Sodium in PDB 8u2m: Structure of P450BLT From Micromonospora Sp. Mw-13 in Complex with Biarylitide

The structure of Structure of P450BLT From Micromonospora Sp. Mw-13 in Complex with Biarylitide, PDB code: 8u2m was solved by M.H.Hansen, M.J.Cryle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.80 / 1.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.674, 95.607, 105.763, 90, 92.71, 90
R / Rfree (%)	19.9 / 22.9

The structure of Structure of P450BLT From Micromonospora Sp. Mw-13 in Complex with Biarylitide also contains other interesting chemical elements:

Fluorine	(F)	12 atoms
Iron	(Fe)	3 atoms

The binding sites of Sodium atom in the Structure of P450BLT From Micromonospora Sp. Mw-13 in Complex with Biarylitide (pdb code 8u2m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of P450BLT From Micromonospora Sp. Mw-13 in Complex with Biarylitide, PDB code: 8u2m:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Structure of P450BLT From Micromonospora Sp. Mw-13 in Complex with Biarylitide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of P450BLT From Micromonospora Sp. Mw-13 in Complex with Biarylitide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:43.5 occ:1.00 OD2 A:ASP133 2.3 28.7 1.0 O A:ALA386 2.7 28.2 1.0 HA A:GLU387 3.2 34.3 1.0 HB3 A:SER136 3.2 34.0 1.0 CG A:ASP133 3.2 27.7 1.0 HB A:VAL135 3.3 28.8 1.0 O A:HOH602 3.6 36.8 1.0 H A:SER136 3.6 27.3 1.0 HG A:SER136 3.6 33.8 1.0 OD1 A:ASP133 3.7 22.8 1.0 HB2 A:GLU387 3.7 38.1 1.0 C A:ALA386 3.8 30.4 1.0 HG12 A:VAL135 3.8 35.4 1.0 HG3 A:GLU387 4.0 44.5 1.0 CA A:GLU387 4.0 28.6 1.0 CB A:SER136 4.0 28.3 1.0 OG A:SER136 4.1 28.2 1.0 CB A:VAL135 4.2 24.0 1.0 HH12 A:ARG140 4.2 41.5 1.0 CB A:GLU387 4.2 31.7 1.0 N A:SER136 4.2 22.7 1.0 HG11 A:VAL135 4.3 35.4 1.0 CG1 A:VAL135 4.3 29.5 1.0 N A:GLU387 4.3 23.1 1.0 CB A:ASP133 4.4 28.0 1.0 HB3 A:ASP133 4.5 33.5 1.0 NH1 A:ARG140 4.5 34.6 1.0 HB2 A:ASP133 4.5 33.5 1.0 CG A:GLU387 4.6 37.1 1.0 CA A:SER136 4.7 26.3 1.0 HB2 A:SER136 4.8 34.0 1.0 HH11 A:ARG140 4.8 41.5 1.0 HG21 A:VAL135 4.8 25.9 1.0 HH22 A:ARG140 4.9 38.2 1.0 H A:LEU388 4.9 29.3 1.0 HA A:ALA386 5.0 34.3 1.0

Sodium binding site 2 out of 5 in the Structure of P450BLT From Micromonospora Sp. Mw-13 in Complex with Biarylitide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of P450BLT From Micromonospora Sp. Mw-13 in Complex with Biarylitide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:55.3 occ:1.00 H A:ALA159 2.3 49.0 1.0 OD1 A:ASP157 2.6 57.8 1.0 HB1 A:ALA159 3.1 59.0 1.0 HB3 A:ALA159 3.1 59.0 1.0 N A:ALA159 3.1 40.8 1.0 H A:GLY158 3.2 51.5 1.0 CG A:ASP157 3.2 57.9 1.0 OD2 A:ASP157 3.4 57.6 1.0 CB A:ALA159 3.5 49.1 1.0 N A:GLY158 3.6 42.9 1.0 CA A:ALA159 3.9 45.3 1.0 HA3 A:GLY158 4.0 41.2 1.0 C A:GLY158 4.1 39.3 1.0 CA A:GLY158 4.1 34.3 1.0 H A:GLY160 4.3 51.1 1.0 C A:ASP157 4.3 46.6 1.0 HA A:ASP157 4.3 49.0 1.0 HB2 A:ALA159 4.4 59.0 1.0 CB A:ASP157 4.5 50.5 1.0 HA A:ALA159 4.5 54.3 1.0 CA A:ASP157 4.6 40.8 1.0 N A:GLY160 4.9 42.6 1.0 C A:ALA159 5.0 50.8 1.0 HB2 A:ASP157 5.0 60.6 1.0

Sodium binding site 3 out of 5 in the Structure of P450BLT From Micromonospora Sp. Mw-13 in Complex with Biarylitide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of P450BLT From Micromonospora Sp. Mw-13 in Complex with Biarylitide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:51.5 occ:1.00 OD1 A:ASP303 2.4 27.3 1.0 O A:ARG301 3.0 29.6 1.0 O A:HOH690 3.2 45.8 1.0 HA3 A:GLY302 3.3 33.7 1.0 H A:ASP303 3.3 31.5 1.0 N A:ASP303 3.3 26.2 1.0 CG A:ASP303 3.5 31.1 1.0 C A:GLY302 3.5 28.5 1.0 HB2 A:ARG300 3.6 41.4 1.0 HA A:ASP303 3.7 27.9 1.0 CA A:GLY302 3.8 28.1 1.0 C A:ARG301 3.9 32.7 1.0 CA A:ASP303 4.0 23.3 1.0 O A:ARG300 4.0 24.9 1.0 O A:GLY302 4.1 26.1 1.0 N A:GLY302 4.2 29.2 1.0 CB A:ASP303 4.3 24.4 1.0 OD2 A:ASP303 4.3 27.9 1.0 HB3 A:ARG300 4.4 41.4 1.0 O A:ACT405 4.4 46.0 0.9 CB A:ARG300 4.4 34.5 1.0 C A:ARG300 4.5 28.0 1.0 HA2 A:GLY302 4.7 33.7 1.0 HB2 A:ASP303 4.7 29.3 1.0

Sodium binding site 4 out of 5 in the Structure of P450BLT From Micromonospora Sp. Mw-13 in Complex with Biarylitide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of P450BLT From Micromonospora Sp. Mw-13 in Complex with Biarylitide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na408 b:51.0 occ:1.00 OE1 B:GLU54 2.7 29.1 1.0 O B:HOH657 2.7 31.9 1.0 HG21 B:THR37 3.0 42.5 1.0 HB3 B:ALA53 3.1 43.5 1.0 OE2 B:GLU54 3.2 51.0 1.0 HA3 B:GLY51 3.2 32.0 1.0 CD B:GLU54 3.3 30.4 1.0 H B:ALA53 3.4 31.8 1.0 CG2 B:THR37 3.9 35.4 1.0 CA B:GLY51 4.0 26.6 1.0 H B:GLU54 4.0 39.1 1.0 CB B:ALA53 4.0 36.2 1.0 HA2 B:GLY51 4.0 32.0 1.0 HB2 B:ALA53 4.0 43.5 1.0 H B:TYR52 4.1 31.8 1.0 HB B:THR37 4.1 39.4 1.0 N B:ALA53 4.1 26.5 1.0 HG22 B:THR37 4.2 42.5 1.0 OD2 B:ASP315 4.2 33.0 1.0 N B:TYR52 4.3 26.5 1.0 C B:GLY51 4.3 28.8 1.0 CB B:THR37 4.4 32.8 1.0 OG1 B:THR37 4.5 37.1 1.0 HG23 B:THR37 4.6 42.5 1.0 CA B:ALA53 4.6 28.4 1.0 O B:HOH750 4.6 48.7 1.0 N B:GLU54 4.7 32.6 1.0 HB1 B:ALA53 4.7 43.5 1.0 CG B:GLU54 4.8 30.4 1.0

Sodium binding site 5 out of 5 in the Structure of P450BLT From Micromonospora Sp. Mw-13 in Complex with Biarylitide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of P450BLT From Micromonospora Sp. Mw-13 in Complex with Biarylitide within 5.0Å range: probe atom residue distance (Å) B Occ C:Na404 b:50.1 occ:1.00 O C:HOH632 2.5 47.2 1.0 OD2 C:ASP133 2.7 38.5 1.0 O C:ALA386 2.7 38.0 1.0 HB3 C:SER136 3.3 35.5 1.0 HA C:GLU387 3.4 39.4 1.0 HB C:VAL135 3.5 41.1 1.0 HB2 C:GLU387 3.6 40.3 1.0 O C:HOH587 3.7 36.9 1.0 CG C:ASP133 3.7 38.2 1.0 HG13 C:VAL135 3.7 31.7 1.0 HH12 C:ARG140 3.8 53.3 1.0 C C:ALA386 3.9 34.3 1.0 H C:SER136 3.9 38.0 1.0 HG C:SER136 3.9 43.5 1.0 HG3 C:GLU387 4.0 56.3 1.0 OD1 C:ASP133 4.1 34.0 1.0 CB C:SER136 4.1 29.6 1.0 CA C:GLU387 4.1 32.8 1.0 NH1 C:ARG140 4.2 44.4 1.0 CB C:GLU387 4.2 33.6 1.0 OG C:SER136 4.3 36.3 1.0 CB C:VAL135 4.4 34.3 1.0 CG1 C:VAL135 4.4 26.4 1.0 N C:SER136 4.4 31.7 1.0 HH11 C:ARG140 4.4 53.3 1.0 N C:GLU387 4.5 35.5 1.0 HG12 C:VAL135 4.5 31.7 1.0 CG C:GLU387 4.6 46.9 1.0 HH22 C:ARG140 4.7 48.8 1.0 HB2 C:SER136 4.8 35.5 1.0 CA C:SER136 4.9 30.9 1.0 CZ C:ARG140 4.9 37.8 1.0 CB C:ASP133 4.9 35.6 1.0 HG22 C:VAL135 4.9 32.4 1.0 HB3 C:ASP133 4.9 42.8 1.0 HA C:ALA386 5.0 38.4 1.0

M.H.Hansen, A.Keto, M.Treisman, V.M.Sasi, L.Coe, Y.Zhao, L.Padva, C.Hess, V.Leichthammer, D.L.Machell, R.B.Schittenhelm, C.J.Jackson, J.Tailhades, M.Crusemann, J.J.De Voss, E.H.Krenske, M.J.Cryle. Structural Insights Into A Side Chain Cross-Linking Biarylitide P450 From Ripp Biosynthesis Acs Catalysis 812 2024.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.3C05417