Atomistry » Potassium » PDB 4toh-4wol » 4udj
Atomistry »
  Potassium »
    PDB 4toh-4wol »
      4udj »

Potassium in PDB 4udj: Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose 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 Beta-D- Mannopyranose and Inorganic Phosphate, PDB code: 4udj 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) 108.13 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.880, 140.840, 168.750, 90.00, 90.00, 90.00
R / Rfree (%) 14.955 / 19.333

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 Beta-D- Mannopyranose and Inorganic Phosphate (pdb code 4udj). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate, PDB code: 4udj:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 4udj

Go back to Potassium Binding Sites List in 4udj
Potassium binding site 1 out of 8 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose 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 Beta-D- Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K333

b:61.1
occ:1.00
 O A:HOH493 2.7 23.4 1.0
O A:TRP255 2.7 16.2 1.0
O A:HOH536 2.8 26.3 1.0
O A:VAL197 2.9 12.4 1.0
O A:HIS196 3.1 12.5 1.0
O A:HOH494 3.3 25.1 1.0
O A:HOH546 3.5 21.4 1.0
C A:VAL197 3.7 13.4 1.0
CA A:VAL197 3.9 12.6 1.0
C A:TRP255 3.9 16.0 1.0
C A:HIS196 4.0 12.6 1.0
N A:VAL197 4.3 12.6 1.0
ND1 A:HIS196 4.4 15.0 1.0
CA A:LYS256 4.6 16.1 1.0
CG2 A:VAL257 4.6 15.7 1.0
N A:VAL257 4.7 15.0 1.0
N A:LYS256 4.7 15.5 1.0
CD1 A:TRP255 4.8 19.4 1.0
CB A:TRP255 4.8 17.5 1.0
N A:MET198 4.8 13.6 1.0
CA A:TRP255 4.8 16.3 1.0

Potassium binding site 2 out of 8 in 4udj

Go back to Potassium Binding Sites List in 4udj
Potassium binding site 2 out of 8 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose 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 Beta-D- Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K606

b:36.4
occ:1.00
 O A:HOH609 2.6 12.5 1.0
OD2 A:ASP277 2.6 13.9 1.0
OG A:SER41 2.7 9.2 1.0
O A:ASP304 2.7 10.4 1.0
CB A:SER41 3.4 9.8 1.0
CG A:ASP277 3.5 14.7 1.0
CB A:ASP277 3.5 13.7 1.0
CE1 A:PHE43 3.6 12.7 0.5
ND2 A:ASN40 3.6 10.1 1.0
NH2 A:ARG65 3.6 12.7 1.0
CE1 A:PHE43 3.7 10.9 0.5
C A:ASP304 3.9 10.6 1.0
CZ A:PHE43 3.9 12.2 0.5
CZ A:PHE43 3.9 10.6 0.5
CZ A:ARG65 4.1 13.0 1.0
CB A:ASP304 4.2 11.6 1.0
CD1 A:PHE43 4.3 12.5 0.5
OD2 A:ASP61 4.3 9.3 1.0
NE A:ARG65 4.3 12.4 1.0
O A:HOH457 4.4 14.1 1.0
CD1 A:PHE43 4.5 10.8 0.5
CB A:ASP61 4.7 9.3 1.0
OD1 A:ASP277 4.7 17.3 1.0
CA A:ASP304 4.7 10.9 1.0
CG A:ASP61 4.8 9.2 1.0
O A:HOH375 4.8 8.2 1.0
NH1 A:ARG65 4.8 12.9 1.0
CA A:SER41 4.9 9.9 1.0
N A:THR305 4.9 10.2 1.0
CG A:ASN40 4.9 10.4 1.0
CE2 A:PHE43 4.9 10.3 0.5
CE2 A:PHE43 4.9 11.9 0.5
CA A:THR305 5.0 10.7 1.0

Potassium binding site 3 out of 8 in 4udj

Go back to Potassium Binding Sites List in 4udj
Potassium binding site 3 out of 8 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose 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 Beta-D- Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K607

b:44.6
occ:1.00
 OD2 F:ASP277 2.5 23.8 1.0
O F:HOH587 2.6 21.4 1.0
O F:ASP304 2.7 16.8 1.0
OG F:SER41 2.8 17.7 1.0
CG F:ASP277 3.4 24.5 1.0
CB F:SER41 3.5 18.7 1.0
CB F:ASP277 3.5 21.3 1.0
NH2 F:ARG65 3.5 16.0 1.0
ND2 F:ASN40 3.7 18.4 1.0
CE1 F:PHE43 3.7 16.3 0.5
CE1 F:PHE43 3.7 17.5 0.5
C F:ASP304 3.9 17.4 1.0
CZ F:PHE43 4.0 17.3 0.5
CZ F:ARG65 4.0 15.9 1.0
CZ F:PHE43 4.1 16.0 0.5
CB F:ASP304 4.2 16.4 1.0
O F:HOH457 4.2 20.6 1.0
OD2 F:ASP61 4.3 19.1 1.0
NE F:ARG65 4.3 15.5 1.0
CD1 F:PHE43 4.4 16.1 0.5
CD1 F:PHE43 4.5 17.4 0.5
OD1 F:ASP277 4.6 25.7 1.0
CA F:ASP304 4.7 17.1 1.0
CB F:ASP61 4.8 19.1 1.0
NH1 F:ARG65 4.8 16.0 1.0
O F:HOH375 4.8 13.5 1.0
CG F:ASP61 4.9 18.6 1.0
N F:THR305 4.9 17.9 1.0
CA F:SER41 4.9 18.4 1.0
CA F:THR305 5.0 18.5 1.0
CA F:ASP277 5.0 21.5 1.0
CG F:ASN40 5.0 17.9 1.0

Potassium binding site 4 out of 8 in 4udj

Go back to Potassium Binding Sites List in 4udj
Potassium binding site 4 out of 8 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose 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 Beta-D- Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K333

b:61.2
occ:1.00
 O B:TRP255 2.7 16.2 1.0
O B:HOH493 2.8 24.4 1.0
O B:HOH536 2.8 25.8 1.0
O B:HIS196 2.9 12.8 1.0
O B:VAL197 3.0 12.4 1.0
O B:HOH494 3.1 22.7 1.0
C B:VAL197 3.7 12.9 1.0
CA B:VAL197 3.8 12.4 1.0
C B:TRP255 3.8 15.9 1.0
C B:HIS196 3.9 12.6 1.0
O B:HOH546 4.0 36.7 1.0
N B:VAL197 4.3 11.8 1.0
CA B:LYS256 4.3 17.2 1.0
N B:LYS256 4.5 15.8 1.0
ND1 B:HIS196 4.5 14.0 1.0
N B:VAL257 4.5 16.5 1.0
CD1 B:TRP255 4.7 18.2 1.0
CG2 B:VAL257 4.7 18.7 1.0
CA B:TRP255 4.8 15.4 1.0
CB B:TRP255 4.8 16.8 1.0
N B:MET198 4.9 13.7 1.0
C B:LYS256 5.0 17.3 1.0

Potassium binding site 5 out of 8 in 4udj

Go back to Potassium Binding Sites List in 4udj
Potassium binding site 5 out of 8 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose 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 Beta-D- Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K333

b:60.7
occ:1.00
 O C:TRP255 2.6 14.8 1.0
O C:HOH536 2.8 24.7 1.0
O C:VAL197 2.9 10.7 1.0
O C:HOH493 2.9 18.1 1.0
O C:HIS196 3.0 10.6 1.0
O C:HOH494 3.4 23.0 1.0
C C:VAL197 3.6 11.4 1.0
O C:HOH546 3.6 27.2 1.0
CA C:VAL197 3.7 10.5 1.0
C C:TRP255 3.8 15.0 1.0
C C:HIS196 3.9 10.5 1.0
N C:VAL197 4.2 10.0 1.0
CA C:LYS256 4.3 14.6 1.0
N C:VAL257 4.5 14.8 1.0
ND1 C:HIS196 4.5 11.9 1.0
N C:LYS256 4.5 13.9 1.0
CG2 C:VAL257 4.6 16.9 1.0
CD1 C:TRP255 4.8 16.0 1.0
CA C:TRP255 4.8 14.3 1.0
N C:MET198 4.8 11.9 1.0
CB C:TRP255 4.9 15.2 1.0
C C:LYS256 4.9 14.5 1.0
CB C:VAL197 5.0 10.6 1.0

Potassium binding site 6 out of 8 in 4udj

Go back to Potassium Binding Sites List in 4udj
Potassium binding site 6 out of 8 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose 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 Beta-D- Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K333

b:56.7
occ:1.00
 O D:HOH536 2.5 27.5 1.0
O D:TRP255 2.7 20.1 1.0
O D:HOH493 2.9 25.9 1.0
O D:HIS196 3.2 13.9 1.0
O D:HOH494 3.2 24.5 1.0
O D:VAL197 3.3 15.4 1.0
C D:TRP255 3.9 19.6 1.0
C D:VAL197 4.0 16.0 1.0
CA D:VAL197 4.2 14.8 1.0
C D:HIS196 4.2 14.2 1.0
CA D:LYS256 4.3 19.5 1.0
N D:VAL257 4.5 18.5 1.0
N D:LYS256 4.5 18.7 1.0
CD1 D:TRP255 4.6 20.7 1.0
ND1 D:HIS196 4.6 17.4 1.0
N D:VAL197 4.7 14.0 1.0
CG2 D:VAL257 4.7 18.3 1.0
CB D:TRP255 4.9 21.2 1.0
CA D:TRP255 4.9 20.0 1.0
C D:LYS256 4.9 19.2 1.0

Potassium binding site 7 out of 8 in 4udj

Go back to Potassium Binding Sites List in 4udj
Potassium binding site 7 out of 8 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K333

b:57.4
occ:1.00
 O E:TRP255 2.6 18.0 1.0
O E:HOH536 2.6 27.4 1.0
O E:HOH493 3.1 24.0 1.0
O E:VAL197 3.1 13.6 1.0
O E:HOH494 3.1 18.4 1.0
O E:HIS196 3.2 12.1 1.0
C E:TRP255 3.7 18.7 1.0
O E:HOH597 3.8 31.1 1.0
C E:VAL197 3.9 13.6 1.0
CA E:VAL197 4.0 13.1 1.0
C E:HIS196 4.1 12.3 1.0
CA E:LYS256 4.2 18.7 1.0
N E:LYS256 4.4 18.1 1.0
N E:VAL257 4.4 19.2 1.0
CD1 E:TRP255 4.5 19.1 1.0
N E:VAL197 4.5 12.2 1.0
CB E:TRP255 4.7 17.9 1.0
CG2 E:VAL257 4.7 21.3 1.0
CA E:TRP255 4.7 18.5 1.0
ND1 E:HIS196 4.7 14.7 1.0
C E:LYS256 4.8 19.4 1.0

Potassium binding site 8 out of 8 in 4udj

Go back to Potassium Binding Sites List in 4udj
Potassium binding site 8 out of 8 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K333

b:64.1
occ:1.00
 O F:HOH536 2.7 24.4 1.0
O F:TRP255 2.7 19.0 1.0
O F:HOH493 2.7 19.0 1.0
O F:VAL197 3.0 17.1 1.0
O F:HIS196 3.1 14.7 1.0
O F:HOH494 3.3 27.1 1.0
C F:VAL197 3.8 17.5 1.0
C F:TRP255 3.8 19.1 1.0
CA F:VAL197 3.9 16.6 1.0
C F:HIS196 4.1 15.4 1.0
CA F:LYS256 4.3 20.6 1.0
N F:VAL197 4.5 15.0 1.0
N F:LYS256 4.5 19.0 1.0
ND1 F:HIS196 4.5 19.0 1.0
N F:VAL257 4.5 19.8 1.0
CD1 F:TRP255 4.7 17.8 1.0
CG2 F:VAL257 4.7 18.4 1.0
CA F:TRP255 4.8 18.4 1.0
CB F:TRP255 4.9 19.2 1.0
C F:LYS256 4.9 20.4 1.0
N F:MET198 5.0 16.4 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: Mon Aug 12 12:14:47 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy