Calcium in PDB 8xph: Marine Planctomycetes Laminarinase Ptlam

Protein crystallography data

The structure of Marine Planctomycetes Laminarinase Ptlam, PDB code: 8xph was solved by J.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.47 / 2.20
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.096, 77.336, 90.191, 90, 90, 90
R / Rfree (%) 22.1 / 26.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Marine Planctomycetes Laminarinase Ptlam (pdb code 8xph). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Marine Planctomycetes Laminarinase Ptlam, PDB code: 8xph:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 8xph

Go back to Calcium Binding Sites List in 8xph
Calcium binding site 1 out of 4 in the Marine Planctomycetes Laminarinase Ptlam


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Marine Planctomycetes Laminarinase Ptlam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:8.2
occ:1.00
 O A:HOH566 2.3 15.5 1.0
O A:HOH519 2.4 10.8 1.0
O A:GLU46 2.4 8.0 1.0
O A:GLY86 2.5 15.1 1.0
O A:ASP278 2.5 3.7 1.0
OD1 A:ASP278 2.6 11.7 1.0
C A:GLY86 3.4 11.1 1.0
C A:GLU46 3.5 9.6 1.0
C A:ASP278 3.6 8.2 1.0
CG A:ASP278 3.7 13.0 1.0
CA A:GLY86 3.9 16.0 1.0
CA A:ASP278 4.1 10.3 1.0
CA A:GLU46 4.2 10.5 1.0
CB A:GLU46 4.4 16.2 1.0
O A:PHE47 4.4 14.9 1.0
OE1 A:GLU46 4.4 14.4 1.0
CB A:ASP278 4.5 12.6 1.0
O A:HOH681 4.5 9.0 1.0
OD2 A:ASP278 4.5 10.1 1.0
C A:PHE47 4.6 8.3 1.0
O A:HOH517 4.6 18.9 1.0
N A:ASN87 4.6 9.8 1.0
N A:PHE47 4.6 10.0 1.0
CD1 A:TRP279 4.6 6.7 1.0
CB A:TRP279 4.7 8.5 1.0
N A:TRP279 4.7 13.7 1.0
CB A:PHE47 4.8 11.7 1.0
CA A:PHE47 4.9 7.6 1.0

Calcium binding site 2 out of 4 in 8xph

Go back to Calcium Binding Sites List in 8xph
Calcium binding site 2 out of 4 in the Marine Planctomycetes Laminarinase Ptlam


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Marine Planctomycetes Laminarinase Ptlam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:3.9
occ:1.00
 O A:ALA182 2.3 3.6 1.0
O A:GLU235 2.3 6.5 1.0
O A:HOH633 2.3 9.8 1.0
O A:HOH569 2.4 8.1 1.0
OE1 A:GLU238 2.4 11.9 1.0
OE2 A:GLU238 2.4 13.7 1.0
CD A:GLU238 2.6 21.9 1.0
O A:HOH630 2.7 23.0 1.0
C A:GLU235 3.3 6.7 1.0
C A:ALA182 3.4 6.4 1.0
CG A:GLU238 3.9 26.5 1.0
CA A:GLU235 3.9 21.4 1.0
CB A:ALA182 4.1 10.8 1.0
CA A:ALA182 4.2 7.2 1.0
N A:MET236 4.2 9.4 1.0
N A:ALA182 4.4 6.9 1.0
CB A:GLU235 4.4 14.6 1.0
O A:GLY183 4.4 22.3 1.0
O A:HOH601 4.4 8.0 1.0
N A:GLY183 4.5 12.7 1.0
OE1 A:GLU186 4.5 3.5 1.0
CA A:MET236 4.6 9.1 1.0
OE2 A:GLU186 4.7 7.5 1.0
N A:LYS237 4.7 13.4 1.0
CD2 A:PHE181 4.7 8.0 1.0
CA A:GLY183 4.8 23.6 1.0
C A:GLY183 4.9 30.9 1.0
CD A:GLU186 4.9 6.0 1.0
N A:GLU238 5.0 7.6 1.0

Calcium binding site 3 out of 4 in 8xph

Go back to Calcium Binding Sites List in 8xph
Calcium binding site 3 out of 4 in the Marine Planctomycetes Laminarinase Ptlam


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Marine Planctomycetes Laminarinase Ptlam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:19.5
occ:1.00
 O B:HOH589 2.3 17.3 1.0
O B:GLU235 2.3 18.3 1.0
O B:ALA182 2.4 10.8 1.0
OE1 B:GLU238 2.4 35.1 1.0
O B:HOH626 2.5 8.7 1.0
OE2 B:GLU238 2.6 46.6 1.0
CD B:GLU238 2.6 38.7 1.0
C B:GLU235 3.2 26.4 1.0
C B:ALA182 3.5 17.6 1.0
CA B:GLU235 3.9 22.3 1.0
CG B:GLU238 3.9 44.0 1.0
CB B:ALA182 4.1 20.2 1.0
N B:MET236 4.2 21.8 1.0
CA B:ALA182 4.3 18.3 1.0
CB B:GLU235 4.3 24.4 1.0
O B:GLY183 4.4 36.0 1.0
N B:ALA182 4.5 15.5 1.0
CA B:MET236 4.5 23.3 1.0
N B:GLY183 4.6 15.0 1.0
O B:HOH635 4.6 15.1 1.0
N B:LYS237 4.7 19.8 1.0
CA B:GLY183 4.9 22.4 1.0
CD2 B:PHE181 4.9 17.1 1.0
C B:GLY183 4.9 32.0 1.0
N B:GLU238 4.9 15.8 1.0

Calcium binding site 4 out of 4 in 8xph

Go back to Calcium Binding Sites List in 8xph
Calcium binding site 4 out of 4 in the Marine Planctomycetes Laminarinase Ptlam


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Marine Planctomycetes Laminarinase Ptlam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:19.6
occ:1.00
 O B:HOH541 2.1 11.6 1.0
O B:GLU46 2.3 6.9 1.0
O B:GLY86 2.3 10.6 1.0
OD1 B:ASP48 2.5 21.7 1.0
O B:ASP278 2.7 36.2 1.0
OD1 B:ASP278 2.7 15.3 1.0
O B:HOH530 2.8 15.4 1.0
C B:GLY86 3.2 12.2 1.0
C B:GLU46 3.5 15.5 1.0
CA B:GLY86 3.5 9.4 1.0
CG B:ASP48 3.5 42.5 1.0
C B:ASP278 3.8 13.4 1.0
CG B:ASP278 3.9 17.6 1.0
OD2 B:ASP48 4.1 35.8 1.0
O B:PHE47 4.2 20.9 1.0
C B:PHE47 4.2 17.1 1.0
CA B:ASP278 4.3 20.4 1.0
CA B:GLU46 4.3 16.2 1.0
N B:ASN87 4.3 18.1 1.0
CB B:GLU46 4.5 14.7 1.0
N B:PHE47 4.5 22.3 1.0
N B:ASP48 4.5 29.7 1.0
CB B:PHE47 4.7 31.7 1.0
CB B:ASP278 4.7 14.3 1.0
CB B:ASP48 4.7 27.1 1.0
CA B:PHE47 4.7 18.5 1.0
CA B:ASP48 4.7 21.0 1.0
OE1 B:GLU46 4.7 19.5 1.0
OD2 B:ASP278 4.8 21.5 1.0
O B:HOH501 4.9 14.0 1.0
CA B:ASN87 4.9 6.8 1.0
N B:TRP279 4.9 17.1 1.0
CD1 B:TRP279 4.9 10.8 1.0
CB B:TRP279 4.9 21.3 1.0
N B:GLY86 5.0 16.9 1.0

Reference:

J.Yang, J.Yang. N/A N/A.
Page generated: Sat Sep 28 09:20:25 2024

Last articles

As in 9E9G
Al in 9B2D
Al in 9ED3
Zn in 9IRQ
Zn in 9IYX
Zn in 9J8P
Zn in 9IUU
Zn in 9GBF
Zn in 9G2V
Zn in 9G2L
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy