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Sodium in PDB 7xcl: Crystal Structure of Trimethylamine Methyltransferase Mttb From Methanosarcina Barkeri at 2.5 A Resolution

Enzymatic activity of Crystal Structure of Trimethylamine Methyltransferase Mttb From Methanosarcina Barkeri at 2.5 A Resolution

All present enzymatic activity of Crystal Structure of Trimethylamine Methyltransferase Mttb From Methanosarcina Barkeri at 2.5 A Resolution:
2.1.1.250;

Protein crystallography data

The structure of Crystal Structure of Trimethylamine Methyltransferase Mttb From Methanosarcina Barkeri at 2.5 A Resolution, PDB code: 7xcl was solved by J.Li, M.K.Chan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 175.492, 175.492, 300.996, 90, 90, 120
R / Rfree (%) 17.5 / 21.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Trimethylamine Methyltransferase Mttb From Methanosarcina Barkeri at 2.5 A Resolution (pdb code 7xcl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Trimethylamine Methyltransferase Mttb From Methanosarcina Barkeri at 2.5 A Resolution, PDB code: 7xcl:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 7xcl

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Sodium binding site 1 out of 6 in the Crystal Structure of Trimethylamine Methyltransferase Mttb From Methanosarcina Barkeri at 2.5 A Resolution


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 Trimethylamine Methyltransferase Mttb From Methanosarcina Barkeri at 2.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:42.4
occ:1.00
 O A:ILE397 2.0 43.0 1.0
O A:LEU13 2.0 37.9 1.0
O A:HOH779 2.4 36.2 1.0
O F:HOH706 2.4 33.9 1.0
O A:HOH773 2.4 35.0 1.0
O A:HOH731 2.4 31.2 1.0
C A:ILE397 3.0 40.5 1.0
C A:LEU13 3.3 31.9 1.0
O F:LEU20 3.7 39.6 1.0
N A:PRO398 3.8 40.5 1.0
CA A:PRO398 3.8 37.3 1.0
OE2 F:GLU25 4.0 34.1 1.0
N A:ILE397 4.0 40.5 1.0
CA A:ILE397 4.1 39.8 1.0
N A:ASN14 4.1 30.7 1.0
CA A:ASN14 4.1 34.8 1.0
N A:VAL399 4.2 34.8 1.0
N A:GLY15 4.3 31.7 1.0
CA A:LEU13 4.4 33.3 1.0
O A:GLY15 4.5 33.0 1.0
C A:PRO398 4.5 36.2 1.0
CD F:GLU25 4.6 38.3 1.0
CB A:LEU13 4.6 37.0 1.0
CB A:ILE397 4.6 51.0 1.0
OE1 F:GLU25 4.6 39.3 1.0
N A:LEU13 4.7 40.5 1.0
C A:ASN14 4.7 33.8 1.0
OD1 A:ASN14 4.8 62.1 1.0
CG2 A:VAL399 4.8 34.3 1.0
CG A:LEU13 4.9 47.2 1.0
C F:LEU20 4.9 38.4 1.0
C A:GLY396 5.0 42.8 1.0

Sodium binding site 2 out of 6 in 7xcl

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Sodium binding site 2 out of 6 in the Crystal Structure of Trimethylamine Methyltransferase Mttb From Methanosarcina Barkeri at 2.5 A Resolution


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 Trimethylamine Methyltransferase Mttb From Methanosarcina Barkeri at 2.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na603

b:34.8
occ:1.00
 O B:ILE397 2.0 34.9 1.0
O B:LEU13 2.0 40.8 1.0
O E:HOH719 2.4 42.2 1.0
O E:HOH745 2.4 23.6 1.0
O B:HOH792 2.4 31.1 1.0
O B:HOH756 2.4 35.0 1.0
C B:ILE397 3.0 31.2 1.0
C B:LEU13 3.3 34.4 1.0
N B:PRO398 3.7 35.1 1.0
CA B:PRO398 3.8 36.3 1.0
O E:LEU20 3.8 33.0 1.0
N B:ILE397 3.9 34.1 1.0
OE2 E:GLU25 4.0 38.3 1.0
CA B:ILE397 4.0 34.0 1.0
N B:ASN14 4.1 28.1 1.0
CA B:ASN14 4.2 37.4 1.0
N B:VAL399 4.2 35.9 1.0
CA B:LEU13 4.3 32.5 1.0
N B:GLY15 4.4 39.4 1.0
C B:PRO398 4.4 34.3 1.0
OE1 E:GLU25 4.5 40.6 1.0
CD E:GLU25 4.5 38.1 1.0
CB B:LEU13 4.5 36.1 1.0
O B:GLY15 4.5 38.7 1.0
CB B:ILE397 4.6 36.1 1.0
N B:LEU13 4.6 37.4 1.0
C B:ASN14 4.7 37.3 1.0
CG2 B:VAL399 4.8 32.0 1.0
OD1 B:ASN14 4.9 58.0 1.0
CD B:PRO398 4.9 33.9 1.0
CG2 B:ILE397 4.9 41.9 1.0
CG B:LEU13 5.0 43.8 1.0
C E:LEU20 5.0 32.5 1.0

Sodium binding site 3 out of 6 in 7xcl

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Sodium binding site 3 out of 6 in the Crystal Structure of Trimethylamine Methyltransferase Mttb From Methanosarcina Barkeri at 2.5 A Resolution


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 Trimethylamine Methyltransferase Mttb From Methanosarcina Barkeri at 2.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na602

b:41.5
occ:1.00
 O C:ILE397 2.0 44.0 1.0
O C:LEU13 2.0 44.2 1.0
O D:HOH714 2.4 41.4 1.0
O C:HOH742 2.4 40.0 1.0
O C:HOH715 2.4 37.4 1.0
O C:HOH754 2.4 36.5 1.0
C C:ILE397 3.0 36.0 1.0
C C:LEU13 3.3 38.7 1.0
O D:LEU20 3.8 32.9 1.0
N C:PRO398 3.8 37.2 1.0
CA C:PRO398 3.9 34.9 1.0
N C:ILE397 4.0 42.6 1.0
OE2 D:GLU25 4.0 29.5 1.0
CA C:ILE397 4.0 36.3 1.0
N C:ASN14 4.1 35.2 1.0
CA C:ASN14 4.2 40.6 1.0
N C:VAL399 4.3 33.4 1.0
CA C:LEU13 4.3 36.5 1.0
N C:GLY15 4.3 34.2 1.0
O C:GLY15 4.5 42.0 1.0
O C:HOH761 4.5 38.1 1.0
CB C:LEU13 4.5 39.6 1.0
C C:PRO398 4.5 34.1 1.0
N C:LEU13 4.6 41.4 1.0
CD D:GLU25 4.6 37.0 1.0
CB C:ILE397 4.6 37.0 1.0
OE1 D:GLU25 4.7 33.0 1.0
C C:ASN14 4.7 39.1 1.0
CG2 C:VAL399 4.8 19.0 1.0
C D:LEU20 4.9 39.4 1.0
OD1 C:ASN14 5.0 51.2 1.0

Sodium binding site 4 out of 6 in 7xcl

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Sodium binding site 4 out of 6 in the Crystal Structure of Trimethylamine Methyltransferase Mttb From Methanosarcina Barkeri at 2.5 A Resolution


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 Trimethylamine Methyltransferase Mttb From Methanosarcina Barkeri at 2.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na604

b:49.6
occ:1.00
 O D:ILE397 2.0 50.1 1.0
O D:LEU13 2.0 46.2 1.0
O C:HOH711 2.4 43.4 1.0
O C:HOH735 2.4 37.5 1.0
O D:HOH758 2.4 40.6 1.0
O D:HOH719 2.4 41.7 1.0
C D:ILE397 3.1 43.6 1.0
C D:LEU13 3.2 37.4 1.0
O C:LEU20 3.7 33.6 1.0
N D:PRO398 3.8 42.4 1.0
CA D:PRO398 3.9 39.2 1.0
OE2 C:GLU25 4.0 45.2 1.0
N D:ILE397 4.1 41.9 1.0
CA D:ILE397 4.1 45.7 1.0
N D:ASN14 4.1 37.4 1.0
N D:GLY15 4.1 39.8 1.0
CA D:ASN14 4.1 37.1 1.0
N D:VAL399 4.3 39.9 1.0
CA D:LEU13 4.3 39.4 1.0
O D:GLY15 4.5 39.0 1.0
C D:PRO398 4.5 43.8 1.0
OE1 C:GLU25 4.6 42.6 1.0
CB D:LEU13 4.6 42.0 1.0
CD C:GLU25 4.6 40.8 1.0
N D:LEU13 4.7 44.3 1.0
C D:ASN14 4.7 40.1 1.0
CB D:ILE397 4.7 53.8 1.0
CG2 D:VAL399 4.7 25.3 1.0
C C:LEU20 4.9 36.6 1.0
CG D:LEU13 5.0 47.6 1.0
OD1 D:ASN14 5.0 60.4 1.0
C D:GLY396 5.0 43.4 1.0

Sodium binding site 5 out of 6 in 7xcl

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Sodium binding site 5 out of 6 in the Crystal Structure of Trimethylamine Methyltransferase Mttb From Methanosarcina Barkeri at 2.5 A Resolution


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 Trimethylamine Methyltransferase Mttb From Methanosarcina Barkeri at 2.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na603

b:39.2
occ:1.00
 O E:ILE397 2.0 39.3 1.0
O E:LEU13 2.0 37.2 1.0
O E:HOH770 2.4 34.7 1.0
O B:HOH730 2.4 36.1 1.0
O B:HOH739 2.4 34.3 1.0
O E:HOH775 2.4 33.1 1.0
C E:ILE397 3.0 34.3 1.0
C E:LEU13 3.3 26.5 1.0
O B:LEU20 3.7 36.5 1.0
N E:PRO398 3.8 26.0 1.0
CA E:PRO398 3.9 31.6 1.0
N E:ILE397 4.0 29.1 1.0
OE2 B:GLU25 4.0 34.3 1.0
CA E:ILE397 4.1 29.2 1.0
N E:ASN14 4.1 20.8 1.0
CA E:ASN14 4.2 29.8 1.0
N E:GLY15 4.3 28.1 1.0
N E:VAL399 4.3 32.4 1.0
CA E:LEU13 4.3 28.9 1.0
O E:HOH784 4.4 36.8 1.0
O E:GLY15 4.5 28.8 1.0
C E:PRO398 4.5 33.5 1.0
CB E:LEU13 4.6 28.6 1.0
CB E:ILE397 4.6 34.4 1.0
N E:LEU13 4.6 38.6 1.0
CD B:GLU25 4.7 32.1 1.0
C E:ASN14 4.7 32.0 1.0
OE1 B:GLU25 4.7 39.9 1.0
CG2 E:VAL399 4.9 25.7 1.0
C B:LEU20 4.9 32.5 1.0

Sodium binding site 6 out of 6 in 7xcl

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Sodium binding site 6 out of 6 in the Crystal Structure of Trimethylamine Methyltransferase Mttb From Methanosarcina Barkeri at 2.5 A Resolution


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 Trimethylamine Methyltransferase Mttb From Methanosarcina Barkeri at 2.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na602

b:38.8
occ:1.00
 O F:ILE397 1.9 38.7 1.0
O F:LEU13 2.0 38.7 1.0
O F:HOH772 2.4 36.1 1.0
O A:HOH717 2.4 31.4 1.0
O F:HOH748 2.4 27.9 1.0
O F:HOH785 2.4 27.8 1.0
C F:ILE397 3.0 35.1 1.0
C F:LEU13 3.3 31.6 1.0
O A:LEU20 3.8 33.9 1.0
N F:PRO398 3.8 33.3 1.0
CA F:PRO398 3.8 34.4 1.0
N F:ILE397 4.0 37.5 1.0
OE2 A:GLU25 4.0 32.3 1.0
CA F:ILE397 4.0 30.6 1.0
N F:ASN14 4.1 31.9 1.0
CA F:ASN14 4.2 38.0 1.0
N F:GLY15 4.3 35.8 1.0
N F:VAL399 4.3 29.2 1.0
CA F:LEU13 4.4 32.3 1.0
O F:HOH759 4.4 38.9 1.0
C F:PRO398 4.5 34.6 1.0
CB F:LEU13 4.6 40.9 1.0
O F:GLY15 4.6 29.1 1.0
CB F:ILE397 4.6 39.0 1.0
CD A:GLU25 4.6 35.5 1.0
N F:LEU13 4.7 33.2 1.0
OE1 A:GLU25 4.7 33.7 1.0
C F:ASN14 4.7 38.3 1.0
CG2 F:VAL399 4.9 14.3 1.0
CD F:PRO398 5.0 34.5 1.0
C A:LEU20 5.0 35.1 1.0
C F:GLY396 5.0 38.6 1.0
OD1 F:ASN14 5.0 49.8 1.0

Reference:

J.Li, P.T.Kang, R.Jiang, J.Y.Lee, J.A.Soares, J.A.Krzycki, M.K.Chan. Insights Into Pyrrolysine Function From Structures of A Trimethylamine Methyltransferase and Its Corrinoid Protein Complex Commun Biol 2023.
ISSN: ESSN 2399-3642
DOI: 10.1038/S42003-022-04397-3
Page generated: Wed Oct 9 09:39:32 2024

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