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Calcium in PDB 3jxs: Crystal Structure of XG34, An Evolved Xyloglucan Binding Cbm

Protein crystallography data

The structure of Crystal Structure of XG34, An Evolved Xyloglucan Binding Cbm, PDB code: 3jxs was solved by C.Divne, T.-C.Tan, H.Brumer, F.Gullfot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.570, 43.760, 93.080, 90.00, 104.27, 90.00
R / Rfree (%) 16.9 / 21.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of XG34, An Evolved Xyloglucan Binding Cbm (pdb code 3jxs). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of XG34, An Evolved Xyloglucan Binding Cbm, PDB code: 3jxs:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3jxs

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Calcium binding site 1 out of 5 in the Crystal Structure of XG34, An Evolved Xyloglucan Binding Cbm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of XG34, An Evolved Xyloglucan Binding Cbm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:23.6
occ:1.00
 OE1 A:GLU52 2.3 13.1 1.0
OD1 A:ASP160 2.3 9.3 1.0
O A:LYS55 2.3 10.9 1.0
O A:GLU52 2.4 11.7 1.0
OE2 A:GLU11 2.4 18.4 1.0
O A:GLY9 2.5 17.6 1.0
OD2 A:ASP160 2.7 12.2 1.0
CG A:ASP160 2.8 10.6 1.0
C A:GLU52 3.4 11.3 1.0
CD A:GLU52 3.4 16.2 1.0
C A:GLY9 3.4 17.4 1.0
CD A:GLU11 3.5 17.6 1.0
C A:LYS55 3.5 10.8 1.0
CA A:GLY9 3.7 16.2 1.0
N A:LYS55 3.8 12.1 1.0
CB A:GLU52 3.9 14.6 1.0
CG A:GLU11 4.0 19.4 1.0
CA A:GLU52 4.1 12.7 1.0
CA A:LYS55 4.2 11.1 1.0
CG A:GLU52 4.2 17.0 1.0
N A:GLY53 4.3 11.4 1.0
CB A:ASP160 4.3 11.0 1.0
CA A:GLY53 4.3 10.7 1.0
OE2 A:GLU52 4.3 23.4 1.0
N A:GLU52 4.4 11.9 1.0
CB A:LYS55 4.6 11.2 1.0
OE1 A:GLU11 4.6 18.0 1.0
N A:VAL56 4.6 10.0 1.0
C A:GLY53 4.6 11.3 1.0
N A:ASN54 4.6 11.7 1.0
CB A:ALA50 4.7 15.5 1.0
N A:PHE10 4.7 16.4 1.0
N A:GLY161 4.8 11.2 1.0
CA A:VAL56 4.9 10.4 1.0
C A:ASN54 5.0 13.4 1.0

Calcium binding site 2 out of 5 in 3jxs

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Calcium binding site 2 out of 5 in the Crystal Structure of XG34, An Evolved Xyloglucan Binding Cbm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of XG34, An Evolved Xyloglucan Binding Cbm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:30.2
occ:1.00
 O A:HOH1093 2.3 20.5 1.0
OD1 A:ASP29 2.3 25.2 1.0
O A:ALA22 2.4 20.5 1.0
O A:HOH1140 2.5 20.1 1.0
O A:HOH1228 2.5 30.5 1.0
O A:TRP28 2.7 18.3 1.0
CG A:ASP29 3.5 24.1 1.0
C A:ALA22 3.6 20.4 1.0
C A:TRP28 3.6 17.0 1.0
CA A:GLU23 4.2 21.7 1.0
OD2 A:ASP29 4.2 30.1 1.0
O A:HOH1134 4.3 22.1 1.0
N A:ASP29 4.3 15.0 1.0
CA A:ASP29 4.3 15.8 1.0
N A:GLU23 4.4 21.0 1.0
N A:TRP28 4.4 16.1 1.0
CG A:GLU23 4.5 24.9 1.0
O A:HOH1028 4.5 15.8 1.0
CB A:ASP29 4.5 15.9 1.0
O A:VAL25 4.5 17.7 1.0
O A:LEU76 4.6 11.0 1.0
CA A:TRP28 4.6 16.1 1.0
CA A:ALA22 4.7 19.3 1.0
CB A:GLU23 4.9 21.9 1.0

Calcium binding site 3 out of 5 in 3jxs

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Calcium binding site 3 out of 5 in the Crystal Structure of XG34, An Evolved Xyloglucan Binding Cbm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of XG34, An Evolved Xyloglucan Binding Cbm within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:26.9
occ:1.00
 OE2 B:GLU11 2.3 15.0 1.0
OE1 B:GLU52 2.3 21.4 1.0
O B:GLY9 2.3 12.0 1.0
O B:LYS55 2.3 19.8 1.0
O B:GLU52 2.3 18.2 1.0
OD1 B:ASP160 2.4 14.6 1.0
OD2 B:ASP160 2.8 14.3 1.0
CG B:ASP160 3.0 13.2 1.0
C B:GLU52 3.3 19.3 1.0
CD B:GLU11 3.3 9.1 1.0
C B:GLY9 3.4 10.7 1.0
CD B:GLU52 3.5 20.8 1.0
C B:LYS55 3.5 19.2 1.0
CA B:GLY9 3.7 10.8 1.0
CB B:GLU52 3.8 18.5 1.0
CG B:GLU11 3.8 12.1 1.0
N B:LYS55 3.9 19.1 1.0
CA B:GLU52 4.1 18.4 1.0
N B:GLY53 4.2 18.5 1.0
CA B:LYS55 4.2 19.4 1.0
CG B:GLU52 4.3 18.7 1.0
N B:GLU52 4.3 18.2 1.0
OE2 B:GLU52 4.4 29.8 1.0
CB B:ASP160 4.4 12.9 1.0
OE1 B:GLU11 4.5 12.4 1.0
CA B:GLY53 4.5 19.6 1.0
N B:VAL56 4.6 17.5 1.0
N B:PHE10 4.6 10.8 1.0
C B:GLY53 4.6 20.4 1.0
N B:ASN54 4.7 20.7 1.0
CB B:ALA50 4.8 16.9 1.0
CB B:LYS55 4.8 20.8 1.0
N B:GLU11 4.8 10.2 1.0
CA B:VAL56 4.8 17.2 1.0
CG1 B:VAL56 4.9 13.1 1.0
N B:GLY161 4.9 14.8 1.0

Calcium binding site 4 out of 5 in 3jxs

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Calcium binding site 4 out of 5 in the Crystal Structure of XG34, An Evolved Xyloglucan Binding Cbm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of XG34, An Evolved Xyloglucan Binding Cbm within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:21.0
occ:1.00
 OE1 C:GLU52 2.3 12.5 1.0
O C:LYS55 2.3 11.6 1.0
OE2 C:GLU11 2.3 14.1 1.0
O C:GLU52 2.4 10.2 1.0
O C:GLY9 2.4 12.4 1.0
OD1 C:ASP160 2.4 11.7 1.0
OD2 C:ASP160 2.7 14.3 1.0
CG C:ASP160 2.9 9.9 1.0
C C:GLU52 3.3 11.9 1.0
C C:GLY9 3.4 12.4 1.0
CD C:GLU11 3.4 12.4 1.0
C C:LYS55 3.5 12.3 1.0
CD C:GLU52 3.5 19.9 1.0
CA C:GLY9 3.7 13.6 1.0
N C:LYS55 3.8 12.0 1.0
CB C:GLU52 3.9 12.5 1.0
CG C:GLU11 3.9 9.8 1.0
CA C:LYS55 4.1 12.0 1.0
CA C:GLU52 4.1 12.2 1.0
CG C:GLU52 4.3 13.8 1.0
N C:GLY53 4.3 11.2 1.0
N C:GLU52 4.3 11.0 1.0
OE2 C:GLU52 4.4 21.7 1.0
CB C:ASP160 4.4 10.5 1.0
CA C:GLY53 4.4 11.5 1.0
CB C:LYS55 4.5 12.1 1.0
OE1 C:GLU11 4.5 13.3 1.0
N C:ASN54 4.6 12.8 1.0
N C:VAL56 4.6 10.9 1.0
C C:GLY53 4.6 12.7 1.0
CB C:ALA50 4.6 10.8 1.0
N C:PHE10 4.6 11.8 1.0
N C:GLY161 4.9 10.2 1.0
CA C:VAL56 4.9 10.2 1.0
C C:ASN54 4.9 13.9 1.0
N C:GLU11 5.0 12.5 1.0

Calcium binding site 5 out of 5 in 3jxs

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Calcium binding site 5 out of 5 in the Crystal Structure of XG34, An Evolved Xyloglucan Binding Cbm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of XG34, An Evolved Xyloglucan Binding Cbm within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:17.8
occ:1.00
 OD1 C:ASP29 2.3 12.5 1.0
O C:ALA22 2.3 11.5 1.0
O C:HOH1039 2.4 13.2 1.0
O A:HOH1125 2.4 13.8 1.0
O C:HOH1029 2.4 12.5 1.0
O C:TRP28 2.5 6.9 1.0
O B:HOH1019 2.6 11.1 1.0
C C:TRP28 3.5 6.9 1.0
CG C:ASP29 3.5 8.6 1.0
C C:ALA22 3.6 11.1 1.0
N C:ASP29 4.0 6.5 1.0
CA C:ASP29 4.1 6.6 1.0
CA C:GLU23 4.1 11.2 1.0
CE1 B:HIS110 4.3 20.1 1.0
N C:GLU23 4.4 9.4 1.0
N C:TRP28 4.4 6.4 1.0
CB C:ASP29 4.4 8.8 1.0
OD2 C:ASP29 4.4 9.2 1.0
O C:HOH1261 4.4 9.8 1.0
O C:HOH1033 4.4 14.0 1.0
CA C:TRP28 4.5 6.8 1.0
O C:VAL25 4.5 10.4 1.0
CG C:GLU23 4.6 11.9 1.0
CA C:ALA22 4.6 9.5 1.0
ND1 B:HIS110 4.6 13.1 1.0
OG B:SER109 4.7 21.9 1.0
O B:HOH1163 4.7 23.6 1.0
O C:HOH1075 4.7 16.1 1.0
O A:HOH1144 4.7 32.5 1.0
O C:LEU76 4.8 8.5 1.0
CB C:GLU23 4.8 11.4 1.0

Reference:

F.Gullfot, T.C.Tan, L.Von Schantz, E.N.Karlsson, M.Ohlin, H.Brumer, C.Divne. The Crystal Structure of Xg-34, An Evolved Xyloglucan-Specific Carbohydrate-Binding Module. Proteins V. 78 785 2009.
ISSN: ISSN 0887-3585
PubMed: 19950365
DOI: 10.1002/PROT.22642
Page generated: Sat Jul 13 11:54:29 2024

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