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Sodium in PDB 6gbn: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Cytophaga Hutchinsonii in Complex with Adenosine

Enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Cytophaga Hutchinsonii in Complex with Adenosine

All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Cytophaga Hutchinsonii in Complex with Adenosine:
3.3.1.1;

Protein crystallography data

The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Cytophaga Hutchinsonii in Complex with Adenosine, PDB code: 6gbn was solved by J.Czyrko, M.Jaskolski, K.Brzezinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.14 / 2.09
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.275, 102.445, 188.919, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 23.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Cytophaga Hutchinsonii in Complex with Adenosine (pdb code 6gbn). 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 S-Adenosyl-L-Homocysteine Hydrolase From Cytophaga Hutchinsonii in Complex with Adenosine, PDB code: 6gbn:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6gbn

Go back to Sodium Binding Sites List in 6gbn
Sodium binding site 1 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Cytophaga Hutchinsonii in Complex with Adenosine


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 S-Adenosyl-L-Homocysteine Hydrolase From Cytophaga Hutchinsonii in Complex with Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:26.8
occ:1.00
 OG1 A:THR354 2.8 19.3 1.0
O A:HOH768 2.9 24.6 1.0
O A:THR354 2.9 20.4 1.0
O A:HIS356 2.9 19.6 1.0
O A:HOH812 3.0 21.4 1.0
OE1 A:GLN60 3.4 22.6 1.0
NE2 A:GLN60 3.4 22.1 1.0
CB A:THR354 3.5 19.9 1.0
CD A:GLN60 3.6 22.4 1.0
O A:GLY355 3.6 18.9 1.0
C A:THR354 3.7 20.0 1.0
C A:HIS356 3.8 19.1 1.0
CA A:PRO357 4.0 18.8 1.0
C A:GLY355 4.1 19.4 1.0
N6 A:ADN501 4.2 22.9 1.0
N A:PRO357 4.2 18.7 1.0
CA A:THR354 4.2 20.0 1.0
O A:HOH791 4.3 22.5 1.0
N A:GLY355 4.6 19.9 1.0
N A:HIS356 4.6 19.6 1.0
CG A:GLN60 4.7 22.5 1.0
C A:PRO357 4.7 19.4 1.0
CG2 A:THR354 4.7 19.9 1.0
CA A:GLY355 4.8 19.9 1.0
NE2 A:GLN86 4.8 24.8 1.0
CA A:HIS356 4.8 19.2 1.0
N A:SER358 4.8 19.7 1.0

Sodium binding site 2 out of 4 in 6gbn

Go back to Sodium Binding Sites List in 6gbn
Sodium binding site 2 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Cytophaga Hutchinsonii in Complex with Adenosine


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 S-Adenosyl-L-Homocysteine Hydrolase From Cytophaga Hutchinsonii in Complex with Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:27.4
occ:1.00
 O B:HOH805 2.8 21.0 1.0
O B:HOH814 2.8 28.6 1.0
O B:HIS356 2.9 22.0 1.0
O B:THR354 2.9 22.0 1.0
OG1 B:THR354 2.9 21.2 1.0
OE1 B:GLN60 3.3 23.0 1.0
NE2 B:GLN60 3.4 23.2 1.0
CD B:GLN60 3.5 23.1 1.0
O B:GLY355 3.6 21.0 1.0
CB B:THR354 3.6 21.7 1.0
C B:HIS356 3.7 21.5 1.0
C B:THR354 3.7 21.8 1.0
CA B:PRO357 4.0 21.2 1.0
N6 B:ADN501 4.0 24.8 1.0
C B:GLY355 4.0 21.5 1.0
N B:PRO357 4.2 21.2 1.0
O B:HOH799 4.3 22.6 1.0
CA B:THR354 4.3 21.8 1.0
N B:HIS356 4.5 21.7 1.0
N B:GLY355 4.6 21.7 1.0
CG B:GLN60 4.6 23.2 1.0
C B:PRO357 4.7 21.6 1.0
CA B:HIS356 4.7 21.5 1.0
CA B:GLY355 4.8 21.8 1.0
NE2 B:GLN86 4.8 24.6 0.5
N B:SER358 4.8 21.8 1.0
CG2 B:THR354 4.8 21.7 1.0

Sodium binding site 3 out of 4 in 6gbn

Go back to Sodium Binding Sites List in 6gbn
Sodium binding site 3 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Cytophaga Hutchinsonii in Complex with Adenosine


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 S-Adenosyl-L-Homocysteine Hydrolase From Cytophaga Hutchinsonii in Complex with Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:41.7
occ:1.00
 O C:HOH660 2.8 27.3 1.0
O C:HOH667 2.9 25.2 1.0
O C:HIS356 2.9 31.7 1.0
OG1 C:THR354 3.0 28.6 1.0
O C:THR354 3.1 31.0 1.0
NE2 C:GLN60 3.3 36.2 1.0
OE1 C:GLN60 3.3 36.9 1.0
CD C:GLN60 3.5 37.0 1.0
CB C:THR354 3.7 29.4 1.0
O C:GLY355 3.7 29.2 1.0
C C:HIS356 3.8 31.1 1.0
C C:THR354 3.9 30.3 1.0
CA C:PRO357 3.9 30.9 1.0
O C:HOH641 4.0 29.5 1.0
N C:PRO357 4.2 30.5 1.0
N6 C:ADN501 4.2 34.2 1.0
C C:GLY355 4.2 30.3 1.0
CA C:THR354 4.5 29.7 1.0
CG C:GLN60 4.6 38.2 1.0
C C:PRO357 4.6 32.4 1.0
N C:SER358 4.6 33.0 1.0
N C:HIS356 4.7 31.2 1.0
N C:GLY355 4.8 30.2 1.0
CA C:HIS356 4.9 31.1 1.0
CG2 C:THR354 4.9 29.1 1.0
CA C:GLY355 4.9 30.8 1.0
NE2 C:GLN86 5.0 37.3 1.0

Sodium binding site 4 out of 4 in 6gbn

Go back to Sodium Binding Sites List in 6gbn
Sodium binding site 4 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Cytophaga Hutchinsonii in Complex with Adenosine


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 S-Adenosyl-L-Homocysteine Hydrolase From Cytophaga Hutchinsonii in Complex with Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na503

b:42.1
occ:1.00
 O D:HOH645 2.8 29.5 1.0
OG1 D:THR354 2.9 34.7 1.0
O D:THR354 2.9 36.1 1.0
O D:HIS356 3.0 36.6 1.0
O D:HOH685 3.1 25.2 1.0
OE1 D:GLN60 3.2 38.2 1.0
NE2 D:GLN60 3.3 38.2 1.0
CD D:GLN60 3.4 38.3 1.0
CB D:THR354 3.5 35.2 1.0
O D:GLY355 3.8 35.1 1.0
C D:THR354 3.8 35.8 1.0
C D:HIS356 3.8 36.1 1.0
O D:HOH620 4.0 29.4 1.0
N6 D:ADN501 4.0 34.6 1.0
CA D:PRO357 4.1 35.7 1.0
C D:GLY355 4.2 35.9 1.0
N D:PRO357 4.3 35.7 1.0
CA D:THR354 4.3 35.4 1.0
CG D:GLN60 4.6 38.8 1.0
N D:GLY355 4.7 35.8 1.0
N D:HIS356 4.7 36.4 1.0
C D:PRO357 4.7 36.6 1.0
NE2 D:GLN86 4.8 38.6 0.5
CG2 D:THR354 4.8 35.0 1.0
N D:SER358 4.8 36.9 1.0
CA D:GLY355 4.9 36.2 1.0
CA D:HIS356 4.9 36.2 1.0
OE1 D:GLN86 5.0 37.6 0.5
OE1 D:GLN86 5.0 37.6 0.5

Reference:

J.Czyrko, M.Jaskolski, K.Brzezinski. Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Cytophaga Hutchinsonii, A Case of Combination of Crystallographic and Non-Crystallographic Symmetry. Croatica Chemica Acta V. 91 2018.
ISSN: ISSN 0011-1643
DOI: 10.5562/CCA3345
Page generated: Tue Dec 15 12:17:00 2020

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