Atomistry » Sodium » PDB 8bai-8byj » 8bh0
Atomistry »
  Sodium »
    PDB 8bai-8byj »
      8bh0 »

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

Go back to Sodium Binding Sites List in 8bh0
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

Go back to Sodium Binding Sites List in 8bh0
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

Go back to Sodium Binding Sites List in 8bh0
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

Go back to Sodium Binding Sites List in 8bh0
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

Go back to Sodium Binding Sites List in 8bh0
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

Go back to Sodium Binding Sites List in 8bh0
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy