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Calcium in PDB 3pdd: Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules

Protein crystallography data

The structure of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules, PDB code: 3pdd was solved by P.M.Alahuhta, V.V.Lunin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.94 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.905, 58.087, 78.842, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 22.6

Other elements in 3pdd:

The structure of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules (pdb code 3pdd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules, PDB code: 3pdd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3pdd

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Calcium binding site 1 out of 4 in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca192

b:9.3
occ:1.00
O A:HOH243 2.4 4.1 1.0
O A:HOH339 2.4 4.1 1.0
O A:PRO50 2.4 8.0 1.0
O A:THR48 2.4 8.1 1.0
OD2 A:ASP46 2.4 9.8 1.0
O A:HOH240 2.4 7.2 1.0
OD1 A:ASP46 2.6 6.9 1.0
OG1 A:THR48 2.6 9.8 1.0
CG A:ASP46 2.9 7.4 1.0
C A:THR48 3.4 8.9 1.0
C A:PRO50 3.5 8.2 1.0
CB A:THR48 3.7 10.3 1.0
CA A:THR48 3.9 8.9 1.0
N A:THR48 4.2 9.2 1.0
O A:HOH327 4.3 11.9 1.0
N A:PRO50 4.3 10.1 1.0
CB A:ASP46 4.3 10.3 1.0
N A:TYR51 4.3 9.5 1.0
CA A:TYR51 4.4 8.2 1.0
C A:ALA49 4.4 9.7 1.0
N A:ALA49 4.4 8.1 1.0
CA A:PRO50 4.5 9.8 1.0
N A:THR52 4.6 7.2 1.0
OG1 A:THR52 4.6 9.8 1.0
CD A:PRO50 4.6 8.7 1.0
CA A:ALA49 4.7 9.4 1.0
O A:ALA49 4.8 11.2 1.0
C A:TYR51 5.0 8.6 1.0

Calcium binding site 2 out of 4 in 3pdd

Go back to Calcium Binding Sites List in 3pdd
Calcium binding site 2 out of 4 in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca193

b:14.2
occ:1.00
O A:VAL90 2.3 12.5 1.0
OD2 A:ASP163 2.3 14.9 1.0
OD2 A:ASP119 2.4 14.1 1.0
OD1 A:ASP119 2.4 14.5 1.0
OD1 A:ASP121 2.4 12.8 1.0
O A:HOH244 2.4 10.7 1.0
O A:HOH428 2.5 3.2 1.0
CG A:ASP119 2.8 13.8 1.0
CG A:ASP163 3.4 14.6 1.0
CG A:ASP121 3.4 16.6 1.0
C A:VAL90 3.5 12.8 1.0
OD2 A:ASP121 3.6 18.5 1.0
CB A:ASP163 3.9 15.0 1.0
OD2 A:ASP165 4.2 15.1 1.0
N A:GLY122 4.2 20.1 1.0
N A:VAL90 4.3 14.4 1.0
CA A:VAL90 4.3 13.8 1.0
CB A:ASP119 4.3 13.0 1.0
OD1 A:ASP163 4.3 12.5 1.0
CB A:VAL90 4.3 13.5 1.0
N A:LYS91 4.6 12.8 1.0
C A:LYS91 4.6 12.5 1.0
N A:PRO92 4.6 11.8 1.0
CA A:GLY122 4.7 18.2 1.0
OD1 A:ASP164 4.7 19.0 1.0
CB A:ASP121 4.7 19.4 1.0
CA A:LYS91 4.7 12.1 0.5
N A:ASP121 4.7 20.0 1.0
CD A:PRO92 4.8 12.7 1.0
CA A:LYS91 4.8 12.6 0.5
C A:ASP121 4.9 21.0 1.0
O A:LYS91 4.9 12.5 1.0
CA A:ASP121 5.0 20.6 1.0

Calcium binding site 3 out of 4 in 3pdd

Go back to Calcium Binding Sites List in 3pdd
Calcium binding site 3 out of 4 in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca194

b:14.9
occ:1.00
O A:GLU141 2.3 18.1 1.0
O A:PRO143 2.3 13.7 1.0
O A:HOH245 2.3 14.2 1.0
O A:HOH297 2.3 17.1 1.0
O A:HOH630 2.4 18.9 1.0
OD2 A:ASP139 2.4 15.9 1.0
OD1 A:ASP139 2.6 18.1 1.0
CG A:ASP139 2.9 14.5 1.0
C A:PRO143 3.4 13.5 1.0
C A:GLU141 3.5 18.2 1.0
O A:HOH343 4.0 7.9 0.5
N A:PRO143 4.1 16.6 1.0
C A:ALA142 4.2 17.9 1.0
CA A:GLU141 4.3 20.1 0.7
CA A:GLU141 4.3 19.0 0.3
N A:TYR144 4.3 13.6 1.0
CB A:GLU141 4.3 21.4 0.7
CA A:PRO143 4.4 15.8 1.0
CB A:ASP139 4.4 15.6 1.0
CA A:TYR144 4.4 12.8 1.0
CB A:GLU141 4.4 19.9 0.3
N A:GLU141 4.4 17.9 1.0
N A:ALA142 4.5 18.6 1.0
N A:GLU145 4.5 13.4 1.0
CA A:ALA142 4.6 17.8 1.0
O A:HOH673 4.6 32.6 1.0
O A:ALA142 4.7 17.9 1.0
CD A:PRO143 4.7 17.2 1.0
OE1 A:GLU145 4.7 27.6 1.0
O A:HOH406 4.7 19.4 1.0
O A:HOH472 4.8 35.5 1.0
CG A:PRO143 4.9 19.4 1.0
C A:TYR144 4.9 13.4 1.0
O A:HOH545 4.9 16.5 0.5

Calcium binding site 4 out of 4 in 3pdd

Go back to Calcium Binding Sites List in 3pdd
Calcium binding site 4 out of 4 in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca195

b:32.5
occ:1.00
O A:HOH224 2.3 19.6 1.0
O A:HOH375 2.3 22.5 1.0
O A:HOH251 2.5 20.1 1.0
OD1 A:ASP172 2.6 15.0 1.0
O A:HOH611 2.6 28.4 1.0
OD2 A:ASP172 2.6 12.8 1.0
O A:HOH494 2.7 22.4 1.0
CG A:ASP172 2.9 12.7 1.0
NZ A:LYS95 3.8 31.6 1.0
CD A:LYS95 3.9 27.1 1.0
CE A:LYS95 4.1 29.4 1.0
O A:HOH521 4.2 14.6 0.3
CB A:ASP172 4.4 9.4 1.0
O A:SER173 4.6 11.9 1.0
O A:LEU96 4.7 17.4 1.0
N A:LEU96 4.9 13.3 1.0
CG A:LYS95 4.9 20.4 1.0
O A:HOH309 4.9 13.4 0.5
O A:HOH309 5.0 19.6 0.5

Reference:

R.Brunecky, M.Alahuhta, Y.J.Bomble, Q.Xu, J.O.Baker, S.Y.Ding, M.E.Himmel, V.V.Lunin. Structure and Function of the Clostridium Thermocellum Cellobiohydrolase A X1-Module Repeat: Enhancement Through Stabilization of the Cbha Complex. Acta Crystallogr.,Sect.D V. 68 292 2012.
ISSN: ISSN 0907-4449
PubMed: 22349231
DOI: 10.1107/S0907444912001680
Page generated: Sat Dec 12 04:24:35 2020

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