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Sodium in PDB 3wsu: Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus

Protein crystallography data

The structure of Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus, PDB code: 3wsu was solved by Y.Kumagai, K.Yamashita, M.Okuyama, T.Hatanaka, M.Yao, A.Kimura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.47 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.864, 100.846, 105.244, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 19.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus (pdb code 3wsu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus, PDB code: 3wsu:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3wsu

Go back to Sodium Binding Sites List in 3wsu
Sodium binding site 1 out of 4 in the Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus


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 Beta-Mannanase From Streptomyces Thermolilacinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:8.6
occ:1.00
 O A:GLY276 2.2 14.2 1.0
O A:PRO284 2.3 8.4 1.0
OD1 A:ASP283 2.3 8.5 1.0
OE1 A:GLU286 2.4 14.4 1.0
O A:HOH539 2.5 10.6 1.0
O A:HOH563 2.5 15.0 1.0
C A:GLY276 3.2 10.2 1.0
CD A:GLU286 3.4 12.5 1.0
CG A:ASP283 3.4 12.1 1.0
C A:PRO284 3.5 8.0 1.0
OE2 A:GLU286 3.7 13.5 1.0
O A:HOH564 3.7 13.7 1.0
CA A:GLY276 3.8 15.3 1.0
N A:PRO284 3.9 7.2 1.0
OD2 A:ASP283 4.0 16.2 1.0
O A:HOH831 4.0 26.8 1.0
CD A:PRO284 4.1 7.4 1.0
CA A:PRO284 4.2 8.5 1.0
C A:ASP283 4.2 7.8 1.0
N A:PRO277 4.3 9.8 1.0
N A:GLU286 4.4 5.6 1.0
CA A:PRO277 4.4 9.4 1.0
CB A:PRO284 4.4 6.5 1.0
O A:HOH534 4.5 12.0 1.0
N A:ASP285 4.5 7.0 1.0
CB A:ASP283 4.6 10.6 1.0
C A:PRO277 4.6 9.2 1.0
CA A:ASP283 4.6 9.5 1.0
O A:ASP283 4.7 8.1 1.0
O A:HOH728 4.7 29.6 1.0
CA A:ASP285 4.7 5.9 1.0
CD A:PRO278 4.7 9.9 1.0
N A:PRO278 4.8 9.8 1.0
CG A:GLU286 4.8 7.7 1.0
CG A:PRO284 4.8 6.7 1.0
N A:GLY276 5.0 18.0 1.0

Sodium binding site 2 out of 4 in 3wsu

Go back to Sodium Binding Sites List in 3wsu
Sodium binding site 2 out of 4 in the Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus


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 Beta-Mannanase From Streptomyces Thermolilacinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:23.6
occ:1.00
 O A:HOH514 2.2 10.9 1.0
O A:HOH909 2.4 22.7 1.0
OE1 A:GLU273 2.4 7.2 1.0
O A:HOH905 2.5 19.9 1.0
OE2 A:GLU178 2.5 6.5 1.0
O A:HOH906 2.9 21.8 1.0
CD A:GLU178 3.3 7.2 1.0
CD A:GLU273 3.4 6.7 1.0
OE1 A:GLU178 3.5 9.7 1.0
OE2 A:GLU273 3.6 7.3 1.0
OH A:TYR246 3.7 7.6 1.0
CE2 A:TYR246 3.8 5.0 1.0
CZ A:TYR246 4.1 6.0 1.0
O A:HOH640 4.2 23.7 1.0
ND1 A:HIS244 4.4 5.0 1.0
CG A:GLU178 4.6 5.0 1.0
CG A:GLU273 4.8 5.8 1.0
ND2 A:ASN177 4.8 5.3 1.0
CD2 A:TYR246 4.8 5.1 1.0

Sodium binding site 3 out of 4 in 3wsu

Go back to Sodium Binding Sites List in 3wsu
Sodium binding site 3 out of 4 in the Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus


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 Beta-Mannanase From Streptomyces Thermolilacinus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:10.4
occ:1.00
 OD1 B:ASP283 2.3 9.8 1.0
O B:PRO284 2.3 6.7 1.0
OE1 B:GLU286 2.4 11.8 1.0
O B:GLY276 2.4 10.8 1.0
O B:HOH572 2.5 13.7 1.0
O B:HOH604 2.5 12.1 1.0
CG B:ASP283 3.3 11.6 1.0
CD B:GLU286 3.3 12.8 1.0
C B:PRO284 3.5 6.0 1.0
OE2 B:GLU286 3.6 12.0 1.0
C B:GLY276 3.6 11.1 1.0
O B:HOH588 3.7 15.8 1.0
OD2 B:ASP283 3.8 16.9 1.0
N B:PRO284 4.0 6.9 1.0
CD B:PRO284 4.1 6.9 1.0
CA B:PRO284 4.2 8.0 1.0
C B:ASP283 4.2 7.8 1.0
N B:GLY276 4.3 16.4 1.0
N B:PRO277 4.4 9.1 1.0
CA B:PRO277 4.4 7.6 1.0
N B:GLU286 4.4 8.1 1.0
CB B:PRO284 4.4 7.1 1.0
O B:HOH529 4.5 9.7 1.0
O B:HOH827 4.5 35.2 1.0
N B:ASP285 4.5 7.6 1.0
CB B:ASP283 4.6 10.5 1.0
CA B:GLY276 4.6 14.9 1.0
C B:PRO277 4.6 8.4 1.0
O B:ASP283 4.6 9.1 1.0
CA B:ASP283 4.7 9.0 1.0
CD B:PRO278 4.7 8.5 1.0
N B:PRO278 4.7 9.2 1.0
CA B:ASP285 4.7 7.2 1.0
O B:HOH730 4.7 28.1 1.0
CG B:GLU286 4.7 9.3 1.0
CG B:PRO284 4.8 6.4 1.0

Sodium binding site 4 out of 4 in 3wsu

Go back to Sodium Binding Sites List in 3wsu
Sodium binding site 4 out of 4 in the Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus


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 Beta-Mannanase From Streptomyces Thermolilacinus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:23.6
occ:1.00
 O B:HOH506 2.3 8.9 1.0
O B:HOH678 2.3 22.2 1.0
OE2 B:GLU178 2.5 6.6 1.0
OE1 B:GLU273 2.5 6.7 1.0
O B:HOH658 2.5 25.9 1.0
O B:HOH620 2.7 15.2 1.0
CD B:GLU178 3.3 7.0 1.0
CD B:GLU273 3.4 8.0 1.0
OE1 B:GLU178 3.5 9.6 1.0
O B:HOH732 3.6 23.2 1.0
OE2 B:GLU273 3.6 6.7 1.0
OH B:TYR246 3.7 6.6 1.0
CE2 B:TYR246 3.7 8.1 1.0
O B:HOH628 4.0 22.2 1.0
CZ B:TYR246 4.1 7.9 1.0
O B:HOH826 4.1 36.0 1.0
O B:HOH811 4.2 41.8 1.0
ND1 B:HIS244 4.3 6.8 1.0
CG B:GLU178 4.6 6.0 1.0
CD2 B:TYR246 4.7 8.5 1.0
ND2 B:ASN177 4.8 5.0 1.0
CG B:GLU273 4.8 7.5 1.0
CE1 B:HIS244 5.0 6.7 1.0

Reference:

Y.Kumagai, K.Yamashita, T.Tagami, K.Kawakami, M.Uraji, M.Okuyama, M.Yao, A.Kimura, T.Hatanaka. Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus To Be Published.
Page generated: Mon Oct 7 14:00:20 2024

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