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Potassium in PDB 4udg: Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with N- Acetylglucosamine and Inorganic Phosphate

Protein crystallography data

The structure of Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with N- Acetylglucosamine and Inorganic Phosphate, PDB code: 4udg was solved by S.Ladeveze, G.Cioci, G.Potocki-Veronese, S.Tranier, L.Mourey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 108.12 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.816, 140.912, 168.598, 90.00, 90.00, 90.00
R / Rfree (%) 15.361 / 18.297

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with N- Acetylglucosamine and Inorganic Phosphate (pdb code 4udg). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with N- Acetylglucosamine and Inorganic Phosphate, PDB code: 4udg:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 4udg

Go back to Potassium Binding Sites List in 4udg
Potassium binding site 1 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with N- Acetylglucosamine and Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with N- Acetylglucosamine and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K333

b:54.0
occ:1.00
 O A:TRP255 2.6 20.2 1.0
O A:HOH493 2.7 29.2 1.0
O A:HOH536 2.8 27.7 1.0
O A:VAL197 2.9 16.0 1.0
O A:HIS196 3.0 16.3 1.0
O A:HOH494 3.2 28.6 1.0
O A:HOH546 3.6 26.9 1.0
C A:VAL197 3.7 16.2 1.0
C A:TRP255 3.8 19.4 1.0
CA A:VAL197 3.9 14.4 1.0
C A:HIS196 4.0 14.5 1.0
N A:VAL197 4.4 14.8 1.0
CA A:LYS256 4.4 17.2 1.0
ND1 A:HIS196 4.5 17.6 1.0
N A:LYS256 4.5 17.4 1.0
CD1 A:TRP255 4.6 25.9 1.0
N A:VAL257 4.6 17.1 1.0
CB A:TRP255 4.6 20.3 1.0
CG2 A:VAL257 4.7 19.4 1.0
CA A:TRP255 4.7 18.2 1.0
N A:MET198 4.9 15.9 1.0

Potassium binding site 2 out of 6 in 4udg

Go back to Potassium Binding Sites List in 4udg
Potassium binding site 2 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with N- Acetylglucosamine and Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with N- Acetylglucosamine and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K333

b:53.0
occ:1.00
 O B:TRP255 2.6 19.4 1.0
O B:HOH536 2.7 32.9 1.0
O B:VAL197 2.8 16.1 1.0
O B:HOH493 2.8 27.6 1.0
O B:HIS196 2.9 15.4 1.0
O B:HOH494 3.1 31.9 1.0
C B:VAL197 3.6 15.7 1.0
CA B:VAL197 3.7 14.7 1.0
C B:TRP255 3.7 18.7 1.0
C B:HIS196 3.9 14.6 1.0
O B:HOH546 3.9 37.4 1.0
N B:VAL197 4.2 13.9 1.0
O B:HOH665 4.3 53.8 1.0
CA B:LYS256 4.4 18.6 1.0
N B:VAL257 4.5 18.9 1.0
ND1 B:HIS196 4.5 17.2 1.0
N B:LYS256 4.5 17.7 1.0
CG2 B:VAL257 4.5 21.0 1.0
CD1 B:TRP255 4.8 21.2 1.0
CA B:TRP255 4.8 19.2 1.0
N B:MET198 4.8 15.6 1.0
CB B:TRP255 4.9 20.1 1.0
C B:LYS256 5.0 18.9 1.0
CB B:VAL197 5.0 14.1 1.0

Potassium binding site 3 out of 6 in 4udg

Go back to Potassium Binding Sites List in 4udg
Potassium binding site 3 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with N- Acetylglucosamine and Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with N- Acetylglucosamine and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K333

b:60.0
occ:1.00
 O C:TRP255 2.6 19.6 1.0
O C:HOH536 2.7 30.6 1.0
O C:VAL197 2.8 14.8 1.0
O C:HOH493 2.9 25.9 1.0
O C:HIS196 3.0 15.7 1.0
O C:HOH494 3.2 29.1 1.0
C C:VAL197 3.6 15.5 1.0
O C:HOH546 3.6 30.9 1.0
CA C:VAL197 3.8 13.8 1.0
C C:TRP255 3.8 18.1 1.0
C C:HIS196 4.0 13.7 1.0
N C:VAL197 4.3 13.0 1.0
CA C:LYS256 4.3 17.9 1.0
N C:VAL257 4.4 17.9 1.0
N C:LYS256 4.5 15.5 1.0
CG2 C:VAL257 4.5 19.8 1.0
ND1 C:HIS196 4.6 16.9 1.0
N C:MET198 4.8 16.2 1.0
CA C:TRP255 4.9 18.0 1.0
C C:LYS256 4.9 17.1 1.0
CD1 C:TRP255 4.9 19.0 1.0
CB C:TRP255 4.9 19.2 1.0

Potassium binding site 4 out of 6 in 4udg

Go back to Potassium Binding Sites List in 4udg
Potassium binding site 4 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with N- Acetylglucosamine and Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with N- Acetylglucosamine and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K333

b:58.5
occ:1.00
 O D:HOH536 2.5 31.1 1.0
O D:TRP255 2.7 23.1 1.0
O D:HOH493 2.9 31.5 1.0
O D:HOH494 3.1 32.0 1.0
O D:VAL197 3.2 19.8 1.0
O D:HIS196 3.2 17.0 1.0
O D:HOH546 3.7 38.3 1.0
C D:TRP255 3.8 24.6 1.0
C D:VAL197 4.0 18.7 1.0
CA D:VAL197 4.1 17.0 1.0
C D:HIS196 4.2 16.6 1.0
CA D:LYS256 4.3 22.5 1.0
N D:LYS256 4.5 21.0 1.0
N D:VAL257 4.5 21.0 0.5
N D:VAL257 4.5 23.8 0.5
N D:VAL197 4.6 15.9 1.0
ND1 D:HIS196 4.7 19.8 1.0
CD1 D:TRP255 4.7 24.2 1.0
CG2 D:VAL257 4.8 16.9 0.5
CA D:TRP255 4.9 23.0 1.0
CB D:TRP255 4.9 24.1 1.0
C D:LYS256 4.9 22.0 1.0
CG1 D:VAL257 5.0 30.2 0.5

Potassium binding site 5 out of 6 in 4udg

Go back to Potassium Binding Sites List in 4udg
Potassium binding site 5 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with N- Acetylglucosamine and Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with N- Acetylglucosamine and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K333

b:51.5
occ:1.00
 O E:TRP255 2.5 22.7 1.0
O E:HOH536 2.7 28.0 1.0
O E:HOH493 2.9 29.1 1.0
O E:VAL197 2.9 18.0 1.0
O E:HIS196 3.0 15.5 1.0
O E:HOH494 3.2 28.1 1.0
C E:TRP255 3.6 20.4 1.0
C E:VAL197 3.7 16.9 1.0
CA E:VAL197 3.8 15.5 1.0
C E:HIS196 4.0 13.9 1.0
CA E:LYS256 4.3 19.7 1.0
N E:VAL197 4.3 14.4 1.0
N E:LYS256 4.4 18.8 1.0
N E:VAL257 4.5 19.2 1.0
ND1 E:HIS196 4.5 16.7 1.0
CD1 E:TRP255 4.6 20.6 1.0
CG2 E:VAL257 4.7 22.2 1.0
CA E:TRP255 4.7 20.7 1.0
CB E:TRP255 4.7 20.4 1.0
C E:LYS256 4.9 20.9 1.0
N E:MET198 5.0 16.5 1.0

Potassium binding site 6 out of 6 in 4udg

Go back to Potassium Binding Sites List in 4udg
Potassium binding site 6 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with N- Acetylglucosamine and Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with N- Acetylglucosamine and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K333

b:62.0
occ:1.00
 O F:HOH536 2.6 28.1 1.0
O F:HOH493 2.8 29.9 1.0
O F:TRP255 2.8 23.4 1.0
O F:VAL197 3.0 18.6 1.0
O F:HOH494 3.1 33.1 1.0
O F:HIS196 3.2 18.8 1.0
O F:HOH546 3.7 35.3 1.0
C F:VAL197 3.8 19.2 1.0
C F:TRP255 3.9 21.5 1.0
CA F:VAL197 4.0 17.9 1.0
C F:HIS196 4.1 18.4 1.0
CA F:LYS256 4.4 22.8 1.0
N F:VAL197 4.5 16.8 1.0
N F:VAL257 4.5 22.4 1.0
ND1 F:HIS196 4.6 20.1 1.0
N F:LYS256 4.6 19.6 1.0
CD1 F:TRP255 4.8 22.1 1.0
CG2 F:VAL257 4.8 21.4 1.0
CA F:TRP255 5.0 21.3 1.0
CB F:TRP255 5.0 22.3 1.0

Reference:

S.Ladeveze, G.Cioci, P.Roblin, L.Mourey, S.Tranier, G.Potocki-Veronese. Structural Bases For N-Glycan Processing By Mannoside Phosphorylase Acta Crystallogr.,Sect.D V. 71 1 2015.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004715006604
Page generated: Sun Dec 13 23:50:00 2020

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