Calcium in PDB 4y9p: PA3825-Eal Ca-Cdg Structure

The structure of PA3825-Eal Ca-Cdg Structure, PDB code: 4y9p was solved by D.Bellini, S.Horrell, A.Wagner, R.Strange, M.A.Walsh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.07 / 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 (%)	18.8 / 24.7

The binding sites of Calcium atom in the PA3825-Eal Ca-Cdg Structure (pdb code 4y9p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the PA3825-Eal Ca-Cdg Structure, PDB code: 4y9p:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 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:97.5 occ:1.00 O A:HOH422 2.5 53.5 1.0 OE1 A:GLU135 3.2 0.3 1.0 O A:ILE99 3.2 72.4 1.0 OE2 A:GLU135 3.4 0.7 1.0 CD A:GLU135 3.7 0.2 1.0 N21 A:C2E304 3.7 64.4 1.0 C A:ILE99 4.0 63.6 1.0 N A:ILE99 4.1 61.2 1.0 CB A:ASN98 4.2 59.1 1.0 N31 A:C2E304 4.2 50.5 1.0 C21 A:C2E304 4.3 50.7 1.0 O A:GLU130 4.4 48.5 1.0 CG2 A:THR132 4.4 56.5 1.0 O2A A:C2E304 4.5 42.7 1.0 C A:ASN98 4.6 56.3 1.0 N A:SER100 4.7 58.5 1.0 CA A:ASN98 4.7 55.7 1.0 OD1 A:ASN98 4.7 54.9 1.0 OE2 A:GLU62 4.7 79.7 1.0 CA A:ILE99 4.8 63.3 1.0 CA A:SER100 4.8 70.6 1.0 N A:THR132 4.9 55.5 1.0 CG A:ASN98 4.9 54.6 1.0

Calcium binding site 2 out of 6 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:92.6 occ:1.00 OD1 A:ASP161 2.2 48.8 1.0 OE1 A:GLU217 2.4 83.7 1.0 O1P A:C2E304 3.0 71.7 1.0 OD1 A:ASP183 3.1 55.3 1.0 CD A:GLU217 3.1 64.2 1.0 OE2 A:GLU217 3.3 82.0 1.0 CG A:ASP161 3.4 70.8 1.0 NE2 A:GLN184 3.6 0.1 1.0 CG A:GLN184 3.6 82.2 1.0 O5' A:C2E304 3.7 58.8 1.0 CD A:GLN184 3.9 98.5 1.0 N A:GLN184 4.0 52.8 1.0 CG A:ASP183 4.1 66.4 1.0 P1 A:C2E304 4.1 56.2 1.0 OD2 A:ASP161 4.1 69.2 1.0 CA A:ASP183 4.3 52.3 1.0 CB A:GLU217 4.4 39.0 1.0 CG A:GLU217 4.4 52.9 1.0 OD1 A:ASP160 4.5 71.9 1.0 CB A:ASP161 4.5 66.1 1.0 CA A:ASP161 4.6 66.3 1.0 CB A:GLN184 4.7 60.1 1.0 CB A:ASP183 4.7 62.5 1.0 C A:ASP183 4.7 46.9 1.0 O A:HOH414 4.7 42.0 1.0 N A:ASP161 4.9 59.5 1.0 OE1 A:GLN184 4.9 88.0 1.0 C5' A:C2E304 4.9 50.4 1.0 OD2 A:ASP183 4.9 68.3 1.0 CA A:GLN184 5.0 59.9 1.0

Calcium binding site 3 out of 6 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:53.6 occ:1.00 O2P A:C2E304 2.2 49.5 1.0 OD2 A:ASP160 2.2 64.0 1.0 OE2 A:GLU39 2.2 43.1 1.0 O A:HOH414 2.3 42.0 1.0 OE1 A:GLU130 2.3 57.9 1.0 OD1 A:ASN98 2.4 54.9 1.0 CG A:ASP160 3.0 58.8 1.0 OD1 A:ASP160 3.1 71.9 1.0 CD A:GLU39 3.2 58.3 1.0 P1 A:C2E304 3.3 56.2 1.0 CG A:ASN98 3.4 54.6 1.0 CD A:GLU130 3.6 55.2 1.0 OE1 A:GLU39 3.7 46.0 1.0 O1P A:C2E304 3.7 71.7 1.0 ND2 A:ASN98 3.7 51.2 1.0 NZ A:LYS181 4.1 47.7 1.0 O5' A:C2E304 4.1 58.8 1.0 OE2 A:GLU130 4.3 51.6 1.0 CB A:ASP160 4.3 55.7 1.0 CB A:GLU130 4.4 52.9 1.0 CG A:GLU39 4.4 58.3 1.0 CG A:GLU130 4.6 57.2 1.0 O3A A:C2E304 4.6 51.0 1.0 O A:HOH422 4.6 53.5 1.0 CB A:ASN98 4.7 59.1 1.0 C5' A:C2E304 4.7 50.4 1.0 OE1 A:GLU217 4.8 83.7 1.0 C2A A:C2E304 4.8 47.4 1.0 C3A A:C2E304 4.9 46.1 1.0

Calcium binding site 4 out of 6 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:94.7 occ:1.00 O B:HOH421 2.5 55.3 1.0 OE1 B:GLU135 2.8 0.4 1.0 O B:ILE99 3.0 60.2 1.0 OE2 B:GLU135 3.0 0.2 1.0 CD B:GLU135 3.3 0.3 1.0 C B:ILE99 3.9 56.8 1.0 CG2 B:THR132 4.3 68.3 1.0 O B:GLU130 4.4 43.0 1.0 N B:ILE99 4.4 51.4 1.0 N2 B:C2E304 4.5 53.2 1.0 N B:SER100 4.5 60.1 1.0 OE2 B:GLU62 4.5 74.5 1.0 CA B:SER100 4.5 72.1 1.0 N B:THR132 4.7 51.5 1.0 CB B:ASN98 4.8 45.1 1.0 CA B:ILE99 4.8 53.7 1.0 O2' B:C2E304 4.8 46.8 1.0 CG B:GLU135 4.8 0.0 1.0 N3 B:C2E304 4.8 51.9 1.0 C B:ASN98 4.9 47.8 1.0 CA B:LEU131 5.0 59.7 1.0

Calcium binding site 5 out of 6 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:45.1 occ:1.00 O21 B:C2E304 2.1 46.2 1.0 OD2 B:ASP160 2.1 48.7 1.0 OE1 B:GLU130 2.2 41.4 1.0 OE2 B:GLU39 2.3 44.3 1.0 OD1 B:ASN98 2.3 43.4 1.0 O B:HOH401 2.3 44.6 1.0 CG B:ASP160 2.9 57.0 1.0 OD1 B:ASP160 3.1 56.9 1.0 CD B:GLU39 3.3 47.2 1.0 CG B:ASN98 3.4 40.7 1.0 P11 B:C2E304 3.4 45.5 1.0 CD B:GLU130 3.4 43.0 1.0 ND2 B:ASN98 3.7 32.6 1.0 OE1 B:GLU39 3.8 44.2 1.0 CA B:CA303 3.9 0.4 0.7 O11 B:C2E304 3.9 68.7 1.0 NZ B:LYS181 4.1 55.2 1.0 O5A B:C2E304 4.2 47.8 1.0 CB B:GLU130 4.2 40.5 1.0 OE2 B:GLU130 4.3 44.7 1.0 CB B:ASP160 4.3 51.5 1.0 OE2 B:GLU217 4.3 86.8 1.0 CG B:GLU130 4.4 42.2 1.0 O B:HOH421 4.4 55.3 1.0 CG B:GLU39 4.5 42.6 1.0 O3' B:C2E304 4.6 35.8 1.0 CB B:ASN98 4.7 45.1 1.0 C5A B:C2E304 4.8 46.9 1.0

Calcium binding site 6 out of 6 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:0.4 occ:0.70 OE1 B:GLU217 2.1 74.5 1.0 OD1 B:ASP161 2.3 46.8 1.0 OD1 B:ASP160 2.3 56.9 1.0 O11 B:C2E304 2.4 68.7 1.0 OE2 B:GLU217 2.6 86.8 1.0 CD B:GLU217 2.6 86.1 1.0 O B:HOH401 2.8 44.6 1.0 P11 B:C2E304 3.3 45.5 1.0 CG B:ASP161 3.4 75.4 1.0 CG B:ASP160 3.4 57.0 1.0 O5A B:C2E304 3.5 47.8 1.0 O21 B:C2E304 3.7 46.2 1.0 N B:ASP161 3.9 47.3 1.0 CA B:CA302 3.9 45.1 1.0 OD2 B:ASP161 3.9 78.6 1.0 OD2 B:ASP160 4.0 48.7 1.0 CG B:GLU217 4.1 55.9 1.0 CA B:ASP161 4.4 66.2 1.0 CB B:ASP161 4.5 63.0 1.0 C5A B:C2E304 4.5 46.9 1.0 CB B:ASP160 4.6 51.5 1.0 O3' B:C2E304 4.7 35.8 1.0 OD1 B:ASP183 4.7 61.7 1.0 CB B:GLU217 4.8 39.4 1.0 C B:ASP160 4.8 46.0 1.0 CA B:ASP160 4.8 55.3 1.0 NZ B:LYS181 5.0 55.2 1.0

D.Bellini, S.Horrell, A.Hutchin, C.W.Phippen, R.W.Strange, Y.Cai, A.Wagner, J.S.Webb, I.Tews, M.A.Walsh. Mucr and PA3825 Eal-Phosphodiesterase Domains From Pseudomonas Aeruginosa Suggest Roles For Three Metals in the Active Site To Be Published.