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Calcium in PDB 5nrk: Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S15I, I16N Mutant

Enzymatic activity of Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S15I, I16N Mutant

All present enzymatic activity of Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S15I, I16N Mutant:
3.2.1.4;

Protein crystallography data

The structure of Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S15I, I16N Mutant, PDB code: 5nrk was solved by P.Bule, S.Najmudin, C.M.G.A.Fontes, V.D.Alves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.03 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.539, 79.809, 112.159, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 17

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S15I, I16N Mutant (pdb code 5nrk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S15I, I16N Mutant, PDB code: 5nrk:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5nrk

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Calcium binding site 1 out of 6 in the Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S15I, I16N Mutant


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 the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S15I, I16N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca101

b:9.8
occ:1.00
 OD1 B:ASP8 2.3 12.6 1.0
OD1 B:ASP6 2.3 11.7 1.0
O B:SER12 2.3 13.2 1.0
OD1 B:ASN10 2.4 12.3 1.0
O B:HOH239 2.4 9.6 1.0
OD1 B:ASP17 2.4 9.4 1.0
OD2 B:ASP17 2.5 9.0 1.0
CG B:ASP17 2.8 8.5 1.0
CG B:ASP8 3.3 14.3 1.0
CG B:ASN10 3.3 13.0 1.0
CG B:ASP6 3.5 12.4 1.0
C B:SER12 3.5 13.3 1.0
OD2 B:ASP8 3.8 18.8 1.0
ND2 B:ASN10 3.9 12.7 1.0
CA B:ASP6 4.1 10.7 1.0
N B:SER12 4.2 15.3 1.0
N B:ASN10 4.2 14.8 1.0
CB B:ASP6 4.2 12.0 1.0
N B:ASP8 4.3 11.8 1.0
CA B:SER12 4.3 16.3 1.0
CB B:ASP17 4.3 7.5 1.0
OD2 B:ASP6 4.4 14.2 1.0
C B:ASP6 4.4 10.3 1.0
N B:ILE13 4.4 12.9 1.0
CB B:ASN10 4.4 14.3 1.0
CA B:ILE13 4.5 11.4 1.0
CB B:ASP8 4.5 13.0 1.0
O B:HOH206 4.6 22.3 1.0
N B:VAL7 4.6 9.7 1.0
OD1 B:ASN14 4.6 9.1 1.0
N B:GLY9 4.6 14.1 1.0
CB B:SER12 4.7 17.6 1.0
CA B:ASP8 4.7 13.3 1.0
CA B:ASN10 4.7 15.1 1.0
C B:ASP8 4.8 14.3 1.0
N B:GLY11 4.8 15.3 1.0
N B:ASN14 4.9 9.7 1.0
CG B:ASN14 5.0 9.9 1.0
C B:ASN10 5.0 15.4 1.0
N B:ASP17 5.0 7.3 1.0
ND2 B:ASN14 5.0 11.2 1.0

Calcium binding site 2 out of 6 in 5nrk

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Calcium binding site 2 out of 6 in the Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S15I, I16N Mutant


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 the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S15I, I16N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca102

b:8.5
occ:1.00
 OD1 B:ASP42 2.3 10.1 1.0
OD1 B:ASP46 2.3 11.4 1.0
O B:SER48 2.3 10.4 1.0
OD1 B:ASN44 2.4 9.7 1.0
O B:HOH210 2.4 9.2 1.0
OD1 B:ASP53 2.5 7.3 1.0
OD2 B:ASP53 2.5 8.2 1.0
CG B:ASP53 2.8 7.7 1.0
CG B:ASP46 3.3 11.7 1.0
CG B:ASN44 3.4 9.7 1.0
CG B:ASP42 3.4 10.3 1.0
C B:SER48 3.5 11.4 1.0
OD2 B:ASP46 3.6 12.9 1.0
ND2 B:ASN44 3.8 9.9 1.0
CA B:ASP42 4.0 8.9 1.0
CB B:ASP42 4.1 10.2 1.0
N B:SER48 4.1 13.8 1.0
OG B:SER48 4.2 24.2 0.5
N B:LEU43 4.3 8.5 1.0
N B:ASN44 4.3 9.9 1.0
CA B:SER48 4.3 12.6 0.5
OD2 B:ASP42 4.3 13.0 1.0
CB B:ASP53 4.3 7.3 1.0
N B:ASP46 4.3 13.4 1.0
CA B:SER48 4.4 14.4 0.5
N B:ILE49 4.4 10.4 1.0
C B:ASP42 4.5 9.5 1.0
CB B:ASP46 4.5 12.5 1.0
CA B:ILE49 4.6 9.6 1.0
CB B:SER48 4.6 12.8 0.5
OD1 B:ASN50 4.6 7.7 1.0
CB B:ASN44 4.7 10.5 1.0
N B:GLY45 4.7 12.7 1.0
N B:LYS47 4.8 14.5 1.0
CA B:ASP46 4.8 13.3 1.0
N B:ASN50 4.8 7.4 1.0
CA B:ASN44 4.8 10.6 1.0
CB B:SER48 4.9 17.3 0.5
N B:ASP53 4.9 6.1 1.0
C B:ASP46 5.0 13.9 1.0
C B:ASN44 5.0 12.6 1.0

Calcium binding site 3 out of 6 in 5nrk

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Calcium binding site 3 out of 6 in the Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S15I, I16N Mutant


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 the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S15I, I16N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca103

b:22.1
occ:1.00
 OD1 B:ASP37 2.4 38.3 1.0
O B:ALA34 2.5 20.3 1.0
O B:PHE32 2.5 15.1 1.0
O B:HOH264 2.5 27.1 1.0
O B:HOH213 2.6 37.8 1.0
OD2 B:ASP31 2.9 32.6 1.0
CG B:ASP37 3.1 28.3 1.0
OD2 B:ASP37 3.1 28.1 1.0
O B:GLU35 3.6 29.4 1.0
C B:PHE32 3.7 14.8 1.0
C B:ALA34 3.7 18.8 1.0
CG B:ASP31 3.7 28.4 1.0
O B:HOH246 3.9 42.4 1.0
N B:PHE32 4.1 15.3 1.0
C B:GLU35 4.1 26.1 1.0
CA B:GLU35 4.2 26.3 1.0
CB B:ASP31 4.3 26.4 1.0
CA B:PHE32 4.4 14.1 1.0
N B:GLU35 4.4 21.1 1.0
C B:PRO33 4.4 16.2 1.0
CB B:ASP37 4.4 22.1 1.0
OD1 B:ASP31 4.5 25.4 1.0
O B:PRO33 4.5 18.6 1.0
N B:ALA34 4.5 15.5 1.0
N B:ASP37 4.6 17.8 1.0
N B:PRO33 4.7 15.3 1.0
CB B:PHE32 4.7 14.7 1.0
CA B:ALA34 4.7 15.9 1.0
CA B:PRO33 4.8 15.4 1.0
O B:HOH245 4.8 33.3 1.0
CA B:ASP37 4.8 19.2 1.0
N B:ASP36 4.9 21.6 1.0
C B:ASP31 5.0 22.6 1.0

Calcium binding site 4 out of 6 in 5nrk

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Calcium binding site 4 out of 6 in the Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S15I, I16N Mutant


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 the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S15I, I16N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca101

b:8.9
occ:1.00
 O D:SER12 2.3 13.6 1.0
OD1 D:ASP6 2.3 11.4 1.0
OD1 D:ASP8 2.3 10.4 1.0
OD1 D:ASN10 2.4 10.6 1.0
O D:HOH227 2.4 8.0 1.0
OD1 D:ASP17 2.5 8.0 1.0
OD2 D:ASP17 2.5 8.7 1.0
CG D:ASP17 2.8 8.3 1.0
CG D:ASP8 3.3 11.5 1.0
CG D:ASN10 3.3 10.5 1.0
C D:SER12 3.4 14.2 1.0
CG D:ASP6 3.5 10.9 1.0
OD2 D:ASP8 3.7 13.4 1.0
ND2 D:ASN10 3.8 11.5 1.0
CA D:ASP6 4.0 9.7 1.0
N D:SER12 4.2 15.6 1.0
CB D:ASP6 4.2 10.7 1.0
N D:ASN10 4.2 10.9 1.0
N D:ASP8 4.3 8.8 1.0
CA D:SER12 4.3 16.2 1.0
CB D:ASP17 4.4 7.8 1.0
N D:ILE13 4.4 13.2 1.0
OD2 D:ASP6 4.4 11.8 1.0
CA D:ILE13 4.4 12.1 1.0
C D:ASP6 4.4 8.9 1.0
CB D:ASN10 4.5 11.0 1.0
CB D:ASP8 4.5 10.3 1.0
N D:GLY9 4.6 9.3 1.0
OD1 D:ASN14 4.6 8.5 1.0
N D:VAL7 4.7 8.4 1.0
CA D:ASP8 4.7 9.1 1.0
CB D:SER12 4.7 17.8 1.0
ND2 D:ASN14 4.7 11.4 1.0
CA D:ASN10 4.8 11.3 1.0
C D:ASP8 4.8 9.6 1.0
N D:GLY11 4.8 13.0 1.0
N D:ASN14 4.8 9.6 1.0
CG D:ASN14 4.9 9.6 1.0
O D:ASP6 5.0 9.6 1.0
C D:ASN10 5.0 12.8 1.0

Calcium binding site 5 out of 6 in 5nrk

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Calcium binding site 5 out of 6 in the Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S15I, I16N Mutant


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 the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S15I, I16N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca102

b:7.2
occ:1.00
 OD1 D:ASP42 2.3 8.9 1.0
OD1 D:ASP46 2.4 8.9 1.0
O D:SER48 2.4 8.6 1.0
O D:HOH211 2.4 7.1 1.0
OD1 D:ASN44 2.4 8.4 1.0
OD1 D:ASP53 2.5 6.9 1.0
OD2 D:ASP53 2.5 6.8 1.0
CG D:ASP53 2.8 7.1 1.0
CG D:ASP46 3.3 9.1 1.0
CG D:ASN44 3.4 9.1 1.0
CG D:ASP42 3.5 9.1 1.0
C D:SER48 3.5 9.4 1.0
OD2 D:ASP46 3.7 9.5 1.0
ND2 D:ASN44 3.8 8.9 1.0
CA D:ASP42 4.0 8.3 1.0
CB D:ASP42 4.1 9.1 1.0
N D:SER48 4.2 10.8 1.0
N D:LEU43 4.2 8.6 1.0
N D:ASN44 4.3 9.4 1.0
CB D:ASP53 4.3 6.1 1.0
CA D:SER48 4.3 10.6 1.0
N D:ASP46 4.4 10.4 1.0
OD2 D:ASP42 4.4 10.4 1.0
N D:ILE49 4.5 8.7 1.0
C D:ASP42 4.5 8.7 1.0
CB D:ASP46 4.6 10.2 1.0
OD1 D:ASN50 4.6 7.0 1.0
CA D:ILE49 4.6 7.9 1.0
CB D:ASN44 4.6 9.6 1.0
CB D:SER48 4.7 12.5 1.0
N D:ASN50 4.7 6.5 1.0
N D:GLY45 4.7 11.3 1.0
CA D:ASN44 4.8 10.4 1.0
CA D:ASP46 4.8 10.8 1.0
N D:LYS47 4.8 11.3 1.0
CG D:ASN50 4.9 6.8 1.0
N D:ASP53 4.9 6.0 1.0
C D:ASN44 5.0 12.1 1.0
C D:ASP46 5.0 11.6 1.0

Calcium binding site 6 out of 6 in 5nrk

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Calcium binding site 6 out of 6 in the Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S15I, I16N Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S15I, I16N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca103

b:16.9
occ:1.00
 OD1 D:ASP31 2.3 22.5 1.0
O D:PHE32 2.3 13.2 1.0
O D:HOH261 2.3 26.8 1.0
O D:HOH259 2.3 24.9 1.0
OD1 D:ASP37 2.3 17.9 1.0
O D:ALA34 2.4 16.2 1.0
CG D:ASP37 3.3 16.7 1.0
CG D:ASP31 3.4 23.2 1.0
C D:PHE32 3.4 11.7 1.0
C D:ALA34 3.6 14.8 1.0
OD2 D:ASP37 3.6 18.0 1.0
N D:PHE32 3.9 12.2 1.0
OD2 D:ASP31 4.0 28.7 1.0
C D:PRO33 4.1 12.5 1.0
CA D:PHE32 4.2 12.2 1.0
N D:ALA34 4.2 11.7 1.0
O D:PRO33 4.3 15.3 1.0
C D:ASP31 4.4 14.8 1.0
O D:HOH255 4.4 24.1 1.0
N D:PRO33 4.5 12.0 1.0
CA D:ALA34 4.5 13.2 1.0
C D:GLU35 4.5 20.2 1.0
N D:GLU35 4.5 16.5 1.0
CA D:GLU35 4.5 19.9 1.0
CB D:PHE32 4.6 11.9 1.0
CA D:PRO33 4.6 12.4 1.0
CB D:ASP37 4.6 13.2 1.0
CB D:ASP31 4.6 19.1 1.0
O D:GLU35 4.7 27.6 1.0
N D:ASP37 4.7 13.2 1.0
CA D:ASP31 4.7 17.1 1.0
N D:ASP36 4.9 15.6 1.0
CA D:ASP37 5.0 12.4 1.0

Reference:

P.Bule, K.Cameron, J.A.M.Prates, L.M.A.Ferreira, S.P.Smith, H.J.Gilbert, E.A.Bayer, S.Najmudin, C.M.G.A.Fontes, V.D.Alves. Structure-Function Analyses Generate Novel Specificities to Assemble the Components of Multienzyme Bacterial Cellulosome Complexes. J. Biol. Chem. V. 293 4201 2018.
ISSN: ESSN 1083-351X
PubMed: 29367338
DOI: 10.1074/JBC.RA117.001241
Page generated: Mon Jul 15 09:34:43 2024

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