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Sodium in PDB 8bh0: O-Methyltransferase PLU4890 in Complex with Sah and Aq-270B

Protein crystallography data

The structure of O-Methyltransferase PLU4890 in Complex with Sah and Aq-270B, PDB code: 8bh0 was solved by E.M.Huber, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.94, 105.62, 124.47, 94.37, 90.22, 104.97
R / Rfree (%) 17.8 / 20.5

Other elements in 8bh0:

The structure of O-Methyltransferase PLU4890 in Complex with Sah and Aq-270B also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the O-Methyltransferase PLU4890 in Complex with Sah and Aq-270B (pdb code 8bh0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the O-Methyltransferase PLU4890 in Complex with Sah and Aq-270B, PDB code: 8bh0:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 8bh0

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Sodium binding site 1 out of 6 in the O-Methyltransferase PLU4890 in Complex with Sah and Aq-270B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of O-Methyltransferase PLU4890 in Complex with Sah and Aq-270B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:45.9
occ:1.00
 OD2 B:ASP168 2.2 32.7 1.0
CG B:ASP168 3.2 30.0 1.0
O B:HOH598 3.3 39.8 1.0
O B:GLY171 3.4 26.3 1.0
CA B:GLY174 3.5 28.8 1.0
C B:GLY174 3.5 28.9 1.0
O B:GLY174 3.6 28.8 1.0
CB B:ASP168 3.6 27.7 1.0
N B:LEU177 3.7 30.4 1.0
CA B:GLY171 3.7 25.8 1.0
CB B:LEU176 3.8 31.0 1.0
N B:LEU176 3.8 29.1 1.0
O B:HOH545 3.8 31.6 1.0
CG2 B:VAL191 3.9 25.2 1.0
C B:GLY171 4.0 25.8 1.0
N B:GLU175 4.1 29.1 1.0
CG1 B:VAL191 4.1 24.7 1.0
CB B:LEU177 4.1 32.4 1.0
CG B:LEU177 4.1 33.3 1.0
CA B:LEU176 4.2 29.9 1.0
OD1 B:ASP168 4.3 32.8 1.0
N B:GLY174 4.3 28.1 1.0
C B:LEU176 4.4 29.7 1.0
CA B:LEU177 4.5 31.5 1.0
CB B:VAL191 4.6 25.0 1.0
C B:GLU175 4.7 29.2 1.0
CD1 B:LEU177 4.8 33.7 1.0
CG B:LEU176 4.9 31.8 1.0
CD2 B:LEU176 5.0 32.2 1.0

Sodium binding site 2 out of 6 in 8bh0

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Sodium binding site 2 out of 6 in the O-Methyltransferase PLU4890 in Complex with Sah and Aq-270B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of O-Methyltransferase PLU4890 in Complex with Sah and Aq-270B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:34.8
occ:1.00
 OD1 B:ASP168 2.3 32.8 1.0
O B:VAL169 2.6 26.0 1.0
N B:LYS225 3.1 25.1 1.0
N B:SAH401 3.2 30.6 1.0
O B:HOH545 3.3 31.6 1.0
CG B:ASP168 3.4 30.0 1.0
O B:ILE223 3.6 24.4 1.0
C B:VAL169 3.6 25.6 1.0
O B:GLY170 3.8 25.4 1.0
CA B:LEU224 3.8 25.3 1.0
O B:LYS225 3.8 24.5 1.0
C B:GLY170 3.9 25.4 1.0
N B:VAL169 3.9 25.1 1.0
OD2 B:ASP168 3.9 32.7 1.0
C B:LEU224 3.9 25.1 1.0
CA B:LYS225 4.0 25.9 1.0
CB B:LYS225 4.0 27.5 1.0
C B:ILE223 4.0 24.7 1.0
N B:GLY171 4.1 25.5 1.0
CA B:GLY171 4.1 25.8 1.0
N B:LEU224 4.2 24.8 1.0
C B:ASP168 4.3 26.0 1.0
C B:LYS225 4.4 25.6 1.0
CA B:VAL169 4.4 25.5 1.0
CG2 B:ILE223 4.4 26.1 1.0
N B:GLY170 4.4 25.8 1.0
CG2 B:VAL227 4.5 24.3 1.0
CA B:GLY170 4.5 25.6 1.0
CB B:ASP168 4.6 27.7 1.0
CA B:SAH401 4.6 31.3 1.0
CA B:ASP168 4.6 26.5 1.0
CB B:ILE223 4.9 26.2 1.0

Sodium binding site 3 out of 6 in 8bh0

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Sodium binding site 3 out of 6 in the O-Methyltransferase PLU4890 in Complex with Sah and Aq-270B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of O-Methyltransferase PLU4890 in Complex with Sah and Aq-270B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:49.0
occ:1.00
 OG C:SER64 2.2 35.4 1.0
O C:LYS68 3.3 27.2 1.0
CB C:SER64 3.3 32.2 1.0
N C:LYS68 3.6 28.3 1.0
CZ C:PHE69 3.6 30.2 1.0
C C:ASN67 3.6 29.1 1.0
CA C:ASN67 3.7 29.7 1.0
CE2 C:PHE69 3.8 30.4 1.0
CE1 C:PHE69 3.9 30.3 1.0
CA C:SER64 3.9 30.8 1.0
C C:LYS68 4.0 28.1 1.0
O C:ASN67 4.2 29.6 1.0
N C:ASN67 4.3 28.6 1.0
CA C:LYS68 4.3 28.8 1.0
N C:ASN65 4.3 30.1 1.0
CD2 C:PHE69 4.3 29.9 1.0
C C:SER64 4.3 30.4 1.0
CD1 C:PHE69 4.4 29.7 1.0
OD1 C:ASN67 4.4 33.2 1.0
O C:HOH593 4.6 34.0 1.0
CG C:PHE69 4.6 29.0 1.0
O C:ASN65 4.9 28.2 1.0
CB C:ASN67 5.0 30.9 1.0

Sodium binding site 4 out of 6 in 8bh0

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Sodium binding site 4 out of 6 in the O-Methyltransferase PLU4890 in Complex with Sah and Aq-270B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of O-Methyltransferase PLU4890 in Complex with Sah and Aq-270B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na403

b:49.4
occ:1.00
 O D:HOH610 2.4 40.7 1.0
OG D:SER214 2.5 40.9 1.0
CB D:SER214 3.4 38.0 1.0
OG G:SER217 3.6 36.5 1.0
N G:GLY218 3.6 38.1 1.0
N D:PRO216 3.6 31.7 1.0
CA G:GLY218 3.7 39.7 1.0
CB G:SER217 3.8 37.4 1.0
CD D:PRO216 3.9 31.9 1.0
C D:ILE215 3.9 31.9 1.0
CA D:PRO216 3.9 32.0 1.0
O D:HOH552 4.0 36.8 1.0
C G:SER217 4.0 38.1 1.0
CG D:PRO216 4.0 32.3 1.0
C D:SER214 4.0 34.1 1.0
O D:SER214 4.2 34.3 1.0
O D:ILE215 4.2 32.0 1.0
N D:ILE215 4.3 33.0 1.0
CA D:SER214 4.4 36.1 1.0
O G:SER217 4.5 38.7 1.0
CB D:PRO216 4.5 32.2 1.0
CA D:ILE215 4.5 32.2 1.0
CA G:SER217 4.5 36.9 1.0

Sodium binding site 5 out of 6 in 8bh0

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Sodium binding site 5 out of 6 in the O-Methyltransferase PLU4890 in Complex with Sah and Aq-270B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of O-Methyltransferase PLU4890 in Complex with Sah and Aq-270B within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na403

b:48.8
occ:1.00
 O C:HOH505 2.3 37.9 1.0
OG F:SER98 2.9 28.5 0.5
OD1 F:ASN99 2.9 34.8 1.0
O C:HOH600 3.2 38.2 1.0
CG F:ASN99 3.5 31.7 1.0
OG C:SER98 3.7 35.1 1.0
CB F:SER98 3.7 27.7 0.5
CA C:SER95 3.7 27.5 1.0
ND2 F:ASN99 3.8 33.7 1.0
CB C:SER95 3.8 28.6 1.0
CB F:SER98 3.8 27.7 0.5
O F:SER95 3.9 26.9 1.0
CB C:SER98 3.9 30.6 1.0
O C:SER95 4.0 26.5 1.0
OD1 C:ASN99 4.1 33.5 1.0
N F:ASN99 4.1 26.4 1.0
ND2 C:ASN99 4.3 33.2 1.0
C F:SER98 4.4 26.5 0.5
C C:SER95 4.4 26.9 1.0
CG C:ASN99 4.4 31.8 1.0
C F:SER98 4.4 26.2 0.5
CA F:SER95 4.5 27.9 1.0
CA F:ASN99 4.5 27.1 1.0
CB F:ASN99 4.5 29.2 1.0
C F:SER95 4.6 27.0 1.0
CA F:SER98 4.7 26.9 0.5
CB F:SER95 4.7 28.7 1.0
CA F:SER98 4.7 26.9 0.5
CD1 F:LEU102 4.8 30.3 1.0
N C:SER95 4.9 26.7 1.0
OG F:SER98 4.9 27.5 0.5
O F:SER98 4.9 26.9 0.5

Sodium binding site 6 out of 6 in 8bh0

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Sodium binding site 6 out of 6 in the O-Methyltransferase PLU4890 in Complex with Sah and Aq-270B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of O-Methyltransferase PLU4890 in Complex with Sah and Aq-270B within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na403

b:41.2
occ:1.00
 OD1 G:ASP168 2.3 37.3 1.0
O G:VAL169 2.6 27.4 1.0
N G:LYS225 3.2 29.0 1.0
O G:HOH527 3.3 34.8 1.0
CG G:ASP168 3.3 35.5 1.0
N G:SAH401 3.3 32.5 1.0
O G:ILE223 3.4 28.7 1.0
C G:VAL169 3.6 28.3 1.0
N G:VAL169 3.8 28.8 1.0
OD2 G:ASP168 3.8 40.9 1.0
CA G:LEU224 3.8 28.5 1.0
O G:LYS225 3.9 28.3 1.0
O G:GLY170 3.9 28.4 1.0
C G:GLY170 3.9 28.8 1.0
CB G:LYS225 4.0 31.1 1.0
C G:ILE223 4.0 28.3 1.0
C G:LEU224 4.0 28.6 1.0
CA G:GLY171 4.0 29.3 1.0
CA G:LYS225 4.0 29.8 1.0
N G:GLY171 4.1 28.8 1.0
C G:ASP168 4.2 30.3 1.0
N G:LEU224 4.2 28.3 1.0
CA G:VAL169 4.3 29.0 1.0
CG2 G:ILE223 4.4 29.0 1.0
CB G:ASP168 4.4 33.1 1.0
C G:LYS225 4.5 29.1 1.0
N G:GLY170 4.5 28.6 1.0
CA G:ASP168 4.5 30.6 1.0
CG2 G:VAL227 4.5 29.3 1.0
CA G:GLY170 4.6 28.8 1.0
CA G:SAH401 4.7 33.4 1.0
CB G:ILE223 4.8 29.3 1.0
O G:ASP168 4.9 31.3 1.0

Reference:

E.M.Huber, L.Kreling, A.K.Heinrich, M.Duennebacke, A.Poethig, H.B.Bode, M.Groll. A Set of Closely Related Methyltransferases For Site-Specific Tailoring of Anthraquinone Pigments Structure 2023.
ISSN: ISSN 0969-2126
Page generated: Wed Oct 9 10:44:23 2024

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