Calcium in PDB 6khx: Crystal Structure of Prx From Akkermansia Muciniphila

The structure of Crystal Structure of Prx From Akkermansia Muciniphila, PDB code: 6khx was solved by M.Li, J.Wang, W.Xu, Y.Wang, M.Zhang, M.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.10 / 2.58
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	132.733, 211.371, 92.802, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.8

The binding sites of Calcium atom in the Crystal Structure of Prx From Akkermansia Muciniphila (pdb code 6khx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Prx From Akkermansia Muciniphila, PDB code: 6khx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of Prx From Akkermansia Muciniphila


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 Prx From Akkermansia Muciniphila within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:81.2 occ:1.00 O B:ASN106 4.6 32.6 1.0 OE2 B:GLU120 4.7 75.7 1.0 O B:LYS107 4.8 33.2 1.0 CG1 E:VAL128 4.9 74.6 1.0 CB B:LYS107 5.0 27.6 1.0 CB B:ALA111 5.0 19.8 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of Prx From Akkermansia Muciniphila


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 Prx From Akkermansia Muciniphila within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:76.8 occ:1.00 OE1 C:GLU120 4.5 64.9 1.0 CD2 C:LEU116 4.5 22.9 1.0 CB C:ALA111 4.7 23.7 1.0 OE2 C:GLU120 4.8 76.0 1.0 O C:LYS107 4.8 29.2 1.0 O C:ASN106 4.9 33.0 1.0 CB C:LYS107 4.9 32.0 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of Prx From Akkermansia Muciniphila


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 Prx From Akkermansia Muciniphila within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:78.2 occ:1.00 O D:ASN106 4.2 35.1 1.0 OE2 D:GLU120 4.4 77.5 1.0 O D:LYS107 4.6 31.8 1.0 CB D:LYS107 4.7 29.2 1.0 C D:LYS107 4.8 35.8 1.0 CG1 G:VAL128 4.9 83.2 1.0 CB D:ALA111 5.0 28.6 1.0 CD2 D:LEU116 5.0 24.6 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of Prx From Akkermansia Muciniphila


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 Prx From Akkermansia Muciniphila within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca301 b:84.1 occ:1.00 O I:HOH469 2.6 54.3 1.0 O I:HOH473 3.7 45.4 1.0 OE2 F:GLU120 3.9 79.6 1.0 O F:ASN106 4.6 30.0 1.0 CB F:LYS107 4.8 25.7 1.0 CD F:GLU120 4.8 75.7 1.0 O F:LYS107 4.9 25.8 1.0 CD2 F:LEU116 4.9 19.6 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of Prx From Akkermansia Muciniphila


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 Prx From Akkermansia Muciniphila within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca301 b:74.0 occ:1.00 O G:ASN106 4.0 32.0 1.0 O G:LYS107 4.4 34.0 1.0 CB G:LYS107 4.4 32.8 1.0 C G:LYS107 4.6 32.7 1.0 OE2 G:GLU120 4.7 68.7 1.0 CG2 G:THR108 4.8 30.0 1.0 N G:THR108 4.9 33.1 1.0 CB G:ALA111 4.9 24.4 1.0 CD2 G:LEU116 5.0 24.6 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of Prx From Akkermansia Muciniphila


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Prx From Akkermansia Muciniphila within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca301 b:80.6 occ:1.00 OE2 J:GLU120 3.9 82.7 1.0 OE2 H:GLU120 4.5 69.6 1.0 O H:ASN106 4.6 26.2 1.0 CG1 J:VAL128 4.7 87.2 1.0 CD J:GLU120 4.9 76.2 1.0 O H:LYS107 5.0 26.1 1.0 CB H:LYS107 5.0 20.8 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of Prx From Akkermansia Muciniphila


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Prx From Akkermansia Muciniphila within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca301 b:70.0 occ:1.00 O I:HOH473 3.9 45.4 1.0 OE2 I:GLU120 4.2 70.0 1.0 O F:HOH447 4.4 49.4 1.0 O I:ASN106 4.5 22.8 1.0 O I:LYS107 4.6 26.1 1.0 CB I:ALA111 4.6 16.1 1.0 CD2 I:LEU116 4.7 18.7 1.0 CB I:LYS107 4.8 22.5 1.0 C I:LYS107 4.9 26.6 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of Prx From Akkermansia Muciniphila


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Prx From Akkermansia Muciniphila within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca301 b:70.3 occ:1.00 OE1 J:GLU120 3.5 80.7 1.0 O J:ASN106 4.5 21.2 1.0 CD J:GLU120 4.5 76.2 1.0 O J:LYS107 4.7 31.8 1.0 CB J:LYS107 4.8 22.4 1.0 OE2 J:GLU120 4.8 82.7 1.0 CB J:ALA111 4.8 20.0 1.0 C J:LYS107 4.9 25.6 1.0 CD2 J:LEU116 5.0 22.9 1.0

M.Li, J.Wang, W.Xu, Y.Wang, M.Zhang, M.Wang. Crystal Structure of Akkermansia Muciniphila Peroxiredoxin Reveals A Novel Regulatory Mechanism of Typical 2-Cys Prxs By A Distinct Loop. Febs Lett. 2020.
ISSN: ISSN 0014-5793
PubMed: 32027024
DOI: 10.1002/1873-3468.13753