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Strontium in PDB 6jcl: Crystal Structure of Cofactor-Bound RV0187 From Mtb

Protein crystallography data

The structure of Crystal Structure of Cofactor-Bound RV0187 From Mtb, PDB code: 6jcl was solved by J.Kim, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.23 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.300, 75.920, 329.839, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 20.7

Other elements in 6jcl:

The structure of Crystal Structure of Cofactor-Bound RV0187 From Mtb also contains other interesting chemical elements:

Sodium (Na) 1 atom

Strontium Binding Sites:

The binding sites of Strontium atom in the Crystal Structure of Cofactor-Bound RV0187 From Mtb (pdb code 6jcl). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 10 binding sites of Strontium where determined in the Crystal Structure of Cofactor-Bound RV0187 From Mtb, PDB code: 6jcl:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 10 in 6jcl

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Strontium binding site 1 out of 10 in the Crystal Structure of Cofactor-Bound RV0187 From Mtb


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Crystal Structure of Cofactor-Bound RV0187 From Mtb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr302

b:18.1
occ:0.85
 O C:HOH444 2.5 21.6 1.0
OD2 A:ASP165 2.5 18.4 1.0
OD1 A:ASP139 2.5 18.2 1.0
O A:HOH438 2.5 20.6 1.0
OD2 C:ASP178 2.6 17.4 1.0
OD1 A:ASN166 2.6 16.8 1.0
OD2 A:ASP139 2.6 17.9 1.0
CG A:ASP139 2.9 17.0 1.0
CG A:ASP165 3.5 17.9 1.0
CG C:ASP178 3.5 18.9 1.0
CG A:ASN166 3.5 19.7 1.0
OD1 C:ASP178 3.8 18.4 1.0
ND2 A:ASN166 3.8 16.5 1.0
CB A:ASP165 3.9 16.3 1.0
O A:HOH439 4.1 19.3 1.0
O A:ILE42 4.3 18.5 1.0
O A:HOH409 4.3 24.7 1.0
NZ A:LYS209 4.3 20.7 1.0
NZ A:LYS142 4.3 23.8 1.0
CB A:ASP139 4.4 16.2 1.0
OD1 A:ASP165 4.6 19.3 1.0
O C:HOH458 4.7 38.8 1.0
CB A:SAH301 4.7 15.6 1.0
OXT A:SAH301 4.9 18.5 1.0
CB C:ASP178 4.9 15.3 1.0
CB A:ASN166 4.9 18.7 1.0

Strontium binding site 2 out of 10 in 6jcl

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Strontium binding site 2 out of 10 in the Crystal Structure of Cofactor-Bound RV0187 From Mtb


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Crystal Structure of Cofactor-Bound RV0187 From Mtb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr304

b:17.0
occ:0.85
 O C:HOH421 2.5 29.1 1.0
OD1 A:ASP181 2.5 50.8 1.0
OD1 C:ASP179 2.5 26.2 1.0
OD1 A:ASP179 2.5 32.3 1.0
O C:HOH508 2.6 31.9 1.0
OD1 C:ASP181 2.7 34.5 1.0
OD2 A:ASP181 2.7 40.1 1.0
OD2 C:ASP179 2.7 38.9 1.0
CG A:ASP181 2.9 23.9 1.0
CG C:ASP179 2.9 20.6 1.0
OD2 A:ASP179 3.1 34.6 1.0
CG A:ASP179 3.1 25.5 1.0
CG C:ASP181 3.2 28.5 1.0
OD2 C:ASP181 3.3 40.8 1.0
CB C:ASP179 4.4 17.5 1.0
CB A:ASP181 4.4 16.2 1.0
CB A:ASP179 4.5 20.8 1.0
CB C:ASP181 4.5 17.8 1.0
N C:ASP181 4.6 15.7 1.0
NH2 A:ARG169 4.6 19.5 1.0
N A:ASP181 4.6 17.5 1.0
NH2 C:ARG169 4.6 17.7 1.0
NE C:ARG169 4.7 18.8 1.0
NE A:ARG169 4.7 18.1 1.0
N C:ALA182 4.9 16.0 1.0
CA A:ASP179 4.9 19.9 1.0
CA C:ASP179 4.9 17.2 1.0
N A:ALA182 5.0 16.9 1.0
C C:ASP179 5.0 15.4 1.0

Strontium binding site 3 out of 10 in 6jcl

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Strontium binding site 3 out of 10 in the Crystal Structure of Cofactor-Bound RV0187 From Mtb


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Crystal Structure of Cofactor-Bound RV0187 From Mtb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr305

b:18.9
occ:0.85
 OD1 C:ASP139 2.4 22.2 1.0
OD2 C:ASP165 2.5 22.1 1.0
O A:HOH475 2.5 20.6 1.0
OD2 A:ASP178 2.5 25.2 1.0
O C:HOH424 2.5 20.3 1.0
OD1 C:ASN166 2.6 20.2 1.0
OD2 C:ASP139 2.7 18.7 1.0
CG C:ASP139 2.9 20.5 1.0
CG C:ASP165 3.5 19.9 1.0
CG A:ASP178 3.5 24.2 1.0
CG C:ASN166 3.5 19.7 1.0
OD1 A:ASP178 3.8 23.3 1.0
ND2 C:ASN166 3.8 18.2 1.0
CB C:ASP165 3.9 16.3 1.0
O C:HOH440 4.1 17.8 1.0
NZ C:LYS209 4.2 17.4 1.0
O C:HOH404 4.2 32.7 1.0
O C:ILE42 4.3 21.7 1.0
NZ C:LYS142 4.4 26.3 1.0
CB C:ASP139 4.4 19.2 1.0
OD1 C:ASP165 4.5 19.7 1.0
O A:HOH488 4.7 28.2 1.0
CB C:SAH301 4.8 20.0 1.0
CB A:ASP178 4.9 24.1 1.0
O C:SAH301 4.9 20.6 1.0
CB C:ASN166 4.9 16.7 1.0

Strontium binding site 4 out of 10 in 6jcl

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Strontium binding site 4 out of 10 in the Crystal Structure of Cofactor-Bound RV0187 From Mtb


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Crystal Structure of Cofactor-Bound RV0187 From Mtb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr302

b:18.7
occ:0.85
 O E:HOH417 2.4 21.3 1.0
OD2 B:ASP165 2.5 19.9 1.0
OD1 B:ASP139 2.5 21.2 1.0
O B:HOH450 2.5 20.5 1.0
OD2 E:ASP178 2.5 25.0 1.0
OD1 B:ASN166 2.6 19.6 1.0
OD2 B:ASP139 2.6 18.1 1.0
CG B:ASP139 2.9 20.5 1.0
CG E:ASP178 3.5 24.7 1.0
CG B:ASP165 3.5 19.0 1.0
CG B:ASN166 3.6 18.1 1.0
OD1 E:ASP178 3.7 25.9 1.0
ND2 B:ASN166 3.8 16.9 1.0
O B:HOH439 3.9 21.4 1.0
CB B:ASP165 4.0 15.2 1.0
O B:ILE42 4.3 24.2 1.0
NZ B:LYS209 4.3 18.2 1.0
O B:HOH405 4.3 29.6 1.0
NZ B:LYS142 4.3 20.2 1.0
CB B:ASP139 4.4 17.8 1.0
OD1 B:ASP165 4.5 18.3 1.0
O E:HOH496 4.7 43.2 1.0
CB B:SAH301 4.7 21.2 1.0
O B:SAH301 4.8 21.1 1.0
CB E:ASP178 4.9 23.4 1.0
CB B:ASN166 4.9 14.9 1.0

Strontium binding site 5 out of 10 in 6jcl

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Strontium binding site 5 out of 10 in the Crystal Structure of Cofactor-Bound RV0187 From Mtb


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Crystal Structure of Cofactor-Bound RV0187 From Mtb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr306

b:19.1
occ:0.85
 OD1 E:ASP139 2.5 20.4 1.0
O E:HOH439 2.5 19.8 1.0
OD2 B:ASP178 2.5 29.2 1.0
OD2 E:ASP165 2.6 20.6 1.0
OD1 E:ASN166 2.6 19.2 1.0
O B:HOH433 2.6 23.7 1.0
OD2 E:ASP139 2.6 20.9 1.0
CG E:ASP139 2.9 20.9 1.0
CG B:ASP178 3.5 27.7 1.0
CG E:ASP165 3.5 22.4 1.0
CG E:ASN166 3.6 20.7 1.0
OD1 B:ASP178 3.7 26.9 1.0
ND2 E:ASN166 3.8 19.3 1.0
CB E:ASP165 3.9 18.0 1.0
O E:HOH419 3.9 23.0 1.0
O E:ILE42 4.3 22.8 1.0
O E:HOH436 4.3 24.6 1.0
NZ E:LYS209 4.3 21.5 1.0
CB E:ASP139 4.4 18.7 1.0
NZ E:LYS142 4.4 27.4 1.0
OD1 E:ASP165 4.6 23.3 1.0
O B:HOH498 4.6 33.8 1.0
CB E:SAH301 4.7 18.7 1.0
OXT E:SAH301 4.8 21.8 1.0
CB B:ASP178 4.9 27.0 1.0
CB E:ASN166 4.9 18.2 1.0

Strontium binding site 6 out of 10 in 6jcl

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Strontium binding site 6 out of 10 in the Crystal Structure of Cofactor-Bound RV0187 From Mtb


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Crystal Structure of Cofactor-Bound RV0187 From Mtb within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sr302

b:33.4
occ:0.85
 OD1 D:ASP139 2.4 33.8 1.0
O D:HOH430 2.5 26.4 1.0
OD2 D:ASP165 2.5 37.2 1.0
O H:HOH427 2.5 28.1 1.0
OD2 H:ASP178 2.5 31.6 1.0
OD2 D:ASP139 2.6 34.7 1.0
OD1 D:ASN166 2.6 32.6 1.0
CG D:ASP139 2.9 36.1 1.0
CG H:ASP178 3.5 34.6 1.0
CG D:ASP165 3.5 32.3 1.0
CG D:ASN166 3.6 29.8 1.0
OD1 H:ASP178 3.8 34.0 1.0
ND2 D:ASN166 3.8 28.4 1.0
CB D:ASP165 4.0 33.3 1.0
O D:HOH443 4.0 28.8 1.0
O D:HOH427 4.2 39.9 1.0
O D:ILE42 4.3 36.5 1.0
CB D:ASP139 4.3 35.0 1.0
NZ D:LYS209 4.4 32.8 1.0
NZ D:LYS142 4.4 39.2 1.0
OD1 D:ASP165 4.6 30.1 1.0
CB D:SAH301 4.8 38.2 1.0
O H:HOH419 4.8 51.7 1.0
O D:SAH301 4.8 37.8 1.0
CB H:ASP178 4.8 34.7 1.0
CB D:ASN166 5.0 28.4 1.0

Strontium binding site 7 out of 10 in 6jcl

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Strontium binding site 7 out of 10 in the Crystal Structure of Cofactor-Bound RV0187 From Mtb


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Crystal Structure of Cofactor-Bound RV0187 From Mtb within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sr304

b:34.6
occ:0.85
 OD1 H:ASP139 2.5 39.1 1.0
O D:HOH406 2.5 37.0 1.0
OD2 H:ASP165 2.5 35.2 1.0
O H:HOH433 2.5 29.4 1.0
OD1 H:ASN166 2.5 33.4 1.0
OD2 D:ASP178 2.5 35.8 1.0
OD2 H:ASP139 2.7 36.7 1.0
CG H:ASP139 2.9 36.8 1.0
CG H:ASP165 3.5 33.7 1.0
CG D:ASP178 3.5 36.6 1.0
CG H:ASN166 3.5 32.4 1.0
OD1 D:ASP178 3.7 37.0 1.0
ND2 H:ASN166 3.8 31.5 1.0
CB H:ASP165 3.9 34.7 1.0
O H:HOH432 3.9 30.7 1.0
NZ H:LYS209 4.3 31.9 1.0
O H:ILE42 4.3 41.2 1.0
O H:HOH404 4.3 39.8 1.0
NZ H:LYS142 4.3 35.7 1.0
CB H:ASP139 4.4 38.0 1.0
OD1 H:ASP165 4.5 32.9 1.0
O D:HOH457 4.7 41.1 1.0
CB H:SAH301 4.7 38.0 1.0
O H:SAH301 4.9 38.8 1.0
CB D:ASP178 4.9 34.6 1.0
CB H:ASN166 4.9 32.4 1.0

Strontium binding site 8 out of 10 in 6jcl

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Strontium binding site 8 out of 10 in the Crystal Structure of Cofactor-Bound RV0187 From Mtb


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Crystal Structure of Cofactor-Bound RV0187 From Mtb within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Sr302

b:32.4
occ:0.85
 OD1 G:ASP139 2.5 31.4 1.0
OD2 F:ASP178 2.5 29.9 1.0
OD2 G:ASP165 2.5 34.1 1.0
OD1 G:ASN166 2.5 29.1 1.0
O G:HOH426 2.6 30.8 1.0
OD2 G:ASP139 2.7 32.9 1.0
O F:HOH415 2.7 33.1 1.0
CG G:ASP139 2.9 32.4 1.0
CG F:ASP178 3.5 30.3 1.0
CG G:ASP165 3.5 33.5 1.0
CG G:ASN166 3.5 28.2 1.0
OD1 F:ASP178 3.7 29.6 1.0
ND2 G:ASN166 3.8 27.8 1.0
O G:HOH404 3.8 30.4 1.0
CB G:ASP165 3.9 30.8 1.0
NZ G:LYS209 4.2 29.6 1.0
O G:HOH402 4.3 30.6 1.0
O G:ILE42 4.3 31.7 1.0
CB G:ASP139 4.4 36.5 1.0
NZ G:LYS142 4.5 32.7 1.0
OD1 G:ASP165 4.5 34.3 1.0
O F:HOH438 4.8 45.7 1.0
CB G:SAH301 4.8 37.3 1.0
OXT G:SAH301 4.9 37.8 1.0
CB F:ASP178 4.9 28.1 1.0
CB G:ASN166 4.9 28.6 1.0

Strontium binding site 9 out of 10 in 6jcl

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Strontium binding site 9 out of 10 in the Crystal Structure of Cofactor-Bound RV0187 From Mtb


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of Crystal Structure of Cofactor-Bound RV0187 From Mtb within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Sr304

b:23.5
occ:0.85
 OD1 F:ASP181 2.2 57.4 1.0
O G:HOH445 2.3 34.8 1.0
OD1 F:ASP179 2.5 28.5 1.0
O F:HOH482 2.5 32.6 1.0
OD2 G:ASP181 2.5 41.7 1.0
OD1 G:ASP179 2.5 38.6 1.0
OD2 G:ASP179 2.8 37.9 1.0
OD1 G:ASP181 2.9 47.1 1.0
CG G:ASP181 3.0 33.4 1.0
CG G:ASP179 3.0 26.6 1.0
CG F:ASP181 3.0 40.3 1.0
OD2 F:ASP181 3.1 58.0 1.0
CG F:ASP179 3.4 31.4 1.0
OD2 F:ASP179 3.7 38.4 1.0
CB G:ASP181 4.4 25.4 1.0
CB G:ASP179 4.4 25.5 1.0
CB F:ASP181 4.5 28.2 1.0
NH1 F:ARG169 4.6 25.3 1.0
N G:ASP181 4.6 27.9 1.0
N F:ASP181 4.6 24.1 1.0
CB F:ASP179 4.7 23.1 1.0
NH2 G:ARG169 4.7 30.2 1.0
NE G:ARG169 4.7 25.3 1.0
NE F:ARG169 4.8 23.6 1.0
N F:ALA182 4.9 26.0 1.0
CA F:ASP179 4.9 28.7 1.0
CA G:ASP179 4.9 25.0 1.0
N G:ALA182 5.0 28.3 1.0

Strontium binding site 10 out of 10 in 6jcl

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Strontium binding site 10 out of 10 in the Crystal Structure of Cofactor-Bound RV0187 From Mtb


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 10 of Crystal Structure of Cofactor-Bound RV0187 From Mtb within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Sr305

b:28.1
occ:0.85
 OD1 F:ASP139 2.4 27.6 1.0
O F:HOH413 2.4 25.4 1.0
OD2 F:ASP165 2.5 29.7 1.0
OD2 G:ASP178 2.5 24.1 1.0
O G:HOH423 2.5 28.2 1.0
OD1 F:ASN166 2.5 25.7 1.0
OD2 F:ASP139 2.7 29.8 1.0
CG F:ASP139 2.9 26.7 1.0
CG G:ASP178 3.5 24.1 1.0
CG F:ASP165 3.5 29.8 1.0
CG F:ASN166 3.5 25.6 1.0
OD1 G:ASP178 3.7 24.2 1.0
ND2 F:ASN166 3.8 27.2 1.0
CB F:ASP165 3.9 21.0 1.0
O F:HOH419 4.1 25.8 1.0
O F:ILE42 4.2 29.9 1.0
NZ F:LYS209 4.2 25.6 1.0
O F:HOH402 4.2 40.7 1.0
NZ F:LYS142 4.3 36.6 1.0
CB F:ASP139 4.4 27.2 1.0
OD1 F:ASP165 4.5 27.5 1.0
CB G:ASP178 4.8 26.7 1.0
CB F:SAH301 4.8 30.2 1.0
O G:HOH436 4.9 32.4 1.0
CB F:ASN166 4.9 21.8 1.0
OXT F:SAH301 4.9 31.8 1.0

Reference:

S.Lee, J.Kang, J.Kim. Structural and Biochemical Characterization of RV0187, An O-Methyltransferase From Mycobacterium Tuberculosis. Sci Rep V. 9 8059 2019.
ISSN: ESSN 2045-2322
PubMed: 31147608
DOI: 10.1038/S41598-019-44592-7
Page generated: Fri Oct 11 06:39:38 2024

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