Calcium in PDB 4y8e: PA3825-Eal Ca-Apo Structure

Protein crystallography data

The structure of PA3825-Eal Ca-Apo Structure, PDB code: 4y8e 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) 40.21 / 1.61
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.440, 59.820, 96.690, 90.00, 116.94, 90.00
R / Rfree (%) 18.5 / 22.3

Calcium Binding Sites:

The binding sites of Calcium atom in the PA3825-Eal Ca-Apo Structure (pdb code 4y8e). 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-Apo Structure, PDB code: 4y8e:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4y8e

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Calcium binding site 1 out of 6 in the PA3825-Eal Ca-Apo 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-Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:21.6
occ:1.00
 OD1 A:ASN98 2.3 24.1 1.0
O A:HOH467 2.3 20.4 1.0
OE2 A:GLU135 2.4 21.5 1.0
O A:ILE99 2.4 19.9 1.0
O A:HOH535 2.5 26.6 1.0
O A:HOH520 2.5 23.2 1.0
OE1 A:GLU135 2.6 25.1 1.0
CD A:GLU135 2.8 24.0 1.0
CG A:ASN98 3.4 22.8 1.0
C A:ILE99 3.4 20.7 1.0
ND2 A:ASN98 4.0 25.3 1.0
N A:ILE99 4.0 20.3 1.0
O A:GLU130 4.1 19.0 1.0
N A:SER100 4.2 20.5 1.0
O A:HOH497 4.2 39.8 1.0
CA A:SER100 4.3 21.8 1.0
CG A:GLU135 4.3 23.2 1.0
C A:ASN98 4.4 19.9 1.0
CA A:ILE99 4.4 20.5 1.0
CB A:ASN98 4.7 20.2 1.0
CG2 A:THR132 4.7 22.3 1.0
O A:HOH402 4.7 40.5 1.0
N A:THR132 4.7 21.3 1.0
O A:HOH445 4.7 73.9 1.0
OD2 A:ASP160 4.8 23.1 1.0
CA A:ASN98 4.8 18.2 1.0
CA A:LEU131 4.8 19.3 1.0
O A:HOH456 4.8 27.1 1.0
O A:ASN98 4.9 22.8 1.0

Calcium binding site 2 out of 6 in 4y8e

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Calcium binding site 2 out of 6 in the PA3825-Eal Ca-Apo 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-Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:29.8
occ:1.00
 O A:HOH543 2.8 31.6 1.0
N A:GLY218 3.2 16.8 1.0
OE1 A:GLN25 3.3 35.4 1.0
OE1 A:GLN237 3.4 31.4 1.0
CA A:GLY238 3.8 17.9 1.0
CG A:GLN237 3.8 22.3 1.0
O A:GLN237 3.9 18.0 1.0
N A:GLY238 3.9 16.8 1.0
C A:GLN237 3.9 16.3 1.0
CA A:GLY218 4.0 16.6 1.0
CD A:GLN237 4.0 23.6 1.0
C A:GLU217 4.2 16.2 1.0
CB A:GLU217 4.2 16.5 1.0
CD A:GLN25 4.2 27.0 1.0
CA A:GLU217 4.2 16.6 1.0
NE2 A:GLN25 4.3 26.8 1.0
O A:HOH462 4.3 19.6 1.0
CB A:GLN237 4.4 21.1 1.0
O A:HOH552 4.6 48.4 1.0
O A:HOH558 4.7 46.2 1.0
CG A:GLU217 4.8 17.8 1.0
CA A:GLN237 4.8 17.2 1.0
OE1 A:GLU217 4.9 24.6 1.0

Calcium binding site 3 out of 6 in 4y8e

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Calcium binding site 3 out of 6 in the PA3825-Eal Ca-Apo 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-Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:23.4
occ:1.00
 OD1 A:ASP161 2.3 27.5 1.0
O A:HOH489 2.3 32.2 1.0
O A:HOH427 2.3 26.8 1.0
OD1 A:ASP160 2.4 22.4 1.0
OE1 A:GLU217 2.4 24.6 1.0
O A:HOH514 2.4 28.8 1.0
OE2 A:GLU217 2.5 25.1 1.0
CD A:GLU217 2.8 22.1 1.0
CG A:ASP161 3.4 29.9 1.0
CG A:ASP160 3.5 23.1 1.0
OD2 A:ASP160 3.7 23.1 1.0
OD2 A:ASP161 3.8 37.9 1.0
N A:ASP161 4.2 21.4 1.0
O A:HOH455 4.2 27.7 1.0
O A:HOH431 4.2 22.6 1.0
CG A:GLU217 4.3 17.8 1.0
NZ A:LYS181 4.4 23.0 1.0
CB A:ASP161 4.6 23.4 1.0
CA A:ASP161 4.7 22.0 1.0
O A:HOH558 4.8 46.2 1.0
CB A:ASP160 4.8 22.0 1.0
O A:HOH532 4.8 27.6 1.0
O A:HOH548 4.9 50.7 1.0
C A:ASP160 4.9 22.0 1.0

Calcium binding site 4 out of 6 in 4y8e

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Calcium binding site 4 out of 6 in the PA3825-Eal Ca-Apo 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-Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:25.6
occ:1.00
 O B:HOH401 2.2 59.2 1.0
OD1 B:ASN98 2.3 29.8 1.0
O B:HOH529 2.3 29.9 1.0
O B:ILE99 2.4 23.4 1.0
OE2 B:GLU135 2.4 26.6 1.0
O B:HOH456 2.4 24.4 1.0
O B:HOH415 2.4 31.2 1.0
OE1 B:GLU135 2.6 26.3 1.0
CD B:GLU135 2.9 33.6 1.0
C B:ILE99 3.4 25.9 1.0
CG B:ASN98 3.4 23.8 1.0
ND2 B:ASN98 4.0 27.6 1.0
N B:ILE99 4.2 22.6 1.0
N B:SER100 4.2 26.7 1.0
CA B:SER100 4.3 24.2 1.0
O B:GLU130 4.3 21.4 1.0
O B:HOH528 4.3 47.1 1.0
CG B:GLU135 4.4 28.0 1.0
CA B:ILE99 4.4 22.7 1.0
C B:ASN98 4.6 25.1 1.0
OE2 B:GLU62 4.6 45.7 1.0
CB B:ASN98 4.7 21.1 1.0
OD2 B:ASP160 4.7 27.7 1.0
CG2 B:THR132 4.8 24.6 1.0
N B:THR132 4.8 22.2 1.0
CA B:LEU131 4.8 24.2 1.0
CA B:ASN98 4.9 22.2 1.0

Calcium binding site 5 out of 6 in 4y8e

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Calcium binding site 5 out of 6 in the PA3825-Eal Ca-Apo 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-Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:28.7
occ:1.00
 O B:HOH546 3.1 31.2 1.0
O B:HOH531 3.1 47.4 1.0
N B:GLY218 3.3 18.2 1.0
NE2 B:GLN25 3.3 27.5 1.0
NE2 B:GLN237 3.4 26.9 1.0
CG B:GLN237 3.8 24.1 1.0
CA B:GLY238 3.8 18.0 1.0
N B:GLY238 3.9 16.2 1.0
C B:GLN237 3.9 18.3 1.0
O B:GLN237 3.9 17.9 1.0
CA B:GLY218 4.0 19.9 1.0
CD B:GLN237 4.1 26.7 1.0
CB B:GLU217 4.1 19.6 1.0
CA B:GLU217 4.2 17.6 1.0
C B:GLU217 4.2 19.3 1.0
O B:HOH494 4.3 36.2 1.0
CD B:GLN25 4.3 25.6 1.0
CB B:GLN237 4.4 22.6 1.0
OE1 B:GLN25 4.4 28.6 1.0
O B:HOH493 4.4 20.3 1.0
O B:HOH532 4.5 45.6 1.0
CG B:GLU217 4.8 18.9 1.0
CA B:GLN237 4.8 18.8 1.0
OE1 B:GLU217 4.8 31.6 1.0

Calcium binding site 6 out of 6 in 4y8e

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Calcium binding site 6 out of 6 in the PA3825-Eal Ca-Apo 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-Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:27.4
occ:1.00
 O B:HOH503 2.2 45.4 1.0
O B:HOH487 2.3 39.0 1.0
OD1 B:ASP161 2.4 34.0 1.0
OD1 B:ASP160 2.4 28.3 1.0
O B:HOH481 2.5 41.6 1.0
OE1 B:GLU217 2.5 31.6 1.0
OE2 B:GLU217 2.5 27.2 1.0
CD B:GLU217 2.9 26.4 1.0
CG B:ASP160 3.4 28.1 1.0
CG B:ASP161 3.4 37.5 1.0
O B:HOH428 3.5 28.4 1.0
OD2 B:ASP160 3.8 27.7 1.0
OD2 B:ASP161 3.9 38.6 1.0
O B:HOH410 4.0 28.0 1.0
O B:HOH531 4.2 47.4 1.0
O B:HOH418 4.3 44.6 1.0
N B:ASP161 4.3 26.3 1.0
CG B:GLU217 4.4 18.9 1.0
NZ B:LYS181 4.5 23.4 1.0
O B:HOH522 4.7 36.0 1.0
CB B:ASP161 4.7 31.1 1.0
CB B:ASP160 4.8 24.4 1.0
O B:HOH486 4.8 34.8 1.0
CA B:ASP161 4.8 29.1 1.0

Reference:

D.Bellini, S.Horrell, R.Strange, A.Wagner, A.Hitchin, J.S.Webb, I.Tews, M.A.Walch. Structure of PA3825 From P. Aeruginosa Bound to Cyclic Di-Gmp and Pgpg: New Insights For A Potential Three-Metal Catalytic Mechanism of Eal Domains To Be Published.
Page generated: Sat Dec 12 05:13:06 2020

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