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Sodium in PDB 6qlv: Crystal Structure of W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct

Enzymatic activity of Crystal Structure of W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct

All present enzymatic activity of Crystal Structure of W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct:
2.5.1.129;

Protein crystallography data

The structure of Crystal Structure of W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct, PDB code: 6qlv was solved by S.A.Marshall, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 115.40 / 2.39
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 161.533, 164.931, 102.527, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct (pdb code 6qlv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct, PDB code: 6qlv:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 6qlv

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Sodium binding site 1 out of 7 in the Crystal Structure of W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct


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 W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:50.7
occ:1.00
 O B:HOH425 2.5 22.7 1.0
O E:HOH408 2.5 38.5 1.0
OD1 B:ASN117 2.5 39.9 1.0
O B:HOH465 2.7 23.1 1.0
O E:HOH423 2.7 31.7 1.0
O E:HOH452 3.2 38.2 1.0
OE2 E:GLU121 3.4 25.7 1.0
CG B:ASN117 3.6 37.2 1.0
O B:ALA115 4.0 25.0 1.0
ND2 B:ASN117 4.2 37.0 1.0
O E:GLY106 4.3 25.2 1.0
O1P E:FMN301 4.3 25.0 1.0
C E:GLY106 4.4 23.6 1.0
O2P E:FMN301 4.4 22.8 1.0
O B:HOH476 4.5 19.8 1.0
CD E:GLU121 4.6 24.9 1.0
O E:HOH405 4.7 31.9 1.0
CA B:ASN117 4.7 27.9 1.0
CB B:ASN117 4.7 31.1 1.0
CA E:GLY106 4.8 24.8 1.0
O E:HOH451 4.8 30.5 1.0
N E:THR107 4.8 22.6 1.0
P E:FMN301 4.8 24.6 1.0
O5' E:FMN301 4.9 26.5 1.0
O B:CYS116 4.9 35.5 1.0
CB E:ALA110 4.9 19.8 1.0

Sodium binding site 2 out of 7 in 6qlv

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Sodium binding site 2 out of 7 in the Crystal Structure of W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct


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 W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na304

b:56.2
occ:1.00
 OE2 H:GLU121 2.6 28.6 1.0
OD1 C:ASN117 2.8 26.5 1.0
O H:HOH452 3.1 27.2 1.0
O H:HOH401 3.3 43.6 1.0
O H:HOH434 3.4 22.4 1.0
O C:HOH408 3.5 20.4 1.0
CD H:GLU121 3.5 27.1 1.0
CG C:ASN117 3.7 28.8 1.0
OE1 H:GLU121 3.8 29.4 1.0
ND2 C:ASN117 4.0 28.1 1.0
ND2 H:ASN118 4.0 29.5 1.0
O C:HOH467 4.1 20.9 1.0
CB H:ASN117 4.2 26.8 1.0
O C:HOH458 4.4 30.5 1.0
OD1 H:ASN117 4.6 38.9 1.0
CB H:ALA110 4.8 22.2 1.0
CG H:ASN117 4.9 34.0 1.0
CG H:GLU121 4.9 23.9 1.0
O H:HOH431 5.0 24.4 1.0

Sodium binding site 3 out of 7 in 6qlv

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Sodium binding site 3 out of 7 in the Crystal Structure of W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct


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 W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:38.0
occ:1.00
 O C:HOH429 2.4 31.6 1.0
OD1 D:ASN117 2.4 38.1 1.0
O C:HOH433 2.5 30.4 1.0
O D:HOH406 2.6 21.9 1.0
O D:HOH460 2.8 23.3 1.0
O C:HOH456 3.1 43.5 1.0
OE2 C:GLU121 3.4 28.4 1.0
CG D:ASN117 3.5 33.9 1.0
O D:ALA115 4.1 26.5 1.0
ND2 D:ASN117 4.1 28.1 1.0
O1 C:HJN303 4.4 26.7 1.0
O3 C:HJN303 4.4 26.6 1.0
O C:GLY106 4.4 18.5 1.0
O D:HOH488 4.4 26.3 1.0
CD C:GLU121 4.5 25.0 1.0
C C:GLY106 4.6 21.6 1.0
O C:HOH438 4.6 34.4 1.0
CB D:ASN117 4.7 31.6 1.0
O C:HOH409 4.7 31.9 1.0
CA D:ASN117 4.7 28.4 1.0
P1 C:HJN303 4.8 24.6 1.0
O2 C:HJN303 4.9 19.9 1.0
CA C:GLY106 5.0 21.9 1.0

Sodium binding site 4 out of 7 in 6qlv

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Sodium binding site 4 out of 7 in the Crystal Structure of W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct


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 W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na303

b:47.0
occ:1.00
 OD1 F:ASN117 2.4 34.5 1.0
O G:HOH433 2.4 32.7 1.0
O F:HOH416 2.5 17.5 1.0
O G:HOH427 2.5 26.0 1.0
O F:HOH447 2.5 27.9 1.0
O G:HOH405 2.6 35.5 1.0
CG F:ASN117 3.6 34.5 1.0
OE2 G:GLU121 3.6 36.1 1.0
O F:ALA115 3.9 25.6 1.0
O1 G:HJN303 4.2 24.0 1.0
ND2 F:ASN117 4.2 34.8 1.0
O G:HOH431 4.3 33.1 1.0
O G:GLY106 4.3 25.5 1.0
O3 G:HJN303 4.3 20.6 1.0
C G:GLY106 4.4 25.6 1.0
O2 G:HJN303 4.6 23.4 1.0
CA F:ASN117 4.6 29.7 1.0
P1 G:HJN303 4.6 19.2 1.0
CB F:ASN117 4.7 32.0 1.0
CA G:GLY106 4.7 21.8 1.0
O G:HOH402 4.7 38.2 1.0
O F:CYS116 4.7 33.0 1.0
O F:HOH464 4.7 30.1 1.0
O G:HOH418 4.8 19.6 1.0
CD G:GLU121 4.8 35.6 1.0
N G:THR107 4.8 26.5 1.0
N F:ASN117 5.0 27.9 1.0

Sodium binding site 5 out of 7 in 6qlv

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Sodium binding site 5 out of 7 in the Crystal Structure of W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na304

b:72.3
occ:1.00
 O K:HOH407 2.4 44.3 1.0
OD1 G:ASN117 2.5 39.1 1.0
O K:HOH454 2.5 31.7 1.0
O G:HOH425 2.6 23.1 1.0
O K:HOH418 2.6 38.0 1.0
O G:HOH446 2.6 31.6 1.0
OE2 K:GLU121 3.4 30.9 1.0
CG G:ASN117 3.6 36.1 1.0
O G:ALA115 4.1 31.3 1.0
ND2 G:ASN117 4.2 37.9 1.0
O1P K:FMN302 4.2 19.7 1.0
O3P K:FMN302 4.4 20.3 1.0
O K:GLY106 4.4 23.3 1.0
O K:HOH411 4.5 28.1 1.0
C K:GLY106 4.5 23.6 1.0
O G:HOH467 4.6 21.1 1.0
CD K:GLU121 4.6 30.8 1.0
O5' K:FMN302 4.7 25.1 1.0
P K:FMN302 4.7 19.8 1.0
CA G:ASN117 4.7 26.8 1.0
CB G:ASN117 4.7 29.8 1.0
O K:HOH439 4.7 28.0 1.0
CA K:GLY106 4.8 23.3 1.0
N K:THR107 4.9 20.3 1.0
O G:CYS116 5.0 27.8 1.0

Sodium binding site 6 out of 7 in 6qlv

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Sodium binding site 6 out of 7 in the Crystal Structure of W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na301

b:48.0
occ:1.00
 OD1 I:ASN117 2.4 36.6 1.0
O B:HOH429 2.4 22.9 1.0
O I:HOH424 2.5 32.0 1.0
O B:HOH461 2.7 25.7 1.0
O B:HOH442 2.7 29.5 1.0
O B:HOH453 3.0 25.2 1.0
OE2 B:GLU121 3.5 25.8 1.0
CG I:ASN117 3.5 36.2 1.0
O I:ALA115 4.1 26.5 1.0
ND2 I:ASN117 4.2 35.5 1.0
O2P B:FMN301 4.2 24.0 1.0
O B:GLY106 4.3 21.7 1.0
O1P B:FMN301 4.4 23.2 1.0
C B:GLY106 4.5 20.3 1.0
O I:HOH456 4.5 19.1 1.0
O B:HOH443 4.6 24.4 1.0
O B:HOH422 4.6 26.9 1.0
CA I:ASN117 4.7 32.1 1.0
CD B:GLU121 4.7 24.5 1.0
CB I:ASN117 4.7 35.1 1.0
O5' B:FMN301 4.7 24.9 1.0
P B:FMN301 4.7 25.3 1.0
CA B:GLY106 4.8 20.1 1.0
N B:THR107 4.9 19.2 1.0

Sodium binding site 7 out of 7 in 6qlv

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Sodium binding site 7 out of 7 in the Crystal Structure of W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of W200H Ubix in Complex with A Geranyl-Fmn N5 Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na304

b:49.0
occ:1.00
 O L:HOH422 2.4 28.5 1.0
OD1 J:ASN117 2.4 40.0 1.0
O J:HOH403 2.5 29.5 1.0
O L:HOH406 2.5 42.1 1.0
O L:HOH415 2.5 33.9 1.0
O J:HOH456 2.8 22.2 1.0
OE2 L:GLU121 3.4 35.2 1.0
CG J:ASN117 3.5 38.4 1.0
ND2 J:ASN117 4.1 39.6 1.0
O J:ALA115 4.2 26.9 1.0
O2P L:FMN301 4.2 22.2 1.0
O1P L:FMN301 4.4 28.5 1.0
O J:HOH468 4.5 19.7 1.0
O L:HOH404 4.5 21.2 1.0
O L:GLY106 4.5 26.9 1.0
CD L:GLU121 4.6 32.8 1.0
C L:GLY106 4.6 23.4 1.0
CB J:ASN117 4.7 35.1 1.0
O L:HOH445 4.7 33.0 1.0
CA J:ASN117 4.8 33.8 1.0
P L:FMN301 4.8 25.8 1.0
O5' L:FMN301 4.8 26.5 1.0
ND2 L:ASN118 5.0 27.5 1.0
CA L:GLY106 5.0 25.2 1.0
N L:THR107 5.0 21.8 1.0

Reference:

S.A.Marshall, K.A.P.Payne, K.Fisher, M.D.White, A.Ni Cheallaigh, A.Balaikaite, S.E.J.Rigby, D.Leys. The Ubix Flavin Prenyltransferase Reaction Mechanism Resembles Class I Terpene Cyclase Chemistry. Nat Commun V. 10 2357 2019.
ISSN: ESSN 2041-1723
PubMed: 31142738
DOI: 10.1038/S41467-019-10220-1
Page generated: Tue Oct 8 12:55:36 2024

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