Sodium in PDB 7xcm: Crystal Structure of Sulfite Mttb Structure at 3.2 A Resolution

Enzymatic activity of Crystal Structure of Sulfite Mttb Structure at 3.2 A Resolution

All present enzymatic activity of Crystal Structure of Sulfite Mttb Structure at 3.2 A Resolution:
2.1.1.250;

Protein crystallography data

The structure of Crystal Structure of Sulfite Mttb Structure at 3.2 A Resolution, PDB code: 7xcm 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 / 3.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 174.84, 174.84, 300.121, 90, 90, 120
R / Rfree (%) 16.7 / 24.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Sulfite Mttb Structure at 3.2 A Resolution (pdb code 7xcm). 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 Sulfite Mttb Structure at 3.2 A Resolution, PDB code: 7xcm:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 7xcm

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Sodium binding site 1 out of 6 in the Crystal Structure of Sulfite Mttb Structure at 3.2 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 Sulfite Mttb Structure at 3.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:63.3
occ:1.00
 O A:ILE397 1.9 61.2 1.0
O A:LEU13 2.0 59.6 1.0
O F:HOH719 2.4 42.2 1.0
O F:HOH706 2.4 55.8 1.0
O F:HOH714 2.4 70.0 1.0
O A:HOH717 2.4 60.1 1.0
C A:ILE397 3.1 48.1 1.0
C A:LEU13 3.2 47.2 1.0
O F:LEU20 3.7 42.6 1.0
N A:PRO398 3.9 43.9 1.0
CA A:PRO398 3.9 40.0 1.0
N A:ILE397 4.0 61.5 1.0
CA A:ILE397 4.1 49.1 1.0
CA A:ASN14 4.1 56.4 1.0
N A:ASN14 4.1 37.7 1.0
OE2 F:GLU25 4.1 38.3 1.0
CA A:LEU13 4.3 38.6 1.0
N A:VAL399 4.3 42.9 1.0
N A:GLY15 4.3 49.5 1.0
OE1 F:GLU25 4.5 35.7 1.0
N A:LEU13 4.5 43.7 1.0
CB A:LEU13 4.5 24.7 1.0
O A:GLY15 4.6 29.6 1.0
C A:PRO398 4.6 38.6 1.0
CD F:GLU25 4.6 39.9 1.0
OD1 A:ASN14 4.6 52.7 1.0
CB A:ILE397 4.7 45.7 1.0
C A:ASN14 4.7 50.6 1.0
CG2 A:VAL399 4.9 49.9 1.0
C F:LEU20 4.9 41.3 1.0
CG A:LEU13 4.9 24.1 1.0
O A:GLN395 4.9 35.6 1.0
CG2 A:ILE397 5.0 44.8 1.0

Sodium binding site 2 out of 6 in 7xcm

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Sodium binding site 2 out of 6 in the Crystal Structure of Sulfite Mttb Structure at 3.2 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 Sulfite Mttb Structure at 3.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na602

b:44.1
occ:1.00
 O B:ILE397 1.9 56.7 1.0
O B:LEU13 1.9 49.6 1.0
O E:HOH710 2.4 22.5 1.0
O E:HOH703 2.4 50.0 1.0
O B:HOH714 2.4 50.6 1.0
O B:HOH721 2.4 29.5 1.0
C B:ILE397 3.0 46.1 1.0
C B:LEU13 3.2 33.1 1.0
O E:LEU20 3.8 16.1 1.0
N B:PRO398 3.8 45.2 1.0
CA B:PRO398 3.9 37.9 1.0
N B:ILE397 3.9 37.6 1.0
CA B:ILE397 4.1 31.6 1.0
N B:ASN14 4.1 20.1 1.0
CA B:ASN14 4.1 31.7 1.0
N B:VAL399 4.2 35.1 1.0
CA B:LEU13 4.2 21.9 1.0
OE1 E:GLU25 4.3 31.6 1.0
OE2 E:GLU25 4.3 30.2 1.0
N B:GLY15 4.3 50.2 1.0
CB B:LEU13 4.4 10.7 1.0
N B:LEU13 4.5 31.9 1.0
O B:GLY15 4.5 61.2 1.0
C B:PRO398 4.6 41.8 1.0
C B:ASN14 4.6 44.0 1.0
CB B:ILE397 4.7 23.5 1.0
CD E:GLU25 4.7 43.9 1.0
CG2 B:VAL399 4.9 47.9 1.0
C B:GLY396 4.9 31.9 1.0
CG B:LEU13 4.9 16.7 1.0
OD1 B:ASN14 4.9 60.0 1.0
CG2 B:ILE397 5.0 35.3 1.0

Sodium binding site 3 out of 6 in 7xcm

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Sodium binding site 3 out of 6 in the Crystal Structure of Sulfite Mttb Structure at 3.2 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 Sulfite Mttb Structure at 3.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na602

b:56.1
occ:1.00
 O C:LEU13 1.9 64.5 1.0
O C:ILE397 1.9 62.2 1.0
O D:HOH703 2.4 52.9 1.0
O D:HOH707 2.4 48.1 1.0
O C:HOH707 2.4 50.4 1.0
O C:HOH715 2.4 48.1 1.0
C C:ILE397 3.1 54.6 1.0
C C:LEU13 3.2 50.5 1.0
O D:LEU20 3.7 52.0 1.0
N C:PRO398 3.9 53.3 1.0
CA C:PRO398 4.0 45.8 1.0
CA C:ASN14 4.0 35.4 1.0
N C:ASN14 4.0 39.3 1.0
OE2 D:GLU25 4.0 36.3 1.0
N C:ILE397 4.1 50.3 1.0
CA C:ILE397 4.1 49.7 1.0
N C:GLY15 4.2 38.2 1.0
CA C:LEU13 4.3 41.0 1.0
N C:VAL399 4.4 34.0 1.0
O C:GLY15 4.4 36.8 1.0
CB C:LEU13 4.5 20.0 1.0
OE1 D:GLU25 4.6 26.3 1.0
N C:LEU13 4.6 49.0 1.0
C C:ASN14 4.6 36.7 1.0
CD D:GLU25 4.6 31.2 1.0
C C:PRO398 4.7 39.2 1.0
CG C:LEU13 4.7 24.8 1.0
CB C:ILE397 4.7 50.4 1.0
OD1 C:ASN14 4.8 49.2 1.0
C D:LEU20 4.9 44.5 1.0

Sodium binding site 4 out of 6 in 7xcm

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Sodium binding site 4 out of 6 in the Crystal Structure of Sulfite Mttb Structure at 3.2 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 Sulfite Mttb Structure at 3.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na602

b:73.3
occ:1.00
 O D:ILE397 1.9 59.4 1.0
O D:LEU13 1.9 65.2 1.0
O C:HOH709 2.4 61.3 1.0
O D:HOH704 2.4 79.4 1.0
O C:HOH704 2.4 78.4 1.0
O D:HOH721 2.5 56.8 1.0
C D:ILE397 3.0 44.6 1.0
C D:LEU13 3.2 44.4 1.0
N D:PRO398 3.8 39.3 1.0
O C:LEU20 3.9 32.6 1.0
CA D:PRO398 4.0 43.1 1.0
CA D:ILE397 4.0 37.2 1.0
N D:ASN14 4.1 46.9 1.0
N D:ILE397 4.1 51.2 1.0
CA D:ASN14 4.1 49.3 1.0
OE2 C:GLU25 4.1 43.7 1.0
N D:GLY15 4.2 55.0 1.0
CA D:LEU13 4.3 32.6 1.0
N D:VAL399 4.3 42.2 1.0
CB D:LEU13 4.4 41.0 1.0
CG2 D:VAL399 4.5 36.6 1.0
N D:LEU13 4.5 30.6 1.0
O D:GLY15 4.5 51.4 1.0
OE1 C:GLU25 4.5 56.3 1.0
C D:PRO398 4.7 46.9 1.0
CB D:ILE397 4.7 19.4 1.0
C D:ASN14 4.7 52.0 1.0
CD C:GLU25 4.7 56.5 1.0
OD1 D:ASN14 4.8 76.2 1.0
CG D:LEU13 4.9 35.0 1.0
CG2 D:ILE397 5.0 2.3 1.0

Sodium binding site 5 out of 6 in 7xcm

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Sodium binding site 5 out of 6 in the Crystal Structure of Sulfite Mttb Structure at 3.2 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 Sulfite Mttb Structure at 3.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na602

b:62.3
occ:1.00
 O E:ILE397 1.9 55.6 1.0
O E:LEU13 2.0 47.4 1.0
O B:HOH717 2.4 46.8 1.0
O B:HOH703 2.4 54.1 1.0
O E:HOH711 2.4 39.4 1.0
O E:HOH717 2.4 55.4 1.0
C E:ILE397 3.1 45.5 1.0
C E:LEU13 3.2 31.0 1.0
O B:LEU20 3.8 44.4 1.0
N E:PRO398 3.9 36.6 1.0
CA E:PRO398 4.0 34.0 1.0
N E:ILE397 4.0 51.5 1.0
CA E:ILE397 4.1 41.3 1.0
N E:ASN14 4.1 13.0 1.0
CA E:ASN14 4.1 20.1 1.0
N E:GLY15 4.1 33.6 1.0
N E:VAL399 4.2 29.5 1.0
OE2 B:GLU25 4.2 47.3 1.0
CA E:LEU13 4.3 15.7 1.0
OE1 B:GLU25 4.4 24.9 1.0
CB E:LEU13 4.4 29.1 1.0
CG2 E:VAL399 4.5 46.7 1.0
N E:LEU13 4.5 14.8 1.0
O E:GLY15 4.6 40.7 1.0
CB E:ILE397 4.6 49.5 1.0
C E:PRO398 4.6 34.3 1.0
CD B:GLU25 4.6 48.8 1.0
C E:ASN14 4.7 11.8 1.0
CG2 E:ILE397 4.9 65.8 1.0
C B:LEU20 4.9 37.7 1.0
O E:GLN395 4.9 23.4 1.0

Sodium binding site 6 out of 6 in 7xcm

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Sodium binding site 6 out of 6 in the Crystal Structure of Sulfite Mttb Structure at 3.2 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 Sulfite Mttb Structure at 3.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na602

b:50.4
occ:1.00
 O F:ILE397 1.9 43.5 1.0
O F:LEU13 2.0 53.8 1.0
O A:HOH711 2.4 47.3 1.0
O A:HOH704 2.4 45.9 1.0
O F:HOH713 2.4 45.9 1.0
O F:HOH701 2.4 52.3 1.0
C F:ILE397 3.1 29.1 1.0
C F:LEU13 3.2 35.7 1.0
O A:LEU20 3.7 36.2 1.0
OE2 A:GLU25 3.8 43.2 1.0
N F:PRO398 3.9 34.4 1.0
CA F:PRO398 4.0 24.6 1.0
N F:GLY15 4.0 54.8 1.0
CA F:ASN14 4.0 40.9 1.0
N F:ILE397 4.0 28.0 1.0
N F:ASN14 4.1 26.3 1.0
CA F:ILE397 4.1 15.7 1.0
N F:VAL399 4.2 22.9 1.0
CA F:LEU13 4.3 20.1 1.0
O F:GLY15 4.4 53.5 1.0
C F:ASN14 4.5 43.9 1.0
CD A:GLU25 4.5 24.8 1.0
OE1 A:GLU25 4.5 38.8 1.0
N F:LEU13 4.6 26.8 1.0
CB F:LEU13 4.6 11.6 1.0
C F:PRO398 4.6 23.4 1.0
CB F:ILE397 4.7 22.3 1.0
CG2 F:VAL399 4.9 32.6 1.0
C A:LEU20 4.9 40.7 1.0
CA F:GLY15 5.0 59.2 1.0
OD1 F:ASN14 5.0 69.3 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: Fri Apr 7 17:09:11 2023

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