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.
Page generated: Sat Dec 12 07:25:52 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy