Atomistry » Calcium » PDB 5hsa-5i6w » 5i0f
Atomistry »
  Calcium »
    PDB 5hsa-5i6w »
      5i0f »

Calcium in PDB 5i0f: Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate

Protein crystallography data

The structure of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate, PDB code: 5i0f was solved by S.H.Light, G.Minasov, W.F.Anderson, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.59 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 195.127, 103.128, 44.094, 90.00, 92.14, 90.00
R / Rfree (%) 15.9 / 19

Calcium Binding Sites:

The binding sites of Calcium atom in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate (pdb code 5i0f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate, PDB code: 5i0f:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5i0f

Go back to Calcium Binding Sites List in 5i0f
Calcium binding site 1 out of 8 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca805

b:25.5
occ:0.75
O B:HOH1260 2.3 31.6 1.0
O B:HOH1008 2.3 39.2 1.0
OD1 B:ASP66 2.4 40.5 1.0
CG B:ASP66 3.3 41.9 1.0
OD2 B:ASP66 3.6 41.5 1.0
OE1 B:GLU76 4.5 43.9 1.0
OE2 B:GLU76 4.5 44.7 1.0
O B:HOH1249 4.5 45.2 1.0
CB B:ASP66 4.7 42.3 1.0
O B:ASP66 4.7 40.7 1.0
CD B:GLU76 4.9 42.0 1.0

Calcium binding site 2 out of 8 in 5i0f

Go back to Calcium Binding Sites List in 5i0f
Calcium binding site 2 out of 8 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca806

b:43.7
occ:1.00
O B:HOH1495 2.3 33.1 1.0
O B:HOH1433 2.3 34.4 1.0
O B:HOH1020 2.4 25.9 1.0
O B:HOH1283 2.5 26.7 1.0
O B:HOH1417 2.5 37.9 1.0
OD1 B:ASP534 2.5 22.8 1.0
CG B:ASP534 3.3 22.6 1.0
CB B:ASP534 3.9 21.3 1.0
OD2 B:ASP534 4.2 23.7 1.0
O B:SER566 4.4 19.4 1.0
NZ B:LYS201 4.4 24.6 1.0
O B:HOH956 4.5 26.2 1.0
CA B:GLY567 4.5 18.9 1.0
O B:HOH1041 4.6 30.7 1.0
CA B:ASP534 4.7 19.9 1.0
C B:SER566 4.9 18.7 1.0
N B:GLY567 5.0 18.4 1.0

Calcium binding site 3 out of 8 in 5i0f

Go back to Calcium Binding Sites List in 5i0f
Calcium binding site 3 out of 8 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca807

b:48.7
occ:1.00
O B:HOH970 2.3 32.3 1.0
O B:HOH1370 2.4 55.5 1.0
O B:HOH1372 2.4 39.6 1.0
O B:HOH1378 2.4 47.9 1.0
O B:ALA133 2.4 37.4 1.0
O B:HOH1246 2.6 39.3 1.0
C B:ALA133 3.6 37.6 1.0
CA B:ALA133 4.2 36.0 1.0
O B:PRO151 4.3 29.5 1.0
CB B:ALA133 4.3 36.3 1.0
C B:GLU134 4.6 40.8 1.0
O B:HOH1318 4.6 35.8 1.0
N B:GLU134 4.6 38.6 1.0
O B:GLU134 4.7 39.0 1.0
N B:PRO135 4.8 40.9 1.0
CA B:GLU134 4.8 41.4 1.0
O B:ASP149 4.9 30.7 1.0

Calcium binding site 4 out of 8 in 5i0f

Go back to Calcium Binding Sites List in 5i0f
Calcium binding site 4 out of 8 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca808

b:40.2
occ:1.00
O B:HOH994 2.3 33.2 1.0
OD1 B:ASN349 2.4 41.6 1.0
O B:HOH1066 2.5 28.1 1.0
CG B:ASN349 3.5 38.9 1.0
OD2 B:ASP358 3.9 32.6 1.0
ND2 B:ASN349 4.1 38.5 1.0
OD1 B:ASP358 4.1 32.0 1.0
CG B:ASP358 4.1 31.1 1.0
O B:VAL347 4.4 32.6 1.0
ND1 B:HIS354 4.6 28.9 1.0
CE1 B:HIS354 4.7 29.1 1.0
O B:HOH1082 4.7 31.7 1.0
CB B:ASN349 4.8 37.9 1.0
O B:HOH1445 4.8 55.2 1.0
CA B:ASN349 4.8 39.8 1.0
O B:PRO348 4.8 38.9 1.0
CG1 B:VAL347 5.0 34.4 1.0

Calcium binding site 5 out of 8 in 5i0f

Go back to Calcium Binding Sites List in 5i0f
Calcium binding site 5 out of 8 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca809

b:26.4
occ:0.80
O B:HOH1059 2.3 35.3 1.0
O B:GLU76 2.4 32.6 1.0
O B:HOH1197 2.4 36.1 1.0
O B:LEU79 2.4 34.9 1.0
O B:HOH1415 2.6 39.2 1.0
C B:GLU76 3.5 33.5 1.0
C B:LEU79 3.6 35.5 1.0
CA B:GLU76 4.2 34.3 1.0
CB B:GLU76 4.3 37.1 1.0
N B:LEU79 4.4 35.0 1.0
CA B:LEU79 4.4 36.0 1.0
N B:GLY77 4.5 32.1 1.0
N B:ALA80 4.6 34.9 1.0
OE1 B:GLU76 4.7 43.9 1.0
CB B:LEU79 4.7 38.7 1.0
CA B:GLY77 4.7 32.8 1.0
O B:HOH1436 4.7 40.9 1.0
CA B:ALA80 4.8 34.6 1.0
O B:HOH1460 4.8 33.8 1.0
O B:HOH1231 4.9 42.3 1.0
C B:GLY77 4.9 32.2 1.0
CB B:ALA80 5.0 34.3 1.0

Calcium binding site 6 out of 8 in 5i0f

Go back to Calcium Binding Sites List in 5i0f
Calcium binding site 6 out of 8 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca810

b:50.0
occ:1.00
O B:HOH1285 2.3 47.8 1.0
OD1 B:ASP396 2.7 52.8 1.0
OD2 B:ASP396 2.8 55.0 1.0
CG B:ASP396 3.1 53.5 1.0
CB B:ASP396 4.6 53.2 1.0

Calcium binding site 7 out of 8 in 5i0f

Go back to Calcium Binding Sites List in 5i0f
Calcium binding site 7 out of 8 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca811

b:64.5
occ:1.00
O B:HOH930 2.5 28.8 1.0
O B:HOH1035 2.6 34.8 1.0
O B:GLY116 4.2 29.7 1.0
OG1 B:THR118 4.6 33.0 1.0
CD1 B:LEU112 4.8 30.0 1.0

Calcium binding site 8 out of 8 in 5i0f

Go back to Calcium Binding Sites List in 5i0f
Calcium binding site 8 out of 8 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca812

b:42.8
occ:1.00
O B:LEU254 2.3 31.8 1.0
O B:HOH1369 2.3 35.9 1.0
O B:HOH1323 2.5 41.6 1.0
O B:HOH1123 2.5 42.9 1.0
OD1 B:ASP253 2.6 27.7 1.0
OD2 B:ASP253 2.6 28.6 1.0
OD2 B:ASP486 2.8 34.2 1.0
CG B:ASP253 3.0 27.2 1.0
C B:LEU254 3.5 32.6 1.0
CG B:ASP486 3.7 30.1 1.0
O B:GLY255 3.7 51.1 1.0
CB B:ASP486 3.8 27.9 1.0
C B:GLY255 4.1 46.7 1.0
N B:LEU254 4.2 27.6 1.0
CD B:ARG234 4.3 24.3 1.0
N B:GLY255 4.4 35.7 1.0
CA B:GLY255 4.4 40.9 1.0
CB B:ASP253 4.4 25.1 1.0
CA B:LEU254 4.5 29.7 1.0
NE B:ARG234 4.5 25.2 1.0
C B:ASP253 4.7 25.7 1.0
OD1 B:ASP486 4.8 32.1 1.0
O B:HIS161 4.9 26.0 1.0
N B:PHE256 5.0 54.8 1.0

Reference:

S.H.Light, L.A.Cahoon, K.V.Mahasenan, M.Lee, B.Boggess, A.S.Halavaty, S.Mobashery, N.E.Freitag, W.F.Anderson. Transferase Versus Hydrolase: the Role of Conformational Flexibility in Reaction Specificity. Structure V. 25 295 2017.
ISSN: ISSN 1878-4186
PubMed: 28089449
DOI: 10.1016/J.STR.2016.12.007
Page generated: Sat Dec 12 05:29:38 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