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Calcium in PDB 5nrm: Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S51I, L52N Mutant

Enzymatic activity of Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S51I, L52N Mutant

All present enzymatic activity of Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S51I, L52N 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 S51I, L52N Mutant, PDB code: 5nrm 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) 49.05 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 30.490, 59.950, 51.260, 90.00, 106.88, 90.00
R / Rfree (%) 17.8 / 20.5

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 S51I, L52N Mutant (pdb code 5nrm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S51I, L52N Mutant, PDB code: 5nrm:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5nrm

Go back to Calcium Binding Sites List in 5nrm
Calcium binding site 1 out of 3 in the Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S51I, L52N 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 S51I, L52N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca101

b:8.7
occ:1.00
 O B:SER13 2.3 11.4 1.0
OD1 B:ASP7 2.3 10.5 1.0
OD1 B:ASP9 2.4 8.4 1.0
OD2 B:ASP18 2.4 9.1 1.0
OD1 B:ASN11 2.4 9.8 1.0
O B:HOH212 2.4 8.7 1.0
OD1 B:ASP18 2.5 9.3 1.0
CG B:ASP18 2.8 8.9 1.0
CG B:ASP9 3.3 8.8 1.0
CG B:ASN11 3.3 9.3 1.0
CG B:ASP7 3.4 11.1 1.0
C B:SER13 3.5 10.3 1.0
OD2 B:ASP9 3.7 9.3 1.0
ND2 B:ASN11 3.9 9.5 1.0
N B:ASN11 4.0 10.0 1.0
CA B:ASP7 4.2 11.3 1.0
N B:SER13 4.2 10.6 1.0
OD2 B:ASP7 4.2 12.1 1.0
CB B:ASP18 4.3 8.6 1.0
CB B:ASP7 4.3 11.9 1.0
CB B:ASN11 4.3 9.7 1.0
N B:ASP9 4.4 9.8 1.0
N B:ILE14 4.4 10.2 1.0
OD1 B:ASN15 4.4 8.3 1.0
CA B:SER13 4.4 11.1 1.0
CA B:ILE14 4.4 9.9 1.0
N B:GLY10 4.5 9.9 1.0
C B:ASP7 4.5 11.3 1.0
CB B:ASP9 4.6 9.0 1.0
CA B:ASN11 4.6 10.1 1.0
CG B:ASN15 4.6 8.4 1.0
N B:ASN15 4.6 8.2 1.0
N B:GLY12 4.7 10.9 1.0
ND2 B:ASN15 4.7 8.6 1.0
CA B:ASP9 4.8 9.4 1.0
C B:ASP9 4.8 9.7 1.0
N B:VAL8 4.8 11.4 1.0
C B:ASN11 4.9 10.7 1.0
C B:ILE14 5.0 9.2 1.0
N B:ASP18 5.0 7.8 1.0

Calcium binding site 2 out of 3 in 5nrm

Go back to Calcium Binding Sites List in 5nrm
Calcium binding site 2 out of 3 in the Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S51I, L52N 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 S51I, L52N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca102

b:19.2
occ:1.00
 OD1 B:ASP43 2.1 25.0 1.0
OD1 B:ASP47 2.3 31.6 1.0
O B:SER49 2.4 27.5 1.0
OD2 B:ASP54 2.4 25.6 1.0
OD1 B:ASN45 2.4 31.2 1.0
OD1 B:ASP54 2.4 25.6 1.0
O B:HOH202 2.5 23.7 1.0
CG B:ASP54 2.7 25.1 1.0
CG B:ASN45 3.3 32.3 1.0
CG B:ASP47 3.3 34.0 1.0
CG B:ASP43 3.3 25.4 1.0
C B:SER49 3.5 29.3 1.0
OD2 B:ASP47 3.6 34.6 1.0
ND2 B:ASN45 3.7 33.8 1.0
OG B:SER49 4.1 36.5 1.0
N B:SER49 4.2 31.9 1.0
CB B:ASP43 4.2 23.6 1.0
CA B:ASP43 4.3 22.2 1.0
CB B:ASP54 4.3 22.8 1.0
OD1 B:ASN51 4.3 32.3 1.0
N B:ASN45 4.3 27.9 1.0
OD2 B:ASP43 4.3 27.5 1.0
CA B:SER49 4.4 31.3 1.0
N B:ILE50 4.4 28.8 1.0
N B:LEU44 4.4 23.4 1.0
CA B:ILE50 4.4 28.0 1.0
N B:ASP47 4.5 34.1 1.0
N B:ASN51 4.6 28.8 1.0
CB B:ASN45 4.6 31.9 1.0
N B:GLY46 4.6 31.1 1.0
CB B:ASP47 4.7 36.8 1.0
C B:ASP43 4.8 22.8 1.0
CA B:ASN45 4.8 30.7 1.0
CB B:SER49 4.9 34.2 1.0
N B:ASP54 4.9 25.2 1.0
CA B:ASP47 4.9 36.2 1.0
C B:ASN45 5.0 32.5 1.0
C B:ILE50 5.0 29.2 1.0
CA B:ASP54 5.0 23.2 1.0

Calcium binding site 3 out of 3 in 5nrm

Go back to Calcium Binding Sites List in 5nrm
Calcium binding site 3 out of 3 in the Crystal Structure of the Sixth Cohesin From Acetivibrio Cellulolyticus' Scaffoldin B in Complex with CEL5 Dockerin S51I, L52N 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 S51I, L52N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca103

b:20.7
occ:0.80
 OD1 B:ASP38 2.2 23.7 1.0
O B:PHE33 2.2 17.2 1.0
OD1 B:ASP32 2.2 33.3 1.0
O B:ALA35 2.3 25.0 1.0
O B:HOH231 2.3 37.8 1.0
O B:HOH237 2.4 28.7 1.0
CG B:ASP38 3.3 25.2 1.0
C B:PHE33 3.3 16.6 1.0
CG B:ASP32 3.4 32.7 1.0
C B:ALA35 3.5 22.4 1.0
OD2 B:ASP38 3.7 27.6 1.0
N B:PHE33 3.7 20.3 1.0
OD2 B:ASP32 4.0 38.6 1.0
CA B:PHE33 4.0 17.7 1.0
O B:GLU36 4.2 31.6 1.0
C B:PRO34 4.3 17.1 1.0
CB B:PHE33 4.3 17.5 1.0
N B:ALA35 4.3 17.3 1.0
C B:GLU36 4.4 32.2 1.0
C B:ASP32 4.4 22.7 1.0
O B:HOH240 4.4 29.8 1.0
O B:HOH228 4.4 36.1 1.0
N B:ASP38 4.4 26.7 1.0
N B:PRO34 4.4 15.4 1.0
N B:GLU36 4.5 26.8 1.0
CB B:ASP32 4.5 29.2 1.0
CA B:ALA35 4.5 19.8 1.0
O B:PRO34 4.5 18.4 1.0
CB B:ASP38 4.5 25.7 1.0
CA B:ASP32 4.6 26.5 1.0
CA B:GLU36 4.6 31.8 1.0
CA B:PRO34 4.7 15.7 1.0
CA B:ASP38 4.8 25.1 1.0
N B:ASP37 4.9 28.9 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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