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

Potassium in PDB 4udi: Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP)

Protein crystallography data

The structure of Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP), PDB code: 4udi 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) 110.20 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.116, 141.206, 176.245, 90.00, 90.00, 90.00
R / Rfree (%) 15.537 / 18.993

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) (pdb code 4udi). 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 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP), PDB code: 4udi:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 4udi

Go back to Potassium Binding Sites List in 4udi
Potassium binding site 1 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP)


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 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K333

b:50.8
occ:1.00
O A:HOH582 2.3 33.8 1.0
O A:HOH493 2.4 28.2 1.0
O A:HOH536 2.5 29.2 1.0
O A:TRP255 2.6 26.3 1.0
O A:HIS196 2.7 23.1 1.0
O A:VAL197 2.7 21.0 1.0
O A:HOH494 3.2 40.7 1.0
C A:VAL197 3.4 21.5 1.0
CA A:VAL197 3.5 21.2 1.0
C A:HIS196 3.7 22.5 1.0
C A:TRP255 3.7 26.8 1.0
O A:HOH546 4.0 45.3 1.0
N A:VAL197 4.0 20.9 1.0
ND1 A:HIS196 4.3 25.1 1.0
CA A:LYS256 4.4 26.1 1.0
N A:LYS256 4.5 25.6 1.0
N A:MET198 4.6 21.3 1.0
N A:VAL257 4.6 24.4 1.0
CB A:TRP255 4.6 28.0 1.0
CD1 A:TRP255 4.7 31.1 1.0
CA A:TRP255 4.7 26.0 1.0
CG2 A:VAL257 4.7 24.1 1.0
CB A:VAL197 4.8 21.0 1.0
CA A:HIS196 4.9 23.5 1.0

Potassium binding site 2 out of 6 in 4udi

Go back to Potassium Binding Sites List in 4udi
Potassium binding site 2 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP)


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 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K333

b:48.1
occ:1.00
O B:HOH536 2.4 30.7 1.0
O B:TRP255 2.5 25.4 1.0
O B:VAL197 2.6 20.2 1.0
O B:HOH493 2.6 25.7 1.0
O B:HIS196 2.8 21.5 1.0
C B:VAL197 3.4 21.1 1.0
O B:HOH494 3.5 35.6 1.0
CA B:VAL197 3.6 20.6 1.0
C B:TRP255 3.7 26.2 1.0
C B:HIS196 3.8 21.0 1.0
N B:VAL197 4.1 20.0 1.0
O B:HOH546 4.3 45.9 1.0
ND1 B:HIS196 4.4 24.0 1.0
N B:VAL257 4.4 25.4 1.0
CA B:LYS256 4.4 25.9 1.0
N B:LYS256 4.5 24.4 1.0
CG2 B:VAL257 4.5 25.7 1.0
N B:MET198 4.5 20.3 1.0
CA B:TRP255 4.7 25.4 1.0
CB B:TRP255 4.8 27.9 1.0
CB B:VAL197 4.9 20.2 1.0
CD1 B:TRP255 4.9 30.0 1.0
C B:LYS256 4.9 25.9 1.0
CG1 B:VAL197 5.0 21.0 1.0

Potassium binding site 3 out of 6 in 4udi

Go back to Potassium Binding Sites List in 4udi
Potassium binding site 3 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP)


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 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K333

b:50.9
occ:1.00
O C:HOH536 2.4 37.2 1.0
O C:TRP255 2.4 30.1 1.0
O C:HOH493 2.6 28.2 1.0
O C:VAL197 2.7 22.9 1.0
O C:HIS196 2.7 24.3 1.0
O C:HOH494 3.4 42.8 1.0
C C:VAL197 3.5 23.6 1.0
CA C:VAL197 3.6 22.2 1.0
C C:TRP255 3.6 29.8 1.0
C C:HIS196 3.7 23.4 1.0
O C:HOH546 3.9 42.8 1.0
N C:VAL197 4.1 21.9 1.0
CA C:LYS256 4.3 28.1 1.0
ND1 C:HIS196 4.3 27.0 1.0
N C:LYS256 4.4 27.5 1.0
N C:VAL257 4.4 26.6 1.0
CA C:TRP255 4.6 27.5 1.0
CG2 C:VAL257 4.6 26.6 1.0
N C:MET198 4.7 23.1 1.0
CB C:TRP255 4.7 28.5 1.0
CD1 C:TRP255 4.8 31.8 1.0
CB C:VAL197 4.9 21.3 1.0
C C:LYS256 4.9 28.2 1.0
CA C:HIS196 5.0 24.0 1.0

Potassium binding site 4 out of 6 in 4udi

Go back to Potassium Binding Sites List in 4udi
Potassium binding site 4 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP)


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 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K333

b:60.3
occ:1.00
O D:HOH536 2.4 36.8 1.0
O D:TRP255 2.5 33.1 1.0
O D:HOH493 2.7 33.9 1.0
O D:VAL197 2.8 28.3 1.0
O D:HIS196 2.9 26.2 1.0
O D:HOH494 3.4 41.5 1.0
C D:VAL197 3.6 27.6 1.0
C D:TRP255 3.7 34.6 1.0
CA D:VAL197 3.7 27.0 1.0
C D:HIS196 3.9 25.9 1.0
O D:HOH546 4.1 50.5 1.0
CA D:LYS256 4.2 35.2 1.0
O D:HOH540 4.2 48.1 1.0
N D:VAL197 4.3 25.6 1.0
N D:VAL257 4.3 32.4 1.0
N D:LYS256 4.4 34.0 1.0
ND1 D:HIS196 4.5 26.9 1.0
CG2 D:VAL257 4.6 32.0 1.0
CA D:TRP255 4.7 34.1 1.0
CB D:TRP255 4.7 34.0 1.0
N D:MET198 4.8 27.6 1.0
C D:LYS256 4.8 35.0 1.0
CD1 D:TRP255 4.8 34.6 1.0

Potassium binding site 5 out of 6 in 4udi

Go back to Potassium Binding Sites List in 4udi
Potassium binding site 5 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP)


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 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K333

b:61.8
occ:1.00
O E:TRP255 2.5 36.5 1.0
O E:HOH536 2.5 37.3 1.0
O E:HOH493 2.6 32.1 1.0
O E:VAL197 2.8 29.2 1.0
O E:HIS196 2.9 29.6 1.0
O E:HOH494 3.4 39.8 1.0
C E:TRP255 3.6 37.4 1.0
C E:VAL197 3.6 29.3 1.0
CA E:VAL197 3.8 27.8 1.0
C E:HIS196 3.9 28.5 1.0
CA E:LYS256 4.2 36.8 1.0
N E:VAL197 4.3 27.4 1.0
N E:LYS256 4.3 36.6 1.0
N E:VAL257 4.4 36.2 1.0
ND1 E:HIS196 4.5 28.9 1.0
CG2 E:VAL257 4.6 36.9 1.0
CA E:TRP255 4.6 35.9 1.0
CB E:TRP255 4.7 37.4 1.0
CD1 E:TRP255 4.7 38.0 1.0
N E:MET198 4.8 29.6 1.0
C E:LYS256 4.9 37.5 1.0

Potassium binding site 6 out of 6 in 4udi

Go back to Potassium Binding Sites List in 4udi
Potassium binding site 6 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP)


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 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K333

b:63.4
occ:1.00
O F:TRP255 2.4 36.2 1.0
O F:HOH536 2.5 37.9 1.0
O F:VAL197 2.7 27.8 1.0
O F:HOH493 2.7 31.2 1.0
O F:HIS196 2.8 27.4 1.0
O F:HOH494 3.4 41.7 1.0
C F:VAL197 3.5 29.1 1.0
C F:TRP255 3.5 36.8 1.0
CA F:VAL197 3.6 27.9 1.0
C F:HIS196 3.8 26.1 1.0
O F:HOH546 4.0 48.4 1.0
N F:VAL197 4.2 24.7 1.0
CA F:LYS256 4.2 36.0 1.0
N F:LYS256 4.3 33.4 1.0
N F:VAL257 4.3 33.5 1.0
ND1 F:HIS196 4.5 29.9 1.0
CA F:TRP255 4.5 34.7 1.0
CG2 F:VAL257 4.6 31.4 1.0
CB F:TRP255 4.6 35.8 1.0
N F:MET198 4.7 28.0 1.0
CD1 F:TRP255 4.7 35.5 1.0
C F:LYS256 4.8 36.3 1.0
CB F:VAL197 4.9 28.1 1.0
CG1 F:VAL197 5.0 29.8 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

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