Calcium in PDB 4z05: C. Bescii Family 3 Pectate Lyase Mutant E84A

All present enzymatic activity of C. Bescii Family 3 Pectate Lyase Mutant E84A:
4.2.2.2;

The structure of C. Bescii Family 3 Pectate Lyase Mutant E84A, PDB code: 4z05 was solved by P.M.Alahuhta, V.V.Lunin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	35.270, 145.570, 160.077, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 18.6

The structure of C. Bescii Family 3 Pectate Lyase Mutant E84A also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the C. Bescii Family 3 Pectate Lyase Mutant E84A (pdb code 4z05). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the C. Bescii Family 3 Pectate Lyase Mutant E84A, PDB code: 4z05:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the C. Bescii Family 3 Pectate Lyase Mutant E84A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of C. Bescii Family 3 Pectate Lyase Mutant E84A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:7.5 occ:1.00 O A:GLU104 2.3 6.7 1.0 OD1 A:ASP81 2.3 10.0 1.0 O A:VAL82 2.4 6.3 1.0 O A:HOH383 2.4 8.9 1.0 O A:HOH366 2.4 11.4 1.0 O A:HOH403 2.4 8.4 1.0 O A:HOH497 2.4 10.0 1.0 CG A:ASP81 3.4 11.5 1.0 C A:GLU104 3.5 6.5 1.0 C A:VAL82 3.6 6.6 1.0 OD2 A:ASP81 3.9 12.0 1.0 CB A:GLU104 4.0 9.4 1.0 N A:VAL82 4.0 6.4 1.0 O A:HOH414 4.2 10.0 1.0 C A:ASP81 4.2 6.8 1.0 CA A:VAL82 4.3 6.5 1.0 O A:HOH562 4.3 32.2 1.0 O A:HOH392 4.3 10.3 1.0 N A:ALA105 4.4 6.4 1.0 CA A:GLU104 4.4 7.7 1.0 CA A:ALA105 4.4 6.5 1.0 O A:HOH541 4.4 48.5 1.0 N A:ALA106 4.4 7.1 1.0 O A:GLY35 4.4 7.6 1.0 O A:GLY83 4.5 7.5 1.0 N A:GLY83 4.6 6.0 1.0 CB A:ASP81 4.6 9.1 1.0 O A:HOH391 4.6 20.6 1.0 O A:ASP81 4.6 6.8 1.0 CB A:VAL82 4.7 6.5 1.0 CA A:ASP81 4.7 7.6 1.0 CA A:GLY83 4.8 6.2 1.0 O A:LYS103 4.9 6.5 0.5 C A:ALA105 4.9 6.7 1.0 O A:LYS103 4.9 6.5 0.5

Calcium binding site 2 out of 4 in the C. Bescii Family 3 Pectate Lyase Mutant E84A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of C. Bescii Family 3 Pectate Lyase Mutant E84A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:10.2 occ:1.00 OD1 A:ASP64 2.3 11.2 1.0 O A:HOH504 2.4 14.3 1.0 O A:HOH388 2.4 13.1 1.0 OD2 A:ASP85 2.5 10.2 1.0 O A:HOH345 2.5 15.1 1.0 OD1 A:ASP85 2.5 10.0 1.0 CG A:ASP85 2.9 8.2 1.0 CG A:ASP64 3.2 10.9 1.0 OD2 A:ASP64 3.4 12.1 1.0 O A:HOH374 4.1 22.6 1.0 OG1 A:THR88 4.2 10.8 1.0 O A:HOH476 4.2 24.5 1.0 O A:HOH402 4.3 14.3 1.0 CB A:ASP85 4.3 7.8 1.0 CB A:ALA84 4.4 8.1 1.0 NZ A:LYS108 4.5 13.8 1.0 O A:HOH365 4.6 8.5 1.0 CB A:ASP64 4.6 10.1 1.0 O A:HOH445 4.8 11.8 1.0 N A:ASP85 4.8 7.6 1.0 O A:ASP64 4.8 10.4 1.0 CE A:LYS108 4.8 12.0 1.0 CA A:ASP64 4.9 10.2 1.0 C A:ALA84 5.0 8.2 1.0

Calcium binding site 3 out of 4 in the C. Bescii Family 3 Pectate Lyase Mutant E84A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of C. Bescii Family 3 Pectate Lyase Mutant E84A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:21.1 occ:0.86 O B:HOH414 2.2 22.4 1.0 O B:HOH317 2.3 24.1 1.0 O B:HOH402 2.3 25.3 1.0 O B:HOH311 2.3 25.4 1.0 OD1 B:ASP64 2.4 19.1 1.0 OD1 B:ASP85 2.5 19.6 1.0 OD2 B:ASP85 2.6 21.8 1.0 CG B:ASP85 2.9 18.3 1.0 CG B:ASP64 3.1 18.8 1.0 OD2 B:ASP64 3.2 24.0 1.0 OE1 B:GLN111 4.1 17.7 0.5 OG1 B:THR88 4.1 13.8 1.0 OE2 B:GLU39 4.2 59.0 1.0 O B:HOH422 4.3 25.4 0.5 CB B:ALA84 4.3 13.3 1.0 O B:HOH422 4.4 15.8 0.5 CB B:ASP85 4.4 15.7 1.0 O B:HOH349 4.4 21.4 1.0 CB B:ASP64 4.5 16.6 1.0 O B:HOH410 4.6 35.4 1.0 O B:HOH359 4.6 16.9 1.0 O B:HOH352 4.7 19.2 0.7 N B:ASP85 4.8 14.3 1.0 OE1 B:GLU39 4.8 73.1 1.0 CD B:GLN111 4.9 15.0 0.5 CD B:GLU39 4.9 58.0 1.0 CA B:ASP64 4.9 14.4 1.0 C B:ALA84 5.0 14.2 1.0

Calcium binding site 4 out of 4 in the C. Bescii Family 3 Pectate Lyase Mutant E84A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of C. Bescii Family 3 Pectate Lyase Mutant E84A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:14.0 occ:1.00 O B:GLU104 2.3 12.3 1.0 OD1 B:ASP81 2.3 15.5 1.0 O B:HOH465 2.4 19.0 1.0 O B:VAL82 2.4 13.1 1.0 O B:HOH392 2.4 17.6 1.0 O B:HOH379 2.4 18.0 1.0 O B:HOH353 2.5 14.5 1.0 C B:GLU104 3.4 12.6 1.0 CG B:ASP81 3.4 16.0 1.0 C B:VAL82 3.5 11.1 1.0 OD2 B:ASP81 3.9 18.8 1.0 N B:VAL82 3.9 11.4 1.0 CB B:GLU104 4.0 15.2 1.0 C B:ASP81 4.2 12.1 1.0 O B:HOH367 4.3 13.6 1.0 CA B:VAL82 4.3 11.4 1.0 CA B:GLU104 4.3 13.1 1.0 N B:ALA105 4.4 11.8 1.0 CA B:ALA105 4.4 13.6 1.0 O B:HOH450 4.4 24.0 1.0 N B:ALA106 4.5 13.0 1.0 O B:HOH386 4.5 15.0 1.0 O B:GLY83 4.5 12.5 1.0 O B:HOH526 4.5 35.7 1.0 O B:GLY35 4.6 15.7 1.0 N B:GLY83 4.6 11.9 1.0 O B:ASP81 4.6 12.3 1.0 CB B:ASP81 4.7 13.8 1.0 CB B:VAL82 4.7 11.5 1.0 CA B:ASP81 4.7 12.4 1.0 CA B:GLY83 4.7 12.6 1.0 O B:HOH345 4.8 22.9 0.5 C B:ALA105 4.8 13.7 1.0 O B:HOH388 5.0 33.7 0.8 O B:LYS103 5.0 11.2 1.0

M.Alahuhta, L.E.Taylor, R.Brunecky, D.W.Sammond, W.Michener, M.W.Adams, M.E.Himmel, Y.J.Bomble, V.Lunin. The Catalytic Mechanism and Unique Low pH Optimum of Caldicellulosiruptor Bescii Family 3 Pectate Lyase. Acta Crystallogr.,Sect.D V. 71 1946 2015.
ISSN: ESSN 1399-0047
PubMed: 26327384
DOI: 10.1107/S1399004715013760