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Sodium in PDB 3hk7: Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinarate, Monoclinic Crystal Form

Protein crystallography data

The structure of Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinarate, Monoclinic Crystal Form, PDB code: 3hk7 was solved by A.A.Fedorov, E.V.Fedorov, T.T.Nguyen, F.M.Raushel, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.99 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 274.823, 156.516, 185.959, 90.00, 116.20, 90.00
R / Rfree (%) 21.3 / 24.5

Other elements in 3hk7:

The structure of Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinarate, Monoclinic Crystal Form also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Zinc (Zn) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinarate, Monoclinic Crystal Form (pdb code 3hk7). 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 Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinarate, Monoclinic Crystal Form, PDB code: 3hk7:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3hk7

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Sodium binding site 1 out of 4 in the Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinarate, Monoclinic Crystal Form


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 Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinarate, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na432

b:25.7
occ:1.00
 O B:HOH1378 2.3 22.1 1.0
O C:HOH1634 2.3 27.4 1.0
O A:HOH433 2.4 29.0 1.0
O C:HOH466 2.4 17.1 1.0
O A:HOH881 2.5 28.1 1.0
O B:HOH433 2.5 19.9 1.0
OE2 A:GLU332 3.8 28.5 1.0
O A:HOH441 3.9 26.2 1.0
OE2 C:GLU332 4.0 23.7 1.0
OE2 B:GLU332 4.1 20.4 1.0
O B:HOH443 4.1 21.8 1.0
O C:HOH467 4.2 20.4 1.0
OE2 B:GLU336 4.4 24.7 1.0
OE2 A:GLU336 4.5 20.9 1.0
OE2 C:GLU336 4.7 22.1 1.0
CD A:GLU332 4.9 25.5 1.0

Sodium binding site 2 out of 4 in 3hk7

Go back to Sodium Binding Sites List in 3hk7
Sodium binding site 2 out of 4 in the Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinarate, Monoclinic Crystal Form


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 Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinarate, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na431

b:18.4
occ:1.00
 O F:HOH683 2.3 23.5 1.0
O F:HOH450 2.4 18.4 1.0
O D:HOH1832 2.4 24.6 1.0
O D:HOH823 2.5 20.5 1.0
O E:HOH651 2.5 20.6 1.0
O E:HOH1613 2.6 18.2 1.0
OE2 D:GLU332 3.9 21.7 1.0
OE2 F:GLU332 4.0 18.2 1.0
O D:HOH441 4.0 16.3 1.0
OE2 E:GLU332 4.1 18.2 1.0
O F:HOH461 4.1 18.0 1.0
O E:HOH441 4.1 14.8 1.0
OE2 E:GLU336 4.5 21.0 1.0
OE2 D:GLU336 4.5 18.8 1.0
OE2 F:GLU336 4.6 18.5 1.0

Sodium binding site 3 out of 4 in 3hk7

Go back to Sodium Binding Sites List in 3hk7
Sodium binding site 3 out of 4 in the Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinarate, Monoclinic Crystal Form


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 Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinarate, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na431

b:23.1
occ:1.00
 O G:HOH522 2.3 24.0 1.0
O H:HOH1213 2.4 24.0 1.0
O I:HOH438 2.4 23.1 1.0
O I:HOH714 2.4 28.7 1.0
O H:HOH432 2.5 22.7 1.0
O G:HOH1011 2.6 21.6 1.0
OE2 H:GLU332 3.9 21.2 1.0
OE2 G:GLU332 3.9 26.0 1.0
O G:HOH754 4.0 26.4 1.0
O H:HOH443 4.1 21.9 1.0
OE2 I:GLU332 4.1 25.8 1.0
O I:HOH463 4.2 21.7 1.0
OE2 H:GLU336 4.4 22.8 1.0
OE2 I:GLU336 4.5 23.1 1.0
OE2 G:GLU336 4.6 17.1 1.0
CD H:GLU332 5.0 21.0 1.0
CB H:GLU336 5.0 17.5 1.0

Sodium binding site 4 out of 4 in 3hk7

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Sodium binding site 4 out of 4 in the Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinarate, Monoclinic Crystal Form


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 Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinarate, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na430

b:22.8
occ:1.00
 O L:HOH577 2.4 28.5 1.0
O K:HOH462 2.4 16.9 1.0
O L:HOH431 2.4 18.6 1.0
O J:HOH585 2.4 20.1 1.0
O K:HOH1264 2.5 24.4 1.0
O J:HOH1661 2.6 24.3 1.0
OE2 L:GLU332 3.9 18.3 1.0
O L:HOH452 3.9 19.9 1.0
OE2 K:GLU332 4.0 17.9 1.0
O K:HOH439 4.1 18.7 1.0
OE2 J:GLU332 4.1 22.5 1.0
O J:HOH476 4.2 22.4 1.0
OE2 L:GLU336 4.4 21.4 1.0
OE2 J:GLU336 4.4 16.0 1.0
OE2 K:GLU336 4.5 20.4 1.0
CD L:GLU332 4.9 17.6 1.0

Reference:

T.T.Nguyen, A.A.Fedorov, L.Williams, E.V.Fedorov, Y.Li, C.Xu, S.C.Almo, F.M.Raushel. The Mechanism of the Reaction Catalyzed By Uronate Isomerase Illustrates How An Isomerase May Have Evolved From A Hydrolase Within the Amidohydrolase Superfamily. Biochemistry V. 48 8879 2009.
ISSN: ISSN 0006-2960
PubMed: 19678710
DOI: 10.1021/BI901046X
Page generated: Mon Oct 7 10:24:14 2024

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