Atomistry » Calcium » PDB 1dva-1edh » 1ea7
Atomistry »
  Calcium »
    PDB 1dva-1edh »
      1ea7 »

Calcium in PDB 1ea7: Sphericase

Protein crystallography data

The structure of Sphericase, PDB code: 1ea7 was solved by O.Almog, A.Gonzalez, D.Klein, S.Braun, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.30 / 0.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.280, 62.380, 46.120, 90.00, 114.31, 90.00
R / Rfree (%) 9.7 / 11.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Sphericase (pdb code 1ea7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Sphericase, PDB code: 1ea7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1ea7

Go back to Calcium Binding Sites List in 1ea7
Calcium binding site 1 out of 6 in the Sphericase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Sphericase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca311

b:3.5
occ:1.00
OD1 A:ASP287 2.3 5.1 1.0
O A:GLY297 2.3 4.9 1.0
O A:ALA295 2.3 4.3 1.0
OD1 A:ASP299 2.3 4.2 1.0
O A:ILE288 2.3 3.8 1.0
O A:HOH2665 2.4 4.7 1.0
H A:ALA295 3.3 4.8 1.0
C A:GLY297 3.4 4.5 1.0
CG A:ASP287 3.5 5.2 1.0
H A:ILE288 3.5 4.8 1.0
C A:ILE288 3.5 3.6 1.0
CG A:ASP299 3.5 3.6 1.0
C A:ALA295 3.5 3.8 1.0
H A:GLY297 3.6 5.9 1.0
N A:GLY297 3.7 4.9 1.0
OG A:SER302 3.7 4.7 1.0
N A:ILE288 3.8 4.0 1.0
HB3 A:ASP299 3.9 4.7 1.0
HA A:LYS289 4.0 4.2 1.0
N A:ALA295 4.0 4.0 1.0
OD2 A:ASP287 4.1 6.9 1.0
HG2 A:LYS289 4.1 6.9 1.0
HA A:ILE296 4.1 5.2 1.0
C A:ILE296 4.1 4.7 1.0
CA A:GLY297 4.1 6.3 1.0
CA A:ILE288 4.2 3.9 1.0
HB A:ILE288 4.2 4.3 1.0
HA A:ASP287 4.3 5.5 1.0
CB A:ASP299 4.3 4.0 1.0
H A:ASP299 4.3 4.6 1.0
CA A:ALA295 4.4 3.9 1.0
HG3 A:LYS289 4.4 6.9 1.0
OD2 A:ASP299 4.4 4.0 1.0
N A:ILE296 4.4 4.3 1.0
HA A:ASP298 4.4 5.3 1.0
C A:ASP287 4.4 5.2 1.0
CA A:ILE296 4.5 4.4 1.0
N A:LYS289 4.5 3.7 1.0
O A:GLY303 4.5 3.9 1.0
N A:ASP298 4.5 5.0 1.0
N A:ASP299 4.5 3.8 1.0
HA2 A:GLY297 4.6 7.5 1.0
HB3 A:ALA294 4.6 6.9 1.0
CB A:ASP287 4.6 5.5 1.0
CA A:ASP287 4.6 4.6 1.0
HB2 A:ALA295 4.6 7.2 1.0
CA A:LYS289 4.7 3.5 1.0
CG A:LYS289 4.7 5.8 1.0
O A:ILE296 4.7 6.5 1.0
CB A:ILE288 4.8 3.6 1.0
CA A:ASP298 4.8 4.4 1.0
C A:ASP298 4.8 4.5 1.0
HA A:ALA294 4.9 4.6 1.0
HA3 A:GLY297 4.9 7.5 1.0

Calcium binding site 2 out of 6 in 1ea7

Go back to Calcium Binding Sites List in 1ea7
Calcium binding site 2 out of 6 in the Sphericase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Sphericase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca312

b:4.2
occ:1.00
O A:THR214 2.3 5.7 1.0
O A:VAL219 2.3 4.9 1.0
OE1 A:GLN221 2.3 5.5 1.0
OD1 A:ASP224 2.3 4.8 1.0
O A:HOH2662 2.4 5.2 1.0
OD2 A:ASP217 2.4 5.9 1.0
CG A:ASP217 3.3 5.7 1.0
H A:GLN221 3.3 5.5 1.0
CG A:ASP224 3.3 4.1 1.0
CD A:GLN221 3.4 5.0 1.0
HB A:THR214 3.4 7.0 1.0
C A:THR214 3.5 5.0 1.0
OD1 A:ASP217 3.5 8.2 1.0
C A:VAL219 3.5 4.8 1.0
H A:VAL219 3.5 6.3 1.0
HE22 A:GLN221 3.5 8.2 1.0
HA A:ILE220 3.6 5.8 1.0
HA A:ALA215 3.7 7.0 1.0
OD2 A:ASP224 3.8 6.5 1.0
NE2 A:GLN221 3.8 6.8 1.0
H A:ASP217 4.0 6.8 1.0
N A:GLN221 4.1 4.6 1.0
HB2 A:GLN221 4.1 6.7 1.0
O A:HOH2542 4.2 15.2 1.0
CB A:THR214 4.2 5.8 1.0
N A:VAL219 4.2 5.3 1.0
HB A:VAL219 4.2 8.5 1.0
CA A:THR214 4.3 5.3 1.0
CA A:ILE220 4.3 4.8 1.0
N A:ALA215 4.4 5.7 1.0
N A:ILE220 4.4 5.0 1.0
HA A:THR214 4.4 6.3 1.0
CA A:ALA215 4.4 5.8 1.0
CA A:VAL219 4.4 5.7 1.0
HD11 A:ILE220 4.5 9.7 1.0
HB3 A:ASP224 4.5 4.7 1.0
OD1 A:ASP298 4.5 5.1 1.0
H A:GLY216 4.5 7.1 1.0
CB A:ASP224 4.5 3.9 1.0
CG A:GLN221 4.6 6.7 1.0
C A:ILE220 4.6 4.8 1.0
CB A:ASP217 4.6 6.5 1.0
HE21 A:GLN221 4.7 8.2 1.0
CB A:GLN221 4.7 5.6 1.0
HB2 A:ASP224 4.7 4.7 1.0
H A:TYR218 4.7 6.8 1.0
OG1 A:THR214 4.8 6.6 1.0
N A:ASP217 4.8 5.7 1.0
O A:HOH2661 4.8 4.9 1.0
HE1 A:PHE304 4.8 7.7 1.0
CB A:VAL219 4.9 7.1 1.0
C A:ALA215 4.9 5.8 1.0
N A:GLY216 4.9 5.9 1.0
CA A:GLN221 5.0 5.0 1.0
N A:TYR218 5.0 5.7 1.0

Calcium binding site 3 out of 6 in 1ea7

Go back to Calcium Binding Sites List in 1ea7
Calcium binding site 3 out of 6 in the Sphericase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Sphericase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca313

b:4.8
occ:0.77
CA A:CA313 0.0 4.8 0.8
CA A:CA313 0.9 4.9 0.2
O A:HOH2186 1.8 5.7 0.3
O A:HOH2120 2.3 6.1 1.0
OD2 A:ASP98 2.3 5.7 0.8
OD1 A:ASN29 2.3 6.3 1.0
OE1 A:GLU49 2.4 5.9 0.8
O A:HOH2189 2.4 15.1 1.0
O A:HOH2185 2.4 6.7 0.7
OE1 A:GLU49 2.6 7.9 0.2
OE2 A:GLU49 2.6 6.5 0.2
OE2 A:GLU49 2.8 11.6 0.8
CD A:GLU49 2.9 6.1 0.2
CD A:GLU49 2.9 6.2 0.8
OD2 A:ASP98 3.0 11.4 0.2
OD1 A:ASP98 3.2 10.1 0.2
CG A:ASP98 3.3 11.2 0.2
CG A:ASP98 3.4 4.9 0.8
CG A:ASN29 3.5 4.7 1.0
HE1 A:TRP100 3.7 5.2 1.0
HD22 A:ASN29 3.7 7.6 1.0
CB A:ASP98 3.8 9.0 0.2
CB A:ASP98 3.8 4.3 0.8
O A:HOH2341 3.9 20.4 1.0
HG22 A:THR132 4.0 12.5 1.0
ND2 A:ASN29 4.0 6.3 1.0
HZ2 A:TRP100 4.2 5.8 1.0
O A:HOH2066 4.4 15.8 1.0
NE1 A:TRP100 4.4 4.3 1.0
O A:HOH2183 4.4 16.1 0.5
OD1 A:ASP98 4.4 5.7 0.8
CG A:GLU49 4.4 5.5 0.8
CG A:GLU49 4.4 4.8 0.2
O A:HOH2188 4.5 4.8 0.5
HB A:THR132 4.5 8.1 1.0
OG1 A:THR132 4.5 11.1 1.0
O A:GLY27 4.6 5.7 1.0
O A:HOH2044 4.6 11.3 1.0
CB A:ASN29 4.7 4.0 1.0
HA2 A:GLY27 4.7 6.9 1.0
O A:HOH2067 4.8 45.0 1.0
HB3 A:ASN29 4.8 4.8 1.0
CG2 A:THR132 4.8 8.3 1.0
CZ2 A:TRP100 4.9 4.8 1.0
HD21 A:ASN29 4.9 7.6 1.0
CB A:THR132 4.9 6.7 1.0
HA A:ASN29 4.9 4.2 1.0
O A:HOH2181 4.9 5.5 0.5
CE2 A:TRP100 5.0 4.0 1.0

Calcium binding site 4 out of 6 in 1ea7

Go back to Calcium Binding Sites List in 1ea7
Calcium binding site 4 out of 6 in the Sphericase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Sphericase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca313

b:4.9
occ:0.23
CA A:CA313 0.0 4.9 0.2
CA A:CA313 0.9 4.8 0.8
OD2 A:ASP98 1.5 5.7 0.8
OD2 A:ASP98 2.2 11.4 0.2
OE1 A:GLU49 2.3 7.9 0.2
OD1 A:ASP98 2.4 10.1 0.2
OE1 A:GLU49 2.4 5.9 0.8
O A:HOH2189 2.4 15.1 1.0
CG A:ASP98 2.5 11.2 0.2
O A:HOH2120 2.5 6.1 1.0
CG A:ASP98 2.5 4.9 0.8
O A:HOH2186 2.6 5.7 0.3
OD1 A:ASN29 2.6 6.3 1.0
OE2 A:GLU49 2.7 11.6 0.8
OE2 A:GLU49 2.9 6.5 0.2
CD A:GLU49 3.0 6.2 0.8
CD A:GLU49 3.0 6.1 0.2
CB A:ASP98 3.2 9.0 0.2
CB A:ASP98 3.2 4.3 0.8
O A:HOH2185 3.3 6.7 0.7
O A:HOH2341 3.3 20.4 1.0
OD1 A:ASP98 3.6 5.7 0.8
CG A:ASN29 3.8 4.7 1.0
HE1 A:TRP100 4.0 5.2 1.0
O A:HOH2183 4.1 16.1 0.5
HA2 A:GLY27 4.3 6.9 1.0
HD22 A:ASN29 4.3 7.6 1.0
O A:HOH2343 4.4 18.3 0.5
CG A:GLU49 4.4 5.5 0.8
CG A:GLU49 4.4 4.8 0.2
O A:GLY27 4.5 5.7 1.0
ND2 A:ASN29 4.5 6.3 1.0
HG22 A:THR132 4.6 12.5 1.0
CA A:ASP98 4.7 4.3 1.0
O A:HOH2044 4.7 11.3 1.0
NE1 A:TRP100 4.7 4.3 1.0
HA A:ASN29 4.8 4.2 1.0
O A:HOH2181 4.8 5.5 0.5
C A:GLY27 4.8 5.0 1.0
H A:ASP98 4.9 5.0 1.0
CB A:ASN29 4.9 4.0 1.0
O A:HOH2331 4.9 4.0 0.5
CB A:GLU49 4.9 4.8 0.8
HZ2 A:TRP100 4.9 5.8 1.0
CB A:GLU49 4.9 4.2 0.2
O A:HOH2342 5.0 9.9 0.5

Calcium binding site 5 out of 6 in 1ea7

Go back to Calcium Binding Sites List in 1ea7
Calcium binding site 5 out of 6 in the Sphericase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Sphericase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca314

b:7.0
occ:1.00
O A:HOH2374 2.3 7.8 1.0
O A:HOH2214 2.3 6.5 1.0
O A:HOH2210 2.4 10.3 1.0
O A:HOH2212 2.4 11.1 1.0
OD1 A:ASP115 2.4 5.4 1.0
O A:HOH2372 2.4 8.4 1.0
OD2 A:ASP115 2.6 5.3 1.0
CG A:ASP115 2.8 4.5 1.0
HD1 A:TYR112 3.7 8.3 1.0
HA A:THR55 3.9 4.4 1.0
HB2 A:TYR112 4.1 6.5 1.0
O A:HOH2378 4.2 23.2 0.5
OD1 A:ASP114 4.2 6.3 1.0
CD1 A:TYR112 4.3 6.9 1.0
O A:PHE54 4.3 4.0 1.0
CB A:ASP115 4.4 4.0 1.0
OD2 A:ASP114 4.4 8.5 1.0
O A:THR55 4.4 6.4 1.0
O A:HOH2079 4.5 12.0 1.0
O A:HOH2379 4.5 4.1 0.5
O A:GLY56 4.5 5.3 1.0
O A:HOH2077 4.6 17.9 1.0
C A:THR55 4.6 4.3 1.0
CG A:ASP114 4.6 5.9 1.0
CA A:THR55 4.7 3.6 1.0
O A:HOH2147 4.7 32.4 1.0
HB3 A:ASP115 4.7 4.8 1.0
HB2 A:ASP115 4.8 4.8 1.0
CB A:TYR112 4.9 5.5 1.0
H A:ASP115 4.9 4.9 1.0
CG A:TYR112 4.9 6.2 1.0
HE1 A:TYR112 5.0 10.9 1.0
HB3 A:TYR112 5.0 6.5 1.0

Calcium binding site 6 out of 6 in 1ea7

Go back to Calcium Binding Sites List in 1ea7
Calcium binding site 6 out of 6 in the Sphericase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Sphericase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca315

b:7.6
occ:1.00
O A:ALA186 2.3 4.6 1.0
O A:GLY181 2.3 4.0 1.0
O A:LEU183 2.3 4.1 1.0
O A:HOH2564 2.3 4.9 1.0
O A:HOH2566 2.4 3.8 1.0
C A:LEU183 3.4 3.8 1.0
C A:ALA186 3.4 4.0 1.0
HB3 A:ALA188 3.4 5.9 1.0
H A:ALA188 3.4 3.8 1.0
C A:GLY181 3.5 3.8 1.0
HB3 A:ALA186 3.5 7.7 1.0
H A:ALA186 3.6 5.3 1.0
HA A:ALA182 3.6 4.5 1.0
C A:ALA182 3.7 3.8 1.0
N A:LEU183 3.7 3.9 1.0
HG23 A:ILE220 3.7 9.6 1.0
H A:LEU183 3.8 4.7 1.0
N A:ALA188 4.0 3.1 1.0
CA A:ALA182 4.0 3.8 1.0
HH22 A:ARG276 4.0 7.5 1.0
O A:ASP224 4.0 3.8 1.0
O A:ALA182 4.0 4.2 1.0
HA A:PRO184 4.1 6.1 1.0
HA A:ILE187 4.1 3.9 1.0
CA A:ALA186 4.1 4.2 1.0
N A:ALA186 4.1 4.4 1.0
CA A:LEU183 4.1 4.0 1.0
HG22 A:ILE220 4.1 9.6 1.0
CB A:ALA188 4.2 3.9 1.0
N A:ALA182 4.2 3.8 1.0
HB1 A:ALA188 4.2 5.9 1.0
CB A:ALA186 4.2 5.1 1.0
CG2 A:ILE220 4.3 6.4 1.0
N A:PRO184 4.3 4.5 1.0
N A:ILE187 4.4 3.7 1.0
HG21 A:ILE220 4.4 9.6 1.0
HH21 A:ARG276 4.4 7.5 1.0
HA2 A:GLY181 4.4 5.0 1.0
CA A:PRO184 4.5 5.1 1.0
OE1 A:GLU226 4.5 4.5 1.0
C A:PRO184 4.5 4.7 1.0
NH2 A:ARG276 4.5 6.2 1.0
HB2 A:LEU183 4.5 4.9 1.0
CA A:ILE187 4.5 3.3 1.0
O A:PRO184 4.6 5.7 1.0
C A:ILE187 4.6 2.8 1.0
CA A:GLY181 4.6 4.2 1.0
CA A:ALA188 4.6 3.1 1.0
HB1 A:ALA186 4.6 7.7 1.0
O A:PRO180 4.8 4.4 1.0
HA A:LEU183 4.9 4.7 1.0
HD12 A:ILE177 4.9 6.5 1.0
H A:GLY223 4.9 4.9 1.0
HA A:ALA188 4.9 3.7 1.0
CB A:LEU183 5.0 4.1 1.0
HB2 A:GLU226 5.0 4.8 1.0
HB2 A:ALA188 5.0 5.9 1.0
H A:ASP224 5.0 4.5 1.0
HB2 A:ALA186 5.0 7.7 1.0

Reference:

O.Almog, A.Gonzalez, D.Klein, H.M.Greenblat, S.Braun, G.Shoham. The 0.93A Crystal Structure of Sphericase: A Calcium-Loaded Serine Protease From Bacillus Sphaericus J.Mol.Biol. V. 332 1071 2003.
ISSN: ISSN 0022-2836
PubMed: 14499610
DOI: 10.1016/J.JMB.2003.07.011
Page generated: Sat Dec 12 02:54:00 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy