Atomistry » Sodium » PDB 3iwf-3k93 » 3k1s
Atomistry »
  Sodium »
    PDB 3iwf-3k93 »
      3k1s »

Sodium in PDB 3k1s: Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis

Protein crystallography data

The structure of Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis, PDB code: 3k1s was solved by S.M.Anderson, Z.Wawrzak, O.Onopriyenko, K.Kwon, W.F.Anderson, A.Savchenko, Center For Structural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.75 / 2.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 92.887, 92.887, 260.639, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.6

Other elements in 3k1s:

The structure of Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis (pdb code 3k1s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis, PDB code: 3k1s:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in 3k1s

Go back to Sodium Binding Sites List in 3k1s
Sodium binding site 1 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na107

b:48.2
occ:1.00
OH A:TYR99 2.2 41.6 1.0
O C:GLU94 2.6 29.8 1.0
CZ A:TYR99 3.2 30.3 1.0
OE1 C:GLU94 3.3 34.8 1.0
C C:GLU94 3.4 28.3 1.0
CE2 A:TYR99 3.5 28.4 1.0
CA C:GLU94 3.6 27.4 1.0
CG C:LEU98 3.7 35.7 1.0
CB C:GLU94 3.7 26.9 1.0
CE A:LYS31 3.8 33.2 1.0
CB C:ASP97 3.8 37.9 1.0
N C:LEU98 3.9 33.8 1.0
CD1 C:LEU98 4.2 39.1 1.0
NZ A:LYS31 4.3 38.8 1.0
CB C:LEU98 4.3 34.8 1.0
CD C:GLU94 4.3 31.2 1.0
CE1 A:TYR99 4.4 37.6 1.0
CA C:LEU98 4.5 34.1 1.0
C C:ASP97 4.5 35.6 1.0
CD2 C:LEU98 4.6 33.0 1.0
CD1 A:PHE95 4.6 29.3 1.0
CG C:GLU94 4.6 25.5 1.0
N C:PHE95 4.6 27.1 1.0
CA C:ASP97 4.7 36.5 1.0
CD A:LYS31 4.7 42.6 1.0
CG A:LYS31 4.8 41.9 1.0
CE1 A:PHE95 4.8 31.7 1.0
CD2 A:LEU27 4.9 37.0 1.0
CD2 A:TYR99 4.9 31.6 1.0
OD2 C:ASP97 4.9 46.5 1.0
CG C:ASP97 5.0 43.4 1.0

Sodium binding site 2 out of 14 in 3k1s

Go back to Sodium Binding Sites List in 3k1s
Sodium binding site 2 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na108

b:55.3
occ:1.00
OE1 A:GLU47 1.9 32.2 0.5
NE2 E:GLN32 2.8 53.6 1.0
CD A:GLU47 3.0 29.9 0.5
ND2 A:ASN50 3.1 29.8 1.0
O A:HOH353 3.2 26.6 1.0
CB A:ASN50 3.4 22.7 1.0
CG E:GLN28 3.5 52.4 1.0
OE2 A:GLU47 3.6 38.7 0.5
NE2 E:GLN28 3.7 56.1 1.0
CG A:ASN50 3.8 26.7 1.0
CD E:GLN32 3.9 58.8 1.0
O A:GLU47 4.0 27.7 1.0
CA A:GLU47 4.0 24.9 0.5
CA A:GLU47 4.0 24.8 0.5
CD E:GLN28 4.1 59.4 1.0
CG A:GLU47 4.1 25.8 0.5
CB A:GLU47 4.2 26.6 0.5
CG A:GLU47 4.2 25.5 0.5
CB A:GLU47 4.3 26.4 0.5
O E:HOH407 4.4 57.5 1.0
C A:GLU47 4.5 25.6 1.0
OE1 E:GLN32 4.6 61.9 1.0
OE2 A:GLU51 4.7 28.2 1.0
CA A:ASN50 4.8 24.8 1.0
CB E:GLN28 4.9 40.8 1.0
CG E:GLN32 4.9 54.9 1.0
OD1 A:ASN50 5.0 26.1 1.0

Sodium binding site 3 out of 14 in 3k1s

Go back to Sodium Binding Sites List in 3k1s
Sodium binding site 3 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na109

b:60.3
occ:1.00
OE2 A:GLU63 2.3 40.1 1.0
CD A:GLU63 3.0 44.2 1.0
N A:THR69 3.1 46.1 1.0
CG A:GLU63 3.2 37.8 1.0
CD A:LYS68 3.3 64.2 1.0
NZ A:LYS68 3.3 60.2 1.0
CA A:LYS68 3.7 49.8 1.0
CE A:LYS68 3.7 65.1 1.0
C A:LYS68 3.9 48.1 1.0
O A:HOH378 4.0 40.6 1.0
CB A:THR69 4.0 44.4 1.0
CA A:THR69 4.0 44.3 1.0
O A:THR69 4.1 41.8 1.0
OE1 A:GLU63 4.2 38.2 1.0
CB A:GLU63 4.2 32.3 1.0
CG A:LYS68 4.2 56.1 1.0
CB B:SER72 4.3 23.8 1.0
CA B:SER72 4.3 24.5 1.0
O A:GLU67 4.4 49.0 1.0
CB A:LYS68 4.4 50.6 1.0
N B:VAL73 4.5 23.4 1.0
C A:THR69 4.6 43.2 1.0
OG1 A:THR69 4.7 45.0 1.0
N A:LYS68 4.7 49.7 1.0
CA A:GLU63 4.8 33.4 1.0
O B:ILE71 4.8 29.1 1.0
O A:HOH134 4.9 42.0 1.0
C A:GLU67 5.0 47.9 1.0

Sodium binding site 4 out of 14 in 3k1s

Go back to Sodium Binding Sites List in 3k1s
Sodium binding site 4 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na108

b:35.1
occ:1.00
OH B:TYR99 2.3 28.5 1.0
OE1 A:GLU94 2.7 34.2 1.0
O A:GLU94 2.7 27.5 1.0
CE B:LYS31 3.3 27.2 1.0
CZ B:TYR99 3.4 32.6 1.0
C A:GLU94 3.5 26.4 1.0
CA A:GLU94 3.6 25.9 1.0
CE2 B:TYR99 3.6 27.8 1.0
CB A:GLU94 3.7 25.9 1.0
CD A:GLU94 3.8 36.1 1.0
NZ B:LYS31 3.8 26.6 1.0
CB A:ASP97 3.8 33.9 1.0
N A:LEU98 3.9 32.7 1.0
CD2 B:LEU27 3.9 24.8 1.0
CD1 B:PHE95 4.2 32.5 1.0
CB A:LEU98 4.2 32.6 1.0
CG A:GLU94 4.3 27.1 1.0
CE1 B:PHE95 4.4 27.6 1.0
CA A:LEU98 4.4 32.6 1.0
C A:ASP97 4.5 33.8 1.0
O B:HOH478 4.5 79.9 1.0
CD B:LYS31 4.6 35.8 1.0
CE1 B:TYR99 4.6 35.6 1.0
CA A:ASP97 4.6 33.0 1.0
N A:PHE95 4.8 25.8 1.0
OE2 A:GLU94 4.8 35.3 1.0
CG B:LYS31 4.9 36.8 1.0
N A:GLU94 4.9 24.9 1.0
CG B:PHE95 4.9 26.0 1.0
N A:ASP97 5.0 30.0 1.0
CD2 B:TYR99 5.0 29.5 1.0
CG A:ASP97 5.0 44.3 1.0

Sodium binding site 5 out of 14 in 3k1s

Go back to Sodium Binding Sites List in 3k1s
Sodium binding site 5 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na107

b:35.1
occ:1.00
OH C:TYR99 2.3 30.9 1.0
O B:GLU94 2.8 30.7 1.0
OE1 B:GLU94 2.9 30.6 1.0
CZ C:TYR99 3.3 32.2 1.0
CE C:LYS31 3.4 38.5 1.0
CE2 C:TYR99 3.4 30.1 1.0
CB B:GLU94 3.5 26.8 1.0
C B:GLU94 3.5 27.7 1.0
CA B:GLU94 3.6 27.4 1.0
NZ C:LYS31 3.7 33.2 1.0
CD2 C:LEU27 3.9 32.2 1.0
CD B:GLU94 3.9 35.1 1.0
CB B:ASP97 4.1 38.0 1.0
N B:LEU98 4.1 34.8 1.0
CD1 C:PHE95 4.2 29.1 1.0
CG B:GLU94 4.2 29.1 1.0
CB B:LEU98 4.3 33.2 1.0
CE1 C:PHE95 4.3 36.0 1.0
CA B:LEU98 4.6 35.3 1.0
CE1 C:TYR99 4.6 32.6 1.0
OD2 B:ASP97 4.6 48.0 1.0
CD C:LYS31 4.7 38.4 1.0
C B:ASP97 4.7 37.1 1.0
N B:PHE95 4.8 28.2 1.0
CD2 C:TYR99 4.8 34.2 1.0
CA B:ASP97 4.9 36.7 1.0
CG B:ASP97 4.9 45.2 1.0
CG C:PHE95 4.9 26.5 1.0
CD1 C:LEU27 4.9 31.3 1.0
CD1 B:LEU98 5.0 39.5 1.0
N B:GLU94 5.0 27.2 1.0

Sodium binding site 6 out of 14 in 3k1s

Go back to Sodium Binding Sites List in 3k1s
Sodium binding site 6 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na107

b:55.0
occ:1.00
OE1 D:GLU94 2.5 49.2 1.0
OH E:TYR99 2.7 47.5 1.0
O D:GLU94 3.0 33.0 1.0
CB D:GLU94 3.2 33.1 1.0
CA D:GLU94 3.4 31.6 1.0
CE2 E:TYR99 3.4 40.1 1.0
CD D:GLU94 3.5 40.6 1.0
CZ E:TYR99 3.5 46.9 1.0
C D:GLU94 3.5 29.8 1.0
CE E:LYS31 3.7 42.1 1.0
CG D:GLU94 3.9 32.8 1.0
NZ E:LYS31 4.0 43.9 1.0
CB D:ASP97 4.2 37.6 1.0
CD1 E:PHE95 4.3 30.8 1.0
CG D:LEU98 4.4 33.3 1.0
OE2 D:GLU94 4.5 44.9 1.0
CD1 D:LEU98 4.6 36.9 1.0
CD2 E:TYR99 4.7 43.8 1.0
N D:PHE95 4.7 29.0 1.0
OD2 D:ASP97 4.7 45.1 1.0
CE1 E:PHE95 4.8 30.4 1.0
N D:GLU94 4.8 30.9 1.0
CG E:PHE95 4.8 29.4 1.0
CE1 E:TYR99 4.9 47.1 1.0
N D:LEU98 4.9 33.0 1.0

Sodium binding site 7 out of 14 in 3k1s

Go back to Sodium Binding Sites List in 3k1s
Sodium binding site 7 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na108

b:53.9
occ:1.00
OE2 D:GLU51 2.1 43.3 1.0
O B:HOH521 2.9 37.3 1.0
CD D:GLU51 3.0 41.4 1.0
CZ B:PHE29 3.2 44.6 1.0
OE1 D:GLU51 3.3 45.7 1.0
CE2 B:PHE29 3.5 40.4 1.0
O B:HOH523 4.3 37.8 1.0
CG D:GLU51 4.4 32.8 1.0
CE1 B:PHE29 4.5 40.8 1.0
O B:HOH522 4.6 43.4 1.0
OE1 B:GLU25 4.8 43.6 1.0
CD B:GLU25 4.8 39.3 1.0
CD2 B:PHE29 4.8 38.5 1.0
OE2 B:GLU25 4.9 36.0 1.0

Sodium binding site 8 out of 14 in 3k1s

Go back to Sodium Binding Sites List in 3k1s
Sodium binding site 8 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na107

b:48.2
occ:1.00
O F:GLU51 2.3 30.0 1.0
C F:GLU51 3.0 30.6 1.0
OE1 F:GLU51 3.0 33.6 1.0
CE2 F:PHE55 3.1 43.3 1.0
CA F:GLU51 3.2 32.0 1.0
CZ F:PHE55 3.2 46.2 1.0
CB F:GLU51 3.6 30.5 1.0
CD2 F:PHE55 3.8 41.3 1.0
CE1 F:PHE55 3.9 50.5 1.0
CD F:GLU51 4.1 37.9 1.0
CB F:HIS54 4.1 39.0 1.0
N F:ALA52 4.3 30.9 1.0
CG F:PHE55 4.4 41.4 1.0
CG F:GLU51 4.4 30.0 1.0
CD1 F:PHE55 4.5 45.4 1.0
N F:GLU51 4.5 33.3 1.0
CD2 F:HIS54 4.5 45.7 1.0
CG F:HIS54 4.7 42.9 1.0
O F:ASN50 4.7 32.7 1.0
N F:PHE55 4.9 36.4 1.0
CA F:ALA52 4.9 32.3 1.0

Sodium binding site 9 out of 14 in 3k1s

Go back to Sodium Binding Sites List in 3k1s
Sodium binding site 9 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na108

b:46.8
occ:1.00
OH D:TYR99 2.5 36.9 1.0
OE1 F:GLU94 2.7 34.8 1.0
O F:GLU94 2.7 34.4 1.0
C F:GLU94 3.4 31.5 1.0
CZ D:TYR99 3.4 34.8 1.0
CA F:GLU94 3.5 29.8 1.0
CE D:LYS31 3.5 37.9 1.0
CE2 D:TYR99 3.5 31.4 1.0
CB F:GLU94 3.5 33.3 1.0
CD F:GLU94 3.8 36.8 1.0
CB F:ASP97 3.8 40.8 1.0
NZ D:LYS31 4.1 44.8 1.0
N F:LEU98 4.2 38.6 1.0
CG F:GLU94 4.2 32.2 1.0
CG F:LEU98 4.2 36.3 1.0
CD1 F:LEU98 4.5 44.0 1.0
CD D:LYS31 4.5 41.3 1.0
CD1 D:PHE95 4.6 34.9 1.0
N F:PHE95 4.6 29.9 1.0
CB F:LEU98 4.6 38.2 1.0
C F:ASP97 4.6 39.0 1.0
CE1 D:TYR99 4.7 39.2 1.0
CA F:ASP97 4.7 39.1 1.0
CG D:LYS31 4.7 35.9 1.0
CD1 D:LEU27 4.8 36.7 1.0
CA F:LEU98 4.8 38.3 1.0
CE1 D:PHE95 4.8 33.6 1.0
OE2 F:GLU94 4.9 40.4 1.0
CD2 D:TYR99 4.9 31.4 1.0
N F:GLU94 4.9 29.3 1.0
OD2 F:ASP97 4.9 52.6 1.0
CG F:ASP97 4.9 47.5 1.0

Sodium binding site 10 out of 14 in 3k1s

Go back to Sodium Binding Sites List in 3k1s
Sodium binding site 10 out of 14 in the Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na109

b:52.9
occ:1.00
OH F:TYR99 2.4 41.1 1.0
O E:GLU94 2.9 34.3 1.0
OE1 E:GLU94 3.0 39.8 1.0
CE F:LYS31 3.3 46.8 1.0
CZ F:TYR99 3.4 36.6 1.0
CB E:ASP97 3.5 48.7 1.0
CE2 F:TYR99 3.5 36.6 1.0
CA E:GLU94 3.6 33.2 1.0
C E:GLU94 3.6 32.9 1.0
CB E:GLU94 3.6 32.0 1.0
CD2 F:LEU27 3.9 43.0 1.0
NZ F:LYS31 3.9 49.7 1.0
N E:LEU98 4.0 44.9 1.0
CD E:GLU94 4.1 43.1 1.0
CG E:GLU94 4.4 35.6 1.0
CD1 F:PHE95 4.4 31.0 1.0
CB E:LEU98 4.4 45.5 1.0
CD F:LYS31 4.5 51.8 1.0
CA E:LEU98 4.5 46.3 1.0
CG E:ASP97 4.5 56.0 1.0
C E:ASP97 4.5 47.7 1.0
CE1 F:PHE95 4.6 36.6 1.0
CA E:ASP97 4.6 47.6 1.0
OD2 E:ASP97 4.6 62.6 1.0
CE1 F:TYR99 4.6 37.3 1.0
CG F:LYS31 4.8 48.5 1.0
N E:PHE95 4.9 32.5 1.0
CD1 E:LEU98 4.9 51.2 1.0
CD2 F:TYR99 4.9 34.9 1.0
N E:GLU94 5.0 33.1 1.0

Reference:

S.M.Anderson, Z.Wawrzak, O.Onopriyenko, K.Kwon, W.F.Anderson, A.Savchenko, Center For Structural Genomics Of Infectiousdiseases (Csgid). Crystal Structure of the Pts Cellobiose Specific Enzyme Iia From Bacillus Anthracis To Be Published.
Page generated: Tue Dec 15 06:15:52 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy