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Calcium in PDB 6psm: Crystal Structure of PSS1_19B C77S in Complex with Kappa-Neocarrabiose

Protein crystallography data

The structure of Crystal Structure of PSS1_19B C77S in Complex with Kappa-Neocarrabiose, PDB code: 6psm was solved by A.G.Hettle, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.19 / 1.95
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 93.050, 93.050, 300.210, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 21.2

Other elements in 6psm:

The structure of Crystal Structure of PSS1_19B C77S in Complex with Kappa-Neocarrabiose also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Zinc (Zn) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of PSS1_19B C77S in Complex with Kappa-Neocarrabiose (pdb code 6psm). 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 PSS1_19B C77S in Complex with Kappa-Neocarrabiose, PDB code: 6psm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6psm

Go back to Calcium Binding Sites List in 6psm
Calcium binding site 1 out of 6 in the Crystal Structure of PSS1_19B C77S in Complex with Kappa-Neocarrabiose


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 PSS1_19B C77S in Complex with Kappa-Neocarrabiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:26.3
occ:0.80
 OD1 A:ASP37 2.3 25.4 1.0
OD2 A:ASP290 2.4 19.1 1.0
OD1 A:ASP38 2.4 17.5 1.0
O8 A:G4S502 2.5 20.4 1.0
OD1 A:ASN291 2.6 14.8 1.0
OD1 A:ASP290 2.8 16.6 1.0
CG A:ASP290 2.9 17.9 1.0
CG A:ASP38 3.4 19.1 1.0
CG A:ASN291 3.4 14.3 1.0
CG A:ASP37 3.4 22.9 1.0
ND2 A:ASN291 3.5 14.9 1.0
CB A:SER77 3.6 17.6 1.0
N A:ASP38 3.8 15.2 1.0
S A:G4S502 3.8 18.5 1.0
OD2 A:ASP38 4.1 19.1 1.0
CE A:LYS309 4.1 16.5 1.0
OD2 A:ASP37 4.1 23.0 1.0
NZ A:LYS140 4.2 18.7 1.0
CA A:SER77 4.2 16.7 1.0
NZ A:LYS309 4.2 17.2 1.0
O9 A:G4S502 4.3 17.6 1.0
OG A:SER77 4.3 19.3 1.0
CD2 A:HIS233 4.3 15.9 1.0
CB A:ASP38 4.3 16.9 1.0
CA A:ASP38 4.3 17.5 1.0
N A:SER77 4.3 17.0 1.0
CB A:ASP290 4.4 16.3 1.0
CA A:ASP37 4.4 17.7 1.0
C A:ASP37 4.4 16.4 1.0
CB A:ASP37 4.4 19.6 1.0
O7 A:G4S502 4.5 19.4 1.0
CB A:ASN291 4.8 13.6 1.0
NH2 A:ARG81 4.9 14.9 1.0
CD A:LYS309 4.9 15.9 1.0
O4 A:G4S502 4.9 17.7 1.0
NE2 A:HIS233 5.0 16.0 1.0
N A:ASN291 5.0 13.8 1.0

Calcium binding site 2 out of 6 in 6psm

Go back to Calcium Binding Sites List in 6psm
Calcium binding site 2 out of 6 in the Crystal Structure of PSS1_19B C77S in Complex with Kappa-Neocarrabiose


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 PSS1_19B C77S in Complex with Kappa-Neocarrabiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:27.3
occ:0.80
 OD1 B:ASP37 2.2 28.8 1.0
OD2 B:ASP290 2.3 21.7 1.0
OD1 B:ASP38 2.4 19.9 1.0
O9 B:G4S503 2.4 23.7 1.0
OD1 B:ASN291 2.6 17.9 1.0
OD1 B:ASP290 2.8 22.0 1.0
CG B:ASP290 2.9 20.4 1.0
CG B:ASP37 3.4 26.8 1.0
CG B:ASN291 3.4 16.5 1.0
CG B:ASP38 3.4 21.6 1.0
ND2 B:ASN291 3.5 14.3 1.0
CB B:SER77 3.6 17.8 1.0
N B:ASP38 3.8 19.1 1.0
S B:G4S503 3.8 22.6 1.0
OD2 B:ASP37 4.0 29.1 1.0
OD2 B:ASP38 4.1 22.8 1.0
O8 B:G4S503 4.1 20.0 1.0
CE B:LYS309 4.2 17.0 1.0
CA B:SER77 4.2 16.7 1.0
NZ B:LYS140 4.2 20.4 1.0
OG B:SER77 4.3 17.3 1.0
CB B:ASP38 4.3 21.6 1.0
CD2 B:HIS233 4.3 19.3 1.0
CA B:ASP38 4.3 20.0 1.0
CA B:ASP37 4.3 21.5 1.0
NZ B:LYS309 4.3 17.7 1.0
CB B:ASP290 4.3 18.8 1.0
N B:SER77 4.4 17.4 1.0
C B:ASP37 4.4 20.9 1.0
CB B:ASP37 4.4 21.7 1.0
O7 B:G4S503 4.4 21.0 1.0
CB B:ASN291 4.7 16.0 1.0
NH2 B:ARG81 4.8 15.9 1.0
O4 B:G4S503 4.9 20.2 1.0
N B:ASN291 4.9 14.8 1.0
CD B:LYS309 4.9 16.5 1.0
NE2 B:HIS233 5.0 17.6 1.0

Calcium binding site 3 out of 6 in 6psm

Go back to Calcium Binding Sites List in 6psm
Calcium binding site 3 out of 6 in the Crystal Structure of PSS1_19B C77S in Complex with Kappa-Neocarrabiose


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 PSS1_19B C77S in Complex with Kappa-Neocarrabiose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:28.3
occ:0.80
 OD1 C:ASP38 2.2 16.1 1.0
OD1 C:ASP37 2.3 25.1 1.0
O8 C:G4S504 2.4 20.9 1.0
ND2 C:ASN291 2.5 10.7 1.0
OD2 C:ASP290 2.5 17.4 1.0
OD1 C:ASP290 2.9 17.4 1.0
CG C:ASP290 3.0 16.9 1.0
CG C:ASN291 3.3 14.2 1.0
CG C:ASP38 3.3 15.8 1.0
OD1 C:ASN291 3.3 14.2 1.0
CG C:ASP37 3.5 21.1 1.0
CB C:SER77 3.6 14.0 1.0
N C:ASP38 3.8 15.0 1.0
S C:G4S504 3.9 19.7 1.0
CE C:LYS309 4.0 13.6 1.0
OD2 C:ASP38 4.0 15.9 1.0
NZ C:LYS309 4.1 14.9 1.0
OD2 C:ASP37 4.2 21.2 1.0
CA C:SER77 4.2 15.0 1.0
O9 C:G4S504 4.2 17.8 1.0
CB C:ASP38 4.2 13.9 1.0
NZ C:LYS140 4.2 20.2 1.0
CD2 C:HIS233 4.3 14.9 1.0
CA C:ASP38 4.3 14.3 1.0
OG C:SER77 4.3 14.9 1.0
N C:SER77 4.3 14.2 1.0
C C:ASP37 4.4 17.0 1.0
CA C:ASP37 4.4 17.2 1.0
CB C:ASP290 4.5 15.7 1.0
O7 C:G4S504 4.5 17.2 1.0
CB C:ASP37 4.5 18.5 1.0
CB C:ASN291 4.7 13.3 1.0
CD C:LYS309 4.7 14.5 1.0
NE2 C:HIS233 4.9 15.9 1.0
O4 C:G4S504 4.9 16.7 1.0
N C:ASN291 5.0 15.9 1.0
NH2 C:ARG81 5.0 18.2 1.0

Calcium binding site 4 out of 6 in 6psm

Go back to Calcium Binding Sites List in 6psm
Calcium binding site 4 out of 6 in the Crystal Structure of PSS1_19B C77S in Complex with Kappa-Neocarrabiose


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 PSS1_19B C77S in Complex with Kappa-Neocarrabiose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:37.4
occ:0.90
 OD1 D:ASP37 2.3 27.6 1.0
O9 D:G4S506 2.3 27.6 1.0
OD2 D:ASP290 2.4 23.1 1.0
OD1 D:ASP38 2.4 18.3 1.0
OD1 D:ASN291 2.6 18.8 1.0
OD1 D:ASP290 2.9 23.3 1.0
CG D:ASP290 2.9 24.6 1.0
CG D:ASN291 3.4 18.3 1.0
CG D:ASP38 3.4 20.0 1.0
CG D:ASP37 3.4 25.5 1.0
CB D:SER77 3.5 19.3 1.0
ND2 D:ASN291 3.5 18.0 1.0
S D:G4S506 3.8 25.6 1.0
N D:ASP38 3.9 19.4 1.0
CE D:LYS309 4.1 19.8 1.0
OD2 D:ASP37 4.1 27.1 1.0
CA D:SER77 4.1 18.9 1.0
OD2 D:ASP38 4.1 19.0 1.0
NZ D:LYS140 4.1 21.2 1.0
O8 D:G4S506 4.1 23.9 1.0
OG D:SER77 4.2 21.4 1.0
NZ D:LYS309 4.2 21.1 1.0
N D:SER77 4.3 17.7 1.0
CD2 D:HIS233 4.3 25.4 1.0
CB D:ASP38 4.4 19.7 1.0
CA D:ASP38 4.4 19.9 1.0
CB D:ASP290 4.4 21.9 1.0
O7 D:G4S506 4.4 24.7 1.0
CA D:ASP37 4.5 21.5 1.0
CB D:ASP37 4.5 22.8 1.0
C D:ASP37 4.5 22.0 1.0
CB D:ASN291 4.7 17.4 1.0
NH2 D:ARG81 4.8 20.3 1.0
O4 D:G4S506 4.9 23.7 1.0
CD D:LYS309 4.9 18.5 1.0
NE2 D:HIS233 5.0 25.5 1.0

Calcium binding site 5 out of 6 in 6psm

Go back to Calcium Binding Sites List in 6psm
Calcium binding site 5 out of 6 in the Crystal Structure of PSS1_19B C77S in Complex with Kappa-Neocarrabiose


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 PSS1_19B C77S in Complex with Kappa-Neocarrabiose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca501

b:24.7
occ:0.80
 OD1 E:ASP38 2.3 17.0 1.0
OD1 E:ASP37 2.4 29.5 1.0
ND2 E:ASN291 2.4 16.9 1.0
O9 E:G4S506 2.4 22.5 1.0
OD2 E:ASP290 2.4 23.5 1.0
OD1 E:ASP290 2.8 20.8 1.0
CG E:ASP290 2.9 21.1 1.0
CG E:ASN291 3.2 16.8 1.0
OD1 E:ASN291 3.3 17.2 1.0
CG E:ASP38 3.3 20.0 1.0
CG E:ASP37 3.5 26.4 1.0
CB E:SER77 3.6 20.9 1.0
N E:ASP38 3.8 17.8 1.0
S E:G4S506 3.9 20.9 1.0
CE E:LYS309 4.0 16.6 1.0
OD2 E:ASP38 4.1 19.9 1.0
CA E:SER77 4.2 19.5 1.0
NZ E:LYS309 4.2 15.8 1.0
OD2 E:ASP37 4.2 29.6 1.0
NZ E:LYS140 4.3 22.4 1.0
CB E:ASP38 4.3 18.2 1.0
O8 E:G4S506 4.3 18.1 1.0
N E:SER77 4.3 18.2 1.0
CA E:ASP38 4.3 17.4 1.0
OG E:SER77 4.3 22.2 1.0
CD2 E:HIS233 4.3 17.8 1.0
CB E:ASP290 4.4 19.3 1.0
CA E:ASP37 4.5 20.3 1.0
C E:ASP37 4.5 17.5 1.0
O7 E:G4S506 4.5 20.4 1.0
CB E:ASP37 4.5 22.1 1.0
CB E:ASN291 4.6 17.0 1.0
CD E:LYS309 4.7 15.6 1.0
N E:ASN291 4.9 16.4 1.0
O4 E:G4S506 5.0 18.6 1.0
NH2 E:ARG81 5.0 18.3 1.0
NE2 E:HIS233 5.0 17.2 1.0

Calcium binding site 6 out of 6 in 6psm

Go back to Calcium Binding Sites List in 6psm
Calcium binding site 6 out of 6 in the Crystal Structure of PSS1_19B C77S in Complex with Kappa-Neocarrabiose


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 PSS1_19B C77S in Complex with Kappa-Neocarrabiose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca501

b:27.6
occ:0.90
 OD1 F:ASP37 2.2 20.9 1.0
OD1 F:ASP38 2.3 14.5 1.0
O8 F:G4S504 2.5 17.6 1.0
OD2 F:ASP290 2.5 18.7 1.0
OD1 F:ASN291 2.6 12.6 1.0
OD1 F:ASP290 2.9 16.7 1.0
CG F:ASP290 3.0 17.4 1.0
CG F:ASP38 3.3 14.4 1.0
CG F:ASN291 3.4 12.0 1.0
CG F:ASP37 3.4 19.8 1.0
ND2 F:ASN291 3.5 11.4 1.0
CB F:SER77 3.6 18.9 1.0
N F:ASP38 3.8 13.8 1.0
S F:G4S504 3.8 17.5 1.0
OD2 F:ASP38 3.9 15.9 1.0
CE F:LYS309 4.0 12.0 1.0
OD2 F:ASP37 4.1 20.7 1.0
NZ F:LYS309 4.1 13.0 1.0
CD2 F:HIS233 4.2 12.4 1.0
NZ F:LYS140 4.2 15.7 1.0
CB F:ASP38 4.2 14.4 1.0
CA F:SER77 4.3 16.8 1.0
O9 F:G4S504 4.3 17.3 1.0
CA F:ASP38 4.3 13.3 1.0
OG F:SER77 4.3 21.2 1.0
CA F:ASP37 4.4 15.8 1.0
C F:ASP37 4.4 15.1 1.0
N F:SER77 4.4 16.1 1.0
CB F:ASP37 4.4 17.0 1.0
CB F:ASP290 4.5 15.3 1.0
O7 F:G4S504 4.5 16.4 1.0
CB F:ASN291 4.8 11.4 1.0
CD F:LYS309 4.8 12.1 1.0
O4 F:G4S504 4.8 15.2 1.0
NE2 F:HIS233 4.9 11.1 1.0
NH2 F:ARG81 4.9 15.4 1.0

Reference:

A.G.Hettle, J.K.Hobbs, B.Pluvinage, C.Vickers, K.Abe, O.Salama-Alber, B.Mcguire, J.H.Hehemann, J.P.M.Hui, F.Berrue, A.Banskota, J.Zhang, E.Bottos, J.Van Hamme, A.B.Boraston. The Carrageenan Metabolism Pathway of Marine Pseudoalteromonas Species To Be Published.
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