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Calcium in PDB 8ajy: Ruminococcus Flavefaciens Cohesin-Dockerin Structure: Dockerin From Scah Adaptor Scaffoldin in Complex with the Cohesin From Scae Anchoring Scaffoldin

Protein crystallography data

The structure of Ruminococcus Flavefaciens Cohesin-Dockerin Structure: Dockerin From Scah Adaptor Scaffoldin in Complex with the Cohesin From Scae Anchoring Scaffoldin, PDB code: 8ajy was solved by V.D.Alves, P.Bule, C.M.G.A.Fontes, A.L.M.Carvalho, S.Najmudin, M.Duarte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.34 / 1.71
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.81, 120, 65.95, 90, 97.77, 90
R / Rfree (%) 19.4 / 23.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Ruminococcus Flavefaciens Cohesin-Dockerin Structure: Dockerin From Scah Adaptor Scaffoldin in Complex with the Cohesin From Scae Anchoring Scaffoldin (pdb code 8ajy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Ruminococcus Flavefaciens Cohesin-Dockerin Structure: Dockerin From Scah Adaptor Scaffoldin in Complex with the Cohesin From Scae Anchoring Scaffoldin, PDB code: 8ajy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8ajy

Go back to Calcium Binding Sites List in 8ajy
Calcium binding site 1 out of 6 in the Ruminococcus Flavefaciens Cohesin-Dockerin Structure: Dockerin From Scah Adaptor Scaffoldin in Complex with the Cohesin From Scae Anchoring Scaffoldin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ruminococcus Flavefaciens Cohesin-Dockerin Structure: Dockerin From Scah Adaptor Scaffoldin in Complex with the Cohesin From Scae Anchoring Scaffoldin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:13.8
occ:1.00
 OD1 A:ASP137 2.2 15.4 1.0
OD1 A:ASP192 2.3 14.4 1.0
O A:VAL138 2.3 11.5 1.0
O A:TYR190 2.4 13.1 1.0
O A:LYS172 2.4 14.3 1.0
O A:HOH546 2.5 14.1 1.0
C A:LYS172 3.4 14.1 1.0
C A:VAL138 3.4 11.4 1.0
CG A:ASP137 3.4 14.9 1.0
CG A:ASP192 3.5 14.2 1.0
C A:TYR190 3.5 14.3 1.0
N A:VAL138 3.6 12.0 1.0
CA A:ALA191 4.0 13.2 1.0
OD2 A:ASP192 4.0 14.8 1.0
N A:SER173 4.1 14.7 1.0
OD2 A:ASP137 4.1 16.8 1.0
CA A:VAL138 4.1 11.3 1.0
CA A:SER173 4.2 14.9 1.0
N A:ALA191 4.2 13.8 1.0
C A:ALA191 4.2 13.1 1.0
O A:HOH414 4.3 18.3 1.0
CA A:LYS172 4.3 14.6 1.0
N A:ALA139 4.4 11.2 1.0
C A:ASP137 4.4 12.5 1.0
CA A:ASP137 4.5 12.8 1.0
CB A:ASP137 4.5 13.7 1.0
N A:LYS172 4.5 14.0 1.0
CB A:LYS172 4.5 15.2 1.0
CA A:ALA139 4.5 11.7 1.0
O A:ALA191 4.6 13.9 1.0
CA A:TYR190 4.7 15.4 1.0
O A:HOH536 4.7 12.1 1.0
N A:ASP192 4.7 13.1 1.0
CB A:ASP192 4.7 13.7 1.0
CB A:SER173 4.7 14.4 1.0
CB A:VAL138 4.8 11.2 1.0
CD1 A:ILE171 4.9 13.4 1.0
CB A:TYR190 4.9 15.9 1.0
CB A:ALA139 5.0 12.5 1.0

Calcium binding site 2 out of 6 in 8ajy

Go back to Calcium Binding Sites List in 8ajy
Calcium binding site 2 out of 6 in the Ruminococcus Flavefaciens Cohesin-Dockerin Structure: Dockerin From Scah Adaptor Scaffoldin in Complex with the Cohesin From Scae Anchoring Scaffoldin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ruminococcus Flavefaciens Cohesin-Dockerin Structure: Dockerin From Scah Adaptor Scaffoldin in Complex with the Cohesin From Scae Anchoring Scaffoldin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:11.2
occ:1.00
 OD1 B:ASP33 2.3 18.6 1.0
OD1 B:ASP31 2.3 13.3 1.0
O B:HOH325 2.4 10.6 1.0
O B:ILE37 2.4 14.8 1.0
OD1 B:ASN35 2.4 16.4 1.0
OD1 B:ASP42 2.5 11.0 1.0
OD2 B:ASP42 2.6 10.6 1.0
CG B:ASP42 2.9 10.1 1.0
CG B:ASP33 3.2 19.5 1.0
CG B:ASN35 3.3 17.2 1.0
CG B:ASP31 3.3 14.6 1.0
OD2 B:ASP33 3.5 19.6 1.0
C B:ILE37 3.6 13.8 1.0
ND2 B:ASN35 3.8 17.1 1.0
CA B:ASP31 4.1 14.1 1.0
CB B:ASP31 4.2 14.3 1.0
OD2 B:ASP31 4.2 15.8 1.0
N B:ILE37 4.2 15.9 1.0
N B:ASN35 4.2 19.3 1.0
CA B:ILE37 4.3 14.7 1.0
CB B:ASP42 4.4 9.3 1.0
CB B:ILE37 4.4 15.4 1.0
N B:ASP33 4.4 17.4 1.0
C B:ASP31 4.4 15.1 1.0
CB B:ASP33 4.5 19.4 1.0
N B:PHE34 4.5 21.1 1.0
N B:ILE38 4.5 12.6 1.0
OD1 B:ASP39 4.5 11.4 1.0
CB B:ASN35 4.6 18.9 1.0
CA B:ILE38 4.6 11.7 1.0
N B:VAL32 4.6 15.2 1.0
CA B:ASP33 4.7 20.0 1.0
C B:ASP33 4.7 21.3 1.0
CA B:ASN35 4.8 19.7 1.0
N B:GLY36 4.8 18.9 1.0
CG2 B:ILE37 4.9 14.7 1.0
C B:ASN35 4.9 19.6 1.0
N B:ASP39 5.0 11.2 1.0

Calcium binding site 3 out of 6 in 8ajy

Go back to Calcium Binding Sites List in 8ajy
Calcium binding site 3 out of 6 in the Ruminococcus Flavefaciens Cohesin-Dockerin Structure: Dockerin From Scah Adaptor Scaffoldin in Complex with the Cohesin From Scae Anchoring Scaffoldin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ruminococcus Flavefaciens Cohesin-Dockerin Structure: Dockerin From Scah Adaptor Scaffoldin in Complex with the Cohesin From Scae Anchoring Scaffoldin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:16.1
occ:1.00
 OD1 B:ASN72 2.3 15.3 1.0
O B:MET76 2.3 19.5 1.0
OD1 B:ASP70 2.3 15.7 1.0
OD1 B:ASP74 2.3 18.1 1.0
O B:HOH307 2.4 17.0 1.0
OD2 B:ASP81 2.5 13.9 1.0
OD1 B:ASP81 2.5 13.1 1.0
CG B:ASP81 2.8 13.4 1.0
CG B:ASP74 3.2 18.8 1.0
CG B:ASN72 3.4 14.9 1.0
CG B:ASP70 3.5 16.4 1.0
C B:MET76 3.6 20.9 1.0
OD2 B:ASP74 3.6 18.5 1.0
ND2 B:ASN72 3.9 15.8 1.0
CA B:ASP70 4.0 14.8 1.0
N B:MET76 4.2 22.5 1.0
N B:ASP74 4.2 18.6 1.0
CB B:ASP70 4.3 15.9 1.0
CB B:ASP81 4.3 12.5 1.0
OD2 B:ASP70 4.3 17.4 1.0
C B:ASP70 4.4 14.4 1.0
CB B:ASP74 4.4 19.6 1.0
CA B:MET76 4.5 22.8 1.0
N B:ASN72 4.5 12.8 1.0
OD1 B:ASP78 4.5 19.1 1.0
N B:ILE77 4.5 20.1 1.0
CG B:MET76 4.5 24.7 1.0
CA B:ILE77 4.5 18.4 1.0
N B:LYS73 4.5 15.9 1.0
N B:VAL71 4.5 12.9 1.0
CB B:ASN72 4.7 14.1 1.0
CA B:ASP74 4.8 20.2 1.0
C B:ASN72 4.8 15.3 1.0
N B:ASP78 4.8 17.7 1.0
CA B:ASN72 4.9 14.0 1.0
N B:ASN75 4.9 22.2 1.0

Calcium binding site 4 out of 6 in 8ajy

Go back to Calcium Binding Sites List in 8ajy
Calcium binding site 4 out of 6 in the Ruminococcus Flavefaciens Cohesin-Dockerin Structure: Dockerin From Scah Adaptor Scaffoldin in Complex with the Cohesin From Scae Anchoring Scaffoldin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ruminococcus Flavefaciens Cohesin-Dockerin Structure: Dockerin From Scah Adaptor Scaffoldin in Complex with the Cohesin From Scae Anchoring Scaffoldin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:17.5
occ:1.00
 OD1 C:ASP137 2.2 19.5 1.0
O C:LYS172 2.3 18.1 1.0
O C:TYR190 2.3 17.7 1.0
OD1 C:ASP192 2.3 15.5 1.0
O C:VAL138 2.3 15.5 1.0
O C:HOH519 2.4 17.6 1.0
C C:LYS172 3.2 19.5 1.0
C C:VAL138 3.4 15.3 1.0
CG C:ASP137 3.4 19.0 1.0
C C:TYR190 3.5 18.9 1.0
CG C:ASP192 3.5 15.5 1.0
N C:VAL138 3.7 16.0 1.0
N C:SER173 4.0 20.1 1.0
CA C:ALA191 4.1 17.7 1.0
OD2 C:ASP192 4.1 15.7 1.0
CA C:SER173 4.1 20.3 1.0
CA C:VAL138 4.1 15.1 1.0
N C:ALA191 4.2 18.7 1.0
OD2 C:ASP137 4.2 19.9 1.0
CA C:LYS172 4.2 20.2 1.0
C C:ALA191 4.3 17.4 1.0
O C:HOH425 4.4 21.5 1.0
CB C:LYS172 4.4 21.2 1.0
N C:ALA139 4.4 15.3 1.0
N C:LYS172 4.4 19.4 1.0
O C:HOH516 4.5 16.1 1.0
CB C:ASP137 4.5 18.3 1.0
C C:ASP137 4.5 16.2 1.0
CA C:ASP137 4.6 17.4 1.0
O C:ALA191 4.6 17.8 1.0
CB C:SER173 4.6 19.9 1.0
CA C:ALA139 4.6 15.4 1.0
CA C:TYR190 4.6 20.4 1.0
CB C:ASP192 4.7 15.7 1.0
N C:ASP192 4.8 16.9 1.0
CB C:VAL138 4.8 15.1 1.0
CD1 C:ILE171 4.8 17.3 1.0
CB C:TYR190 5.0 20.9 1.0

Calcium binding site 5 out of 6 in 8ajy

Go back to Calcium Binding Sites List in 8ajy
Calcium binding site 5 out of 6 in the Ruminococcus Flavefaciens Cohesin-Dockerin Structure: Dockerin From Scah Adaptor Scaffoldin in Complex with the Cohesin From Scae Anchoring Scaffoldin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Ruminococcus Flavefaciens Cohesin-Dockerin Structure: Dockerin From Scah Adaptor Scaffoldin in Complex with the Cohesin From Scae Anchoring Scaffoldin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:14.1
occ:1.00
 OD1 D:ASP33 2.3 20.6 1.0
OD1 D:ASP31 2.3 15.3 1.0
O D:ILE37 2.3 14.6 1.0
OD1 D:ASP42 2.4 11.7 1.0
OD2 D:ASP42 2.4 10.6 1.0
OD1 D:ASN35 2.5 18.5 1.0
O D:HOH319 2.6 11.3 1.0
CG D:ASP42 2.8 11.2 1.0
CG D:ASP33 3.2 22.7 1.0
CG D:ASP31 3.3 15.6 1.0
CG D:ASN35 3.4 20.4 1.0
C D:ILE37 3.5 15.7 1.0
OD2 D:ASP33 3.6 23.0 1.0
ND2 D:ASN35 3.7 20.7 1.0
CA D:ASP31 4.0 14.8 1.0
CB D:ASP31 4.1 15.2 1.0
OD2 D:ASP31 4.1 16.5 1.0
N D:ILE37 4.2 18.7 1.0
CA D:ILE37 4.3 17.8 1.0
CB D:ASP42 4.3 10.7 1.0
N D:ASP33 4.3 21.6 1.0
C D:ASP31 4.4 16.2 1.0
N D:ASN35 4.4 24.1 1.0
CB D:ILE37 4.4 19.0 1.0
N D:VAL32 4.4 16.7 1.0
N D:ILE38 4.5 14.2 1.0
CB D:ASP33 4.5 23.9 1.0
CA D:ILE38 4.6 13.3 1.0
CB D:ASN35 4.6 22.3 1.0
OD1 D:ASP39 4.6 11.8 1.0
N D:PHE34 4.7 26.5 1.0
C D:ASP33 4.7 26.1 1.0
CA D:ASP33 4.7 24.0 1.0
CG2 D:ILE37 4.8 18.7 1.0
CA D:ASN35 4.9 23.2 1.0
N D:ASP39 4.9 12.0 1.0
N D:GLY36 4.9 21.4 1.0
O D:GLY30 5.0 13.9 1.0

Calcium binding site 6 out of 6 in 8ajy

Go back to Calcium Binding Sites List in 8ajy
Calcium binding site 6 out of 6 in the Ruminococcus Flavefaciens Cohesin-Dockerin Structure: Dockerin From Scah Adaptor Scaffoldin in Complex with the Cohesin From Scae Anchoring Scaffoldin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Ruminococcus Flavefaciens Cohesin-Dockerin Structure: Dockerin From Scah Adaptor Scaffoldin in Complex with the Cohesin From Scae Anchoring Scaffoldin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:16.9
occ:1.00
 O D:HOH308 2.3 20.8 1.0
OD1 D:ASP74 2.3 20.8 1.0
OD1 D:ASP70 2.3 16.8 1.0
O D:MET76 2.3 21.9 1.0
OD2 D:ASP81 2.4 15.6 1.0
OD1 D:ASN72 2.4 17.3 1.0
OD1 D:ASP81 2.5 15.0 1.0
CG D:ASP81 2.7 14.8 1.0
CG D:ASP74 3.2 22.1 1.0
CG D:ASN72 3.4 17.1 1.0
CG D:ASP70 3.4 17.3 1.0
C D:MET76 3.5 22.7 1.0
OD2 D:ASP74 3.6 22.7 1.0
ND2 D:ASN72 3.8 17.2 1.0
CA D:ASP70 4.0 15.6 1.0
N D:MET76 4.1 25.2 1.0
CB D:ASP70 4.2 16.8 1.0
N D:ASP74 4.2 22.4 1.0
CB D:ASP81 4.3 14.0 1.0
CA D:MET76 4.3 25.4 1.0
OD2 D:ASP70 4.3 18.5 1.0
C D:ASP70 4.4 15.2 1.0
CB D:ASP74 4.4 23.2 1.0
N D:ASN72 4.4 15.3 1.0
N D:ILE77 4.4 21.4 1.0
OD1 D:ASP78 4.5 17.9 1.0
CA D:ILE77 4.6 19.7 1.0
N D:VAL71 4.6 14.1 1.0
N D:LYS73 4.6 19.3 1.0
CB D:MET76 4.7 27.3 1.0
CB D:ASN72 4.7 16.6 1.0
CA D:ASP74 4.7 23.7 1.0
N D:ASP78 4.8 18.1 1.0
C D:ASN72 4.9 18.5 1.0
CA D:ASN72 4.9 16.9 1.0
N D:ASN75 4.9 25.3 1.0
C D:ASP74 4.9 25.0 1.0
CG D:ASP78 5.0 18.9 1.0
CA D:ASP81 5.0 13.4 1.0

Reference:

M.Duarte, V.D.Alves, M.Correia, C.Caseiro, L.M.A.Ferreira, M.J.Romao, A.L.Carvalho, S.Najmudin, E.A.Bayer, C.M.G.A.Fontes, P.Bule. Structure-Function Studies Can Improve Binding Affinity of Cohesin-Dockerin Interactions For Multi-Protein Assemblies. Int.J.Biol.Macromol. V. 224 55 2023.
ISSN: ISSN 0141-8130
PubMed: 36252630
DOI: 10.1016/J.IJBIOMAC.2022.10.102
Page generated: Fri Jul 19 06:56:32 2024

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