73 4.6 7.0 1.0 CA A:GLY185 4.6 8.5 1.0 HG2 A:GLU70 4.6 5.5 1.0 CE1 A:HIS73 4.7 8.7 1.0 HG21 A:ILE66 4.7 10.7 1.0 O A:DOD1156 4.7 20.4 1.0 HG22 A:ILE66 4.8 8.1 1.0 HA3 A:GLY185 4.8 8.7 1.0 OE1 A:GLU36 4.9 10.7 1.0 CG2 A:ILE66 4.9 7.2 1.0

Manganese binding site 2 out of 4 in the Xn Joint Refinement of Manganese Catalase From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Xn Joint Refinement of Manganese Catalase From Thermus Thermophilus HB27 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1002 b:7.3 occ:1.00 O A:O1004 2.0 6.8 0.4 OE1 A:GLU36 2.0 10.7 1.0 O A:O1003 2.0 9.8 1.0 OE1 A:GLU70 2.1 9.1 1.0 ND1 A:HIS73 2.2 7.0 1.0 O A:O1005 2.2 10.5 0.7 O A:O1004 2.6 9.4 0.6 O A:O1005 2.8 8.8 0.3 CD A:GLU36 2.9 12.7 1.0 DG1 A:THR39 3.0 10.3 0.8 HG1 A:THR39 3.0 10.1 0.2 CE1 A:HIS73 3.1 8.7 1.0 CD A:GLU70 3.1 7.2 1.0 MN A:MN31001 3.1 7.3 1.0 HE1 A:HIS73 3.2 6.7 1.0 OE2 A:GLU36 3.2 26.6 1.0 CG A:HIS73 3.3 6.0 1.0 OE2 A:GLU70 3.3 8.3 1.0 HB3 A:HIS73 3.5 5.8 1.0 HB2 A:HIS73 3.5 9.7 1.0 CB A:HIS73 3.6 5.7 1.0 HE1 A:HIS188 3.8 6.7 1.0 OG1 A:THR39 3.9 7.8 1.0 DZ2 A:LYS162 4.0 14.2 0.4 HA A:GLU70 4.0 6.7 1.0 HD22 A:LEU181 4.2 8.5 1.0 NE2 A:HIS73 4.2 8.3 1.0 CG A:GLU36 4.3 7.3 1.0 HD13 A:LEU181 4.3 9.1 1.0 CD2 A:HIS73 4.3 7.5 1.0 HA A:GLU36 4.4 10.8 1.0 HG21 A:THR39 4.4 11.7 1.0 CG A:GLU70 4.4 6.5 1.0 HB3 A:GLU36 4.5 5.4 1.0 HG3 A:GLU36 4.5 8.9 1.0 CE1 A:HIS188 4.5 7.5 1.0 ND1 A:HIS188 4.5 6.2 1.0 HB A:THR39 4.6 8.6 1.0 HB3 A:GLU70 4.6 6.9 1.0 NZ A:LYS162 4.7 24.2 0.6 HD21 A:LEU181 4.7 13.3 1.0 CB A:THR39 4.8 6.7 1.0 CB A:GLU36 4.8 7.1 1.0 HB3 A:LEU181 4.9 7.5 1.0 CB A:GLU70 4.9 5.1 1.0 NZ A:LYS162 4.9 11.4 0.4 HE2 A:LYS162 4.9 13.0 0.6 CA A:GLU70 4.9 4.8 1.0 HG3 A:GLU70 4.9 8.2 1.0 CD2 A:LEU181 4.9 11.4 1.0 DZ1 A:LYS162 5.0 16.4 0.4 OE1 A:GLU155 5.0 8.8 1.0

Manganese binding site 3 out of 4 in the Xn Joint Refinement of Manganese Catalase From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Xn Joint Refinement of Manganese Catalase From Thermus Thermophilus HB27 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1001 b:7.4 occ:1.00 O B:O1004 2.1 6.5 0.4 OE2 B:GLU70 2.1 8.2 1.0 OE2 B:GLU155 2.1 8.7 1.0 O B:O1003 2.2 11.0 1.0 ND1 B:HIS188 2.2 6.5 1.0 OE1 B:GLU155 2.6 8.8 1.0 O B:O1004 2.6 10.7 0.6 CD B:GLU155 2.7 8.2 1.0 CE1 B:HIS188 3.1 7.7 1.0 CD B:GLU70 3.1 6.1 1.0 MN B:MN31002 3.1 7.1 1.0 HE1 B:HIS188 3.2 7.9 1.0 CG B:HIS188 3.3 5.6 1.0 HE2 B:TYR43 3.4 8.8 1.0 OE1 B:GLU70 3.4 9.4 1.0 HB2 B:HIS188 3.5 6.6 1.0 HG21 B:THR39 3.5 6.3 1.0 O B:O1005 3.6 10.7 0.3 HA2 B:GLY185 3.6 10.4 1.0 DH B:TYR43 3.6 8.5 0.8 HH B:TYR43 3.7 8.4 0.2 DG1 B:THR39 3.7 11.1 0.8 HB B:THR39 3.7 10.7 1.0 HG1 B:THR39 3.7 10.7 0.1 CB B:HIS188 3.8 5.4 1.0 HB3 B:HIS188 3.8 6.7 1.0 O B:O1005 4.0 8.5 0.7 HE1 B:HIS73 4.1 9.0 1.0 CG B:GLU155 4.2 7.0 1.0 NE2 B:HIS188 4.3 7.4 1.0 CB B:THR39 4.3 6.2 1.0 D2 B:DOD1155 4.3 23.1 1.0 CG2 B:THR39 4.4 9.0 1.0 CD2 B:HIS188 4.4 6.9 1.0 CE2 B:TYR43 4.4 5.5 1.0 CG B:GLU70 4.4 4.9 1.0 OG1 B:THR39 4.5 7.3 1.0 HG3 B:GLU155 4.5 8.5 1.0 HG23 B:ILE66 4.6 7.5 1.0 OH B:TYR43 4.6 8.3 1.0 ND1 B:HIS73 4.6 6.8 1.0 HG3 B:GLU70 4.6 9.0 1.0 HG21 B:ILE66 4.6 7.1 1.0 HG2 B:GLU155 4.6 7.3 1.0 HG2 B:GLU70 4.6 6.2 1.0 CA B:GLY185 4.6 9.3 1.0 CE1 B:HIS73 4.7 7.7 1.0 HG22 B:THR39 4.7 8.1 1.0 HG22 B:ILE66 4.7 6.4 1.0 O B:DOD1155 4.8 24.6 1.0 OE1 B:GLU36 4.9 10.4 1.0 HA3 B:GLY185 4.9 7.8 1.0 CG2 B:ILE66 4.9 6.5 1.0 D1 B:DOD1155 5.0 25.0 1.0

Manganese binding site 4 out of 4 in the Xn Joint Refinement of Manganese Catalase From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Xn Joint Refinement of Manganese Catalase From Thermus Thermophilus HB27 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1002 b:7.1 occ:1.00 OE1 B:GLU36 2.0 10.4 1.0 O B:O1003 2.0 11.0 1.0 O B:O1004 2.1 6.5 0.4 OE1 B:GLU70 2.1 9.4 1.0 ND1 B:HIS73 2.2 6.8 1.0 O B:O1005 2.2 8.5 0.7 O B:O1004 2.6 10.7 0.6 O B:O1005 2.8 10.7 0.3 CD B:GLU36 2.9 11.5 1.0 HG1 B:THR39 2.9 10.7 0.1 DG1 B:THR39 2.9 11.1 0.8 CE1 B:HIS73 3.1 7.7 1.0 CD B:GLU70 3.1 6.1 1.0 MN B:MN31001 3.1 7.4 1.0 HE1 B:HIS73 3.2 9.0 1.0 OE2 B:GLU36 3.2 27.0 1.0 CG B:HIS73 3.2 5.7 1.0 OE2 B:GLU70 3.3 8.2 1.0 HB3 B:HIS73 3.4 5.3 1.0 HB2 B:HIS73 3.6 7.2 1.0 CB B:HIS73 3.6 6.2 1.0 HE1 B:HIS188 3.8 7.9 1.0 OG1 B:THR39 3.9 7.3 1.0 HD22 B:LEU181 3.9 11.8 1.0 HA B:GLU70 4.0 6.1 1.0 NE2 B:HIS73 4.2 7.3 1.0 CG B:GLU36 4.3 7.2 1.0 HD13 B:LEU181 4.3 8.3 1.0 CD2 B:HIS73 4.3 7.3 1.0 HG21 B:THR39 4.4 6.3 1.0 DZ1 B:LYS162 4.4 11.6 0.6 HA B:GLU36 4.4 11.2 1.0 NZ B:LYS162 4.4 18.9 0.4 CG B:GLU70 4.4 4.9 1.0 DZ3 B:LYS162 4.5 14.9 0.6 HB3 B:GLU36 4.5 6.5 1.0 HG3 B:GLU36 4.5 8.3 1.0 CE1 B:HIS188 4.5 7.7 1.0 ND1 B:HIS188 4.5 6.5 1.0 HB B:THR39 4.6 10.7 1.0 HB3 B:GLU70 4.7 5.6 1.0 CB B:THR39 4.8 6.2 1.0 HE2 B:LYS162 4.8 12.8 0.6 HB3 B:LEU181 4.8 10.4 1.0 CB B:GLU36 4.8 5.8 1.0 NZ B:LYS162 4.9 13.5 0.6 CB B:GLU70 4.9 4.7 1.0 CA B:GLU70 4.9 5.0 1.0 CD2 B:LEU181 5.0 11.4 1.0 HG2 B:GLU70 5.0 6.2 1.0 HG3 B:GLU70 5.0 9.0 1.0

T.Yamada, N.Yano, T.Hosoya, K.Kusaka. Single-Crystal Time-of-Flight Neutron Laue Methods: Application to Manganese Catalase From Thermus Thermophilus HB27 J.Appl.Crystallogr. 2019.
ISSN: ESSN 1600-5767
DOI: 10.1107/S1600576719010239