Calcium in PDB 5mkg: PA3825-Eal Ca-Cdg Structure

The structure of PA3825-Eal Ca-Cdg Structure, PDB code: 5mkg was solved by S.Horrell, D.Bellini, R.Strange, A.Wagner, M.Walsh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.29 / 2.44
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.230, 59.400, 92.780, 90.00, 115.03, 90.00
R / Rfree (%)	23.8 / 28.5

The binding sites of Calcium atom in the PA3825-Eal Ca-Cdg Structure (pdb code 5mkg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the PA3825-Eal Ca-Cdg Structure, PDB code: 5mkg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the PA3825-Eal Ca-Cdg Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of PA3825-Eal Ca-Cdg Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:98.0 occ:1.00 O A:HOH426 2.8 53.8 1.0 OE2 A:GLU135 2.9 90.0 0.7 O A:ILE99 3.2 63.2 1.0 OE1 A:GLU135 3.4 87.9 0.7 CD A:GLU135 3.6 88.7 0.7 N21 A:C2E304 3.8 49.8 1.0 C A:ILE99 4.1 60.4 1.0 N31 A:C2E304 4.1 46.1 1.0 C21 A:C2E304 4.3 47.9 1.0 N A:ILE99 4.3 56.2 1.0 O2A A:C2E304 4.4 44.6 1.0 OE2 A:GLU62 4.4 73.0 1.0 CB A:ASN98 4.5 50.5 1.0 CG2 A:THR132 4.6 60.3 1.0 O A:HOH419 4.6 68.3 1.0 O A:GLU130 4.8 46.4 1.0 N A:SER100 4.8 62.3 1.0 C A:ASN98 4.8 52.5 1.0 CA A:SER100 4.8 66.7 1.0 CA A:ILE99 4.9 60.0 1.0 CA A:ASN98 5.0 50.4 1.0

Calcium binding site 2 out of 7 in the PA3825-Eal Ca-Cdg Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of PA3825-Eal Ca-Cdg Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:98.1 occ:1.00 OD1 A:ASP161 2.2 62.2 1.0 O1P A:C2E304 2.8 52.7 1.0 OE1 A:GLU217 2.8 48.4 1.0 O A:HOH421 2.8 61.1 1.0 OD1 A:ASP183 2.9 53.5 1.0 CG A:ASP161 3.3 67.0 1.0 CD A:GLU217 3.5 46.7 1.0 OE2 A:GLU217 3.7 48.3 0.7 O5' A:C2E304 3.8 49.5 1.0 OD2 A:ASP161 3.9 69.7 1.0 CG A:ASP183 4.0 54.0 1.0 P1 A:C2E304 4.0 49.7 1.0 OE1 A:GLN184 4.0 65.1 0.8 N A:GLN184 4.3 51.1 0.8 CB A:ASP161 4.4 64.7 1.0 CA A:ASP183 4.4 50.1 1.0 OD1 A:ASP160 4.4 65.5 1.0 CD A:GLN184 4.4 63.1 0.8 CA A:ASP161 4.5 63.7 1.0 CB A:ASP183 4.6 51.9 1.0 O A:HOH405 4.7 36.9 1.0 CB A:GLU217 4.7 39.1 1.0 CG A:GLU217 4.7 43.1 1.0 N A:ASP161 4.8 60.3 1.0 O3A A:C2E304 4.8 47.2 1.0 OD2 A:ASP183 4.8 54.7 1.0 CB A:GLN184 4.9 55.4 0.8 C A:ASP183 4.9 50.5 1.0 CG A:GLN184 4.9 59.0 0.8

Calcium binding site 3 out of 7 in the PA3825-Eal Ca-Cdg Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of PA3825-Eal Ca-Cdg Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:51.8 occ:1.00 O2P A:C2E304 2.2 46.8 1.0 OE2 A:GLU39 2.3 43.6 1.0 OD2 A:ASP160 2.3 62.3 1.0 OE1 A:GLU130 2.4 50.6 1.0 OD1 A:ASN98 2.4 50.7 1.0 O A:HOH405 2.5 36.9 1.0 CG A:ASP160 3.1 60.3 1.0 OD1 A:ASP160 3.2 65.5 1.0 CD A:GLU39 3.3 45.8 1.0 P1 A:C2E304 3.3 49.7 1.0 CG A:ASN98 3.4 49.7 1.0 CD A:GLU130 3.6 49.7 1.0 O1P A:C2E304 3.6 52.7 1.0 OE1 A:GLU39 3.7 44.1 1.0 ND2 A:ASN98 3.8 48.2 1.0 O5' A:C2E304 4.1 49.5 1.0 NZ A:LYS181 4.3 48.8 1.0 OE2 A:GLU130 4.3 48.7 1.0 CB A:GLU130 4.5 49.0 1.0 CB A:ASP160 4.5 56.7 1.0 CG A:GLU130 4.5 50.3 1.0 CG A:GLU39 4.6 45.3 1.0 O3A A:C2E304 4.6 47.2 1.0 C5' A:C2E304 4.7 47.7 1.0 OE1 A:GLU217 4.7 48.4 1.0 CB A:ASN98 4.8 50.5 1.0 O A:HOH426 4.8 53.8 1.0 C2A A:C2E304 4.9 46.8 1.0

Calcium binding site 4 out of 7 in the PA3825-Eal Ca-Cdg Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of PA3825-Eal Ca-Cdg Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:95.4 occ:1.00 O B:HOH423 2.6 45.0 1.0 OE2 B:GLU135 3.0 85.7 0.7 O B:ILE99 3.1 60.3 1.0 OE1 B:GLU135 3.6 85.1 0.7 CD B:GLU135 3.7 85.8 0.7 C B:ILE99 3.9 59.7 1.0 OE2 B:GLU62 4.3 68.0 1.0 CA B:SER100 4.4 67.9 1.0 N2 B:C2E304 4.5 42.5 1.0 N B:SER100 4.5 63.8 1.0 O B:GLU130 4.5 40.8 1.0 N B:ILE99 4.5 52.6 1.0 CG2 B:THR132 4.6 59.3 1.0 N B:THR132 4.7 53.4 1.0 O2' B:C2E304 4.9 40.4 1.0 CA B:ILE99 4.9 56.3 1.0 N3 B:C2E304 4.9 40.9 1.0 OG1 B:THR132 5.0 57.7 1.0 CB B:ASN98 5.0 46.2 1.0

Calcium binding site 5 out of 7 in the PA3825-Eal Ca-Cdg Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of PA3825-Eal Ca-Cdg Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:38.9 occ:1.00 O21 B:C2E304 2.2 43.1 1.0 OD2 B:ASP160 2.3 50.1 1.0 OE2 B:GLU39 2.3 38.3 1.0 OE1 B:GLU130 2.3 41.4 1.0 OD1 B:ASN98 2.4 42.8 1.0 O B:HOH408 2.4 35.5 1.0 CG B:ASP160 3.1 50.2 1.0 OD1 B:ASP160 3.2 52.0 1.0 CD B:GLU39 3.3 38.3 1.0 CG B:ASN98 3.4 44.5 1.0 P11 B:C2E304 3.5 42.0 1.0 CD B:GLU130 3.5 40.9 1.0 CA B:CA303 3.6 0.1 1.0 OE1 B:GLU39 3.7 37.8 1.0 ND2 B:ASN98 3.8 40.3 1.0 O11 B:C2E304 4.0 49.9 1.0 O5A B:C2E304 4.2 43.6 1.0 NZ B:LYS181 4.2 39.2 1.0 OE2 B:GLU130 4.3 40.2 1.0 CB B:GLU130 4.3 40.0 1.0 CB B:ASP160 4.4 49.4 1.0 CG B:GLU130 4.5 40.3 1.0 OE2 B:GLU217 4.5 43.4 0.7 CG B:GLU39 4.6 36.6 1.0 C5A B:C2E304 4.7 42.8 1.0 O B:HOH423 4.7 45.0 1.0 O3' B:C2E304 4.7 40.1 1.0 CB B:ASN98 4.7 46.2 1.0 C2' B:C2E304 5.0 40.7 1.0

Calcium binding site 6 out of 7 in the PA3825-Eal Ca-Cdg Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of PA3825-Eal Ca-Cdg Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:0.1 occ:1.00 O11 B:C2E304 2.3 49.9 1.0 OE1 B:GLU217 2.4 43.5 0.7 OD1 B:ASP161 2.4 61.6 1.0 OD1 B:ASP160 2.4 52.0 1.0 O B:HOH408 2.8 35.5 1.0 OE2 B:GLU217 2.9 43.4 0.7 CD B:GLU217 3.0 40.8 0.7 P11 B:C2E304 3.0 42.0 1.0 O5A B:C2E304 3.1 43.6 1.0 CG B:ASP160 3.4 50.2 1.0 O21 B:C2E304 3.4 43.1 1.0 CG B:ASP161 3.5 63.6 1.0 CA B:CA302 3.6 38.9 1.0 OD2 B:ASP160 3.7 50.1 1.0 OD2 B:ASP161 4.0 67.9 1.0 N B:ASP161 4.1 53.8 1.0 C5A B:C2E304 4.3 42.8 1.0 CG B:GLU217 4.4 36.8 0.7 O3' B:C2E304 4.5 40.1 1.0 CA B:ASP161 4.6 58.2 1.0 CB B:ASP161 4.6 60.7 1.0 CB B:ASP160 4.7 49.4 1.0 OD1 B:ASP183 4.9 53.9 1.0 C B:ASP160 5.0 51.1 1.0

Calcium binding site 7 out of 7 in the PA3825-Eal Ca-Cdg Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of PA3825-Eal Ca-Cdg Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca305 b:56.8 occ:1.00 O B:HOH410 2.5 34.0 1.0 O B:HOH429 2.6 41.9 1.0 O B:HOH431 2.8 54.5 1.0 OD2 B:ASP234 2.8 48.2 1.0 OD1 B:ASP234 2.9 50.6 1.0 O B:HOH424 2.9 59.0 1.0 CG B:ASP234 3.2 47.5 1.0 O B:GLY232 4.3 44.0 1.0 O B:LEU212 4.5 41.9 1.0 CB B:ASP234 4.7 45.5 1.0 OD1 B:ASP213 5.0 37.2 0.7

D.Bellini, S.Horrell, A.Hutchin, C.W.Phippen, R.W.Strange, Y.Cai, A.Wagner, J.S.Webb, I.Tews, M.A.Walsh. Dimerisation Induced Formation of the Active Site and the Identification of Three Metal Sites in Eal-Phosphodiesterases. Sci Rep V. 7 42166 2017.
ISSN: ESSN 2045-2322
PubMed: 28186120
DOI: 10.1038/SREP42166