Zinc 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
Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of PSS1_19B C77S in Complex with Kappa-Neocarrabiose, PDB code: 6psm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6psm

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Zinc 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 Zinc with other atoms in the Zn 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:Zn505

b:22.6
occ:1.00
O A:HOH618 1.9 17.8 1.0
OD1 A:ASP280 2.1 22.2 1.0
O A:HOH602 2.1 22.5 1.0
CG A:ASP280 2.8 21.6 1.0
OD2 A:ASP280 3.0 24.7 1.0
ZN A:ZN506 3.3 23.3 1.0
OD1 A:ASP281 3.7 19.2 1.0
O A:LYS275 4.2 24.1 1.0
CG A:ASP281 4.2 18.0 1.0
O A:HOH729 4.3 22.8 1.0
CB A:ASP280 4.3 20.0 1.0
CA A:LYS275 4.4 25.3 1.0
OD2 A:ASP281 4.5 20.1 1.0
N A:ASP281 4.5 18.0 1.0
N A:ASP280 4.5 17.8 1.0
CA A:GLY278 4.6 18.2 1.0
CG A:LYS275 4.8 32.7 1.0
CA A:ASP280 4.8 17.7 1.0
C A:LYS275 4.8 26.4 1.0
C A:GLY278 4.9 19.0 1.0
CB A:LYS275 5.0 28.0 1.0
C A:ASP280 5.0 18.2 1.0

Zinc binding site 2 out of 6 in 6psm

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Zinc 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 Zinc with other atoms in the Zn 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
A:Zn506

b:23.3
occ:1.00
OD1 A:ASP281 2.0 19.2 1.0
O A:HOH618 2.0 17.8 1.0
CG A:ASP281 3.0 18.0 1.0
ZN A:ZN505 3.3 22.6 1.0
OD2 A:ASP281 3.3 20.1 1.0
OD2 A:ASP280 3.7 24.7 1.0
O A:HOH737 4.1 20.1 1.0
CB A:ASP281 4.3 18.7 1.0
CG A:ASP280 4.4 21.6 1.0
OD1 A:ASP280 4.5 22.2 1.0
CA A:ASP281 4.6 17.8 1.0
N A:ASP281 4.7 18.0 1.0
CB A:PRO326 4.8 18.4 1.0

Zinc binding site 3 out of 6 in 6psm

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Zinc 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 Zinc with other atoms in the Zn 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
D:Zn503

b:20.7
occ:1.00
O D:HOH642 1.9 17.4 1.0
OD1 D:ASP280 2.1 20.9 1.0
CG D:ASP280 2.9 21.0 1.0
OD2 D:ASP280 3.1 22.3 1.0
ZN D:ZN504 3.3 22.6 1.0
O D:HOH714 3.7 30.8 1.0
OD1 D:ASP281 3.8 19.5 1.0
O D:LYS275 4.2 22.6 1.0
CB D:ASP280 4.3 20.8 1.0
CG D:ASP281 4.3 20.4 1.0
CA D:GLY278 4.4 17.2 1.0
CA D:LYS275 4.4 22.5 1.0
N D:ASP281 4.4 18.3 1.0
N D:ASP280 4.5 20.4 1.0
OD2 D:ASP281 4.7 20.6 1.0
CA D:ASP280 4.8 19.8 1.0
C D:GLY278 4.8 18.6 1.0
C D:LYS275 4.8 23.5 1.0
CG D:LYS275 4.9 23.7 1.0
C D:ASP280 5.0 18.1 1.0
N D:LEU279 5.0 18.7 1.0

Zinc binding site 4 out of 6 in 6psm

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Zinc 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 Zinc with other atoms in the Zn 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:Zn504

b:22.6
occ:1.00
OD1 D:ASP281 1.9 19.5 1.0
CG D:ASP281 2.9 20.4 1.0
OD2 D:ASP281 3.2 20.6 1.0
ZN D:ZN503 3.3 20.7 1.0
OD2 D:ASP280 3.7 22.3 1.0
O D:HOH714 3.9 30.8 1.0
CB D:ASP281 4.3 20.5 1.0
CG D:ASP280 4.4 21.0 1.0
OD1 D:ASP280 4.5 20.9 1.0
CA D:ASP281 4.6 19.1 1.0
N D:ASP281 4.7 18.3 1.0
CB D:PRO326 4.9 15.6 1.0
O D:HOH642 4.9 17.4 1.0

Zinc binding site 5 out of 6 in 6psm

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Zinc 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 Zinc with other atoms in the Zn 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:Zn503

b:22.6
occ:1.00
O E:HOH655 2.0 22.9 1.0
OD1 E:ASP280 2.1 19.7 1.0
CG E:ASP280 2.9 19.8 1.0
OD2 E:ASP280 3.1 20.2 1.0
ZN E:ZN504 3.3 21.6 1.0
OD1 E:ASP281 3.8 19.7 1.0
O E:LYS275 4.2 20.1 1.0
CG E:ASP281 4.3 18.9 1.0
CB E:ASP280 4.3 18.5 1.0
CA E:GLY278 4.4 18.9 1.0
CA E:LYS275 4.5 24.0 1.0
N E:ASP281 4.5 18.8 1.0
N E:ASP280 4.5 18.1 1.0
OD2 E:ASP281 4.6 18.0 1.0
C E:GLY278 4.8 18.8 1.0
CA E:ASP280 4.8 19.4 1.0
CG E:LYS275 4.8 31.6 1.0
C E:LYS275 4.8 22.9 1.0

Zinc binding site 6 out of 6 in 6psm

Go back to Zinc Binding Sites List in 6psm
Zinc 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 Zinc with other atoms in the Zn 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
E:Zn504

b:21.6
occ:1.00
OD1 E:ASP281 1.9 19.7 1.0
CG E:ASP281 2.9 18.9 1.0
OD2 E:ASP281 3.2 18.0 1.0
ZN E:ZN503 3.3 22.6 1.0
OD2 E:ASP280 3.7 20.2 1.0
O E:HOH742 4.2 20.7 1.0
CB E:ASP281 4.2 18.8 1.0
CG E:ASP280 4.4 19.8 1.0
OD1 E:ASP280 4.4 19.7 1.0
CA E:ASP281 4.6 18.9 1.0
N E:ASP281 4.7 18.8 1.0
CB E:PRO326 4.9 16.7 1.0
O E:HOH655 5.0 22.9 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: Wed Dec 16 12:32:10 2020

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