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Sodium in PDB 4w5z: High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina.

Enzymatic activity of High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina.

All present enzymatic activity of High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina.:
3.2.1.14;

Protein crystallography data

The structure of High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina., PDB code: 4w5z was solved by P.H.Malecki, C.E.Vorgias, W.Rypniewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 85.59 / 1.32
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 50.691, 72.686, 171.169, 90.00, 90.00, 90.00
R / Rfree (%) 11.1 / 15

Other elements in 4w5z:

The structure of High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina. also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina. (pdb code 4w5z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina., PDB code: 4w5z:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4w5z

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Sodium binding site 1 out of 8 in the High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:18.6
occ:1.00
 O A:GLY144 2.3 15.7 1.0
OD1 A:ASN105 2.3 16.4 1.0
OD1 A:ASP146 2.3 14.5 1.0
O A:HOH854 2.3 28.4 0.5
O A:THR24 2.4 27.6 1.0
O A:HOH854 2.5 17.9 0.5
CG A:ASP146 3.2 14.7 1.0
CG A:ASN105 3.2 15.8 1.0
HA A:ILE25 3.2 22.6 1.0
C A:GLY144 3.3 14.3 1.0
C A:THR24 3.3 28.9 1.0
HD22 A:ASN105 3.4 17.8 1.0
O A:HOH686 3.5 27.1 1.0
H A:THR24 3.5 39.8 1.0
OD2 A:ASP146 3.5 14.8 1.0
HG1 A:THR26 3.5 27.4 1.0
H A:THR26 3.6 21.1 1.0
ND2 A:ASN105 3.6 14.8 1.0
HA3 A:GLY144 3.8 17.8 1.0
HA2 A:GLY144 3.8 17.8 1.0
O A:PHE145 3.9 15.3 1.0
N A:THR24 3.9 33.2 1.0
CA A:GLY144 3.9 14.9 1.0
CA A:ILE25 4.0 18.9 1.0
C A:PHE145 4.0 14.8 1.0
N A:ILE25 4.0 24.1 1.0
O A:HOH855 4.0 17.4 0.5
HB A:THR26 4.1 19.9 1.0
N A:THR26 4.1 17.6 1.0
HA A:ASP146 4.1 15.2 1.0
CA A:THR24 4.2 32.7 1.0
HG22 A:ILE101 4.2 18.0 1.0
OG1 A:THR26 4.2 22.9 1.0
HA3 A:GLY23 4.2 44.0 1.0
N A:PHE145 4.3 14.8 1.0
HD21 A:ASN105 4.3 17.8 1.0
N A:ASP146 4.3 12.9 1.0
CB A:ASP146 4.4 13.3 1.0
HA A:PHE145 4.5 17.8 1.0
CB A:ASN105 4.5 15.6 1.0
HB3 A:ASN105 4.5 18.8 1.0
C A:ILE25 4.5 19.6 1.0
CA A:PHE145 4.5 14.8 1.0
HG12 A:ILE25 4.5 31.1 1.0
CA A:ASP146 4.6 12.6 1.0
HB A:THR24 4.6 50.1 1.0
CB A:THR26 4.6 16.6 1.0
HG21 A:ILE101 4.7 18.0 1.0
C A:GLY23 4.7 39.6 1.0
HB2 A:ASN105 4.8 18.8 1.0
H A:ILE25 4.8 28.9 1.0
CG2 A:ILE101 4.8 15.0 1.0
H A:ASP146 4.8 15.5 1.0
HG23 A:ILE101 4.8 18.0 1.0
HB3 A:ASP146 4.8 16.0 1.0
HA A:THR24 4.9 39.3 1.0
O A:HOH855 4.9 19.3 0.5
CB A:THR24 5.0 41.7 1.0
CA A:GLY23 5.0 36.6 1.0

Sodium binding site 2 out of 8 in 4w5z

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Sodium binding site 2 out of 8 in the High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:57.4
occ:0.80
 O A:HOH573 2.2 51.5 1.0
O A:HOH509 2.2 44.9 1.0
O A:HOH586 2.7 46.8 1.0
OD1 A:ASP225 2.9 31.1 1.0
CG A:ASP225 3.8 27.2 1.0
OD2 A:ASP225 4.0 32.3 1.0
O A:HOH545 4.6 31.6 1.0
O A:GLN222 4.7 21.6 1.0
H A:ASP225 4.8 23.4 1.0
H A:GLY224 5.0 28.3 1.0

Sodium binding site 3 out of 8 in 4w5z

Go back to Sodium Binding Sites List in 4w5z
Sodium binding site 3 out of 8 in the High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:41.1
occ:0.50
 O A:HOH601 2.2 47.5 1.0
O A:HOH611 2.2 28.0 0.5
O A:HOH792 2.2 48.4 1.0
O A:HOH547 3.8 47.1 1.0
HB3 A:GLU78 3.8 31.0 1.0
O A:HOH705 4.0 41.5 1.0
O A:HOH518 4.3 41.7 1.0
OE2 A:GLU78 4.4 40.5 1.0
HG21 A:THR83 4.4 21.9 1.0
HG2 A:GLU78 4.7 36.4 1.0
CB A:GLU78 4.7 25.8 1.0
CD A:GLU78 4.7 37.4 1.0
CG A:GLU78 4.9 30.3 1.0
O A:GLU78 5.0 24.9 1.0

Sodium binding site 4 out of 8 in 4w5z

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Sodium binding site 4 out of 8 in the High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:50.1
occ:0.80
 O A:HOH603 2.1 55.2 1.0
O A:HOH578 2.1 56.2 1.0
O A:HOH501 2.1 58.2 1.0
O A:HOH507 2.3 33.5 1.0
HZ2 A:LYS57 3.7 44.6 1.0
HZ3 A:LYS57 3.8 44.6 1.0
OE2 A:GLU55 3.8 39.9 1.0
NZ A:LYS57 4.2 37.2 1.0
OE1 A:GLU55 4.3 24.4 1.0
CD A:GLU55 4.5 30.4 1.0
O A:HOH604 4.6 53.2 1.0
HE2 A:LYS57 4.6 37.5 1.0
O A:HOH574 4.8 47.8 1.0
HZ1 A:LYS57 4.9 44.6 1.0
OE1 A:GLU96 5.0 48.2 1.0

Sodium binding site 5 out of 8 in 4w5z

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Sodium binding site 5 out of 8 in the High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:50.6
occ:1.00
 OD2 A:ASP30 2.2 25.3 0.5
O A:HOH557 2.2 57.8 1.0
O A:HOH540 2.4 56.4 1.0
O A:HOH722 2.6 40.4 1.0
CG A:ASP30 3.3 22.1 0.5
OD1 A:ASP30 3.7 18.2 0.5
HB3 A:ASP30 3.9 25.6 0.5
O A:HOH867 3.9 56.1 1.0
O A:HIS339 4.1 23.0 1.0
HB2 A:ASP30 4.3 25.6 0.5
OD2 A:ASP30 4.3 32.5 0.5
HG3 A:PRO343 4.4 42.3 1.0
O A:GLN341 4.4 26.8 1.0
CB A:ASP30 4.4 21.3 0.5
O A:HOH717 4.5 21.6 1.0
CB A:ASP30 4.5 21.7 0.5
CG A:ASP30 4.6 27.7 0.5
HB3 A:ASP30 4.6 26.1 0.5
O A:HOH768 4.7 45.0 1.0
HB2 A:ASP30 4.7 26.1 0.5
HD3 A:PRO343 4.9 37.6 1.0
HD21 A:ASN31 5.0 23.5 0.5

Sodium binding site 6 out of 8 in 4w5z

Go back to Sodium Binding Sites List in 4w5z
Sodium binding site 6 out of 8 in the High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na411

b:66.5
occ:1.00
 O A:HOH864 2.1 56.8 1.0
O A:HOH831 2.3 46.4 1.0
O A:HOH865 2.5 51.1 1.0
O A:HOH742 2.7 36.9 1.0
O A:HOH695 3.6 32.2 1.0
O A:HOH783 3.7 44.5 1.0
OD1 A:ASP290 3.8 23.6 1.0
O A:ALA241 4.2 27.4 1.0
OD2 A:ASP290 4.3 21.5 1.0
HA A:ALA241 4.4 24.0 1.0
CG A:ASP290 4.5 20.6 1.0
C A:ALA241 4.9 21.7 1.0
O A:ASP240 5.0 26.0 1.0

Sodium binding site 7 out of 8 in 4w5z

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Sodium binding site 7 out of 8 in the High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na412

b:36.5
occ:1.00
 O A:HOH870 2.2 46.3 1.0
O A:HOH871 2.2 57.9 1.0
O A:HOH869 2.2 45.2 1.0
NE2 A:HIS266 2.3 21.6 1.0
O A:HOH868 2.4 58.4 1.0
O A:HOH872 2.5 65.3 1.0
CE1 A:HIS266 3.2 21.6 1.0
HE1 A:HIS266 3.3 25.9 1.0
CD2 A:HIS266 3.4 19.9 1.0
HD2 A:HIS266 3.6 23.9 1.0
O A:VAL345 4.2 43.5 1.0
O A:HOH753 4.3 41.5 1.0
ND1 A:HIS266 4.4 17.8 1.0
O A:GLY302 4.4 23.3 1.0
CG A:HIS266 4.5 16.8 1.0
OD1 A:ASP267 4.7 28.3 1.0
HA A:GLN303 4.8 22.1 1.0
HG2 A:GLN303 4.9 25.8 1.0
O A:HOH821 4.9 42.6 1.0
HB3 A:ASP267 5.0 23.6 1.0

Sodium binding site 8 out of 8 in 4w5z

Go back to Sodium Binding Sites List in 4w5z
Sodium binding site 8 out of 8 in the High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na414

b:46.8
occ:0.60
 O A:HOH610 2.2 54.7 1.0
O A:HOH504 2.3 41.2 1.0
OD1 A:ASP75 4.7 26.4 1.0
HB2 A:ALA77 5.0 38.3 1.0

Reference:

P.H.Malecki, C.E.Vorgias, W.Rypniewski. High Resolution Crystal Structure of Catalytic Domain of Chitinase 60 From Psychrophilic Bacteria Moritella Marina. To Be Published.
Page generated: Mon Oct 7 18:49:34 2024

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