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Platinum in PDB 4lq6: Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis

Protein crystallography data

The structure of Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis, PDB code: 4lq6 was solved by A.Kumar, S.Kumar, D.Kumar, A.Mishra, R.P.Dewangan, P.Shrivastava, S.Ramachandran, B.Taneja, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.09 / 1.68
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.350, 103.780, 129.970, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 18.4

Other elements in 4lq6:

The structure of Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Zinc (Zn) 1 atom

Platinum Binding Sites:

The binding sites of Platinum atom in the Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis (pdb code 4lq6). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 9 binding sites of Platinum where determined in the Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis, PDB code: 4lq6:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Platinum binding site 1 out of 9 in 4lq6

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Platinum binding site 1 out of 9 in the Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis


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Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt307

b:50.1
occ:0.15
 PT A:PT307 0.0 50.1 0.1
PT A:PT307 1.4 22.4 0.1
CG A:MET3 2.1 43.3 1.0
CE A:MET3 2.2 44.6 0.4
SD A:MET3 2.4 46.8 0.4
SD A:MET3 2.5 48.3 0.6
PT A:PT307 2.7 0.5 0.4
CE A:MET3 3.2 45.3 0.6
CB A:MET3 3.4 38.3 1.0
N A:MET3 3.8 37.5 1.0
PT A:PT307 3.9 0.8 0.4
CA A:MET3 4.0 35.0 1.0
O A:HOH505 4.3 42.8 1.0
C A:GLY2 4.4 43.7 1.0
CA A:GLY2 4.9 43.2 1.0

Platinum binding site 2 out of 9 in 4lq6

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Platinum binding site 2 out of 9 in the Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt307

b:0.8
occ:0.35
 PT A:PT307 0.0 0.8 0.4
CE A:MET3 2.2 45.3 0.6
PT A:PT307 2.5 22.4 0.1
O A:HOH555 2.6 52.0 1.0
PT A:PT307 2.9 0.5 0.4
O A:GLY65 3.8 28.7 1.0
SD A:MET3 3.8 48.3 0.6
N A:MET3 3.9 37.5 1.0
PT A:PT307 3.9 50.1 0.1
CG A:MET3 4.0 43.3 1.0
N A:GLY2 4.1 44.5 1.0
CB A:MET3 4.1 38.3 1.0
C A:GLY65 4.3 29.3 1.0
O A:LEU64 4.6 32.5 1.0
CA A:MET3 4.6 35.0 1.0
CA A:GLY2 4.7 43.2 1.0
C A:GLY2 4.8 43.7 1.0
CA A:VAL66 4.8 23.3 1.0
N A:VAL66 4.8 24.6 1.0
CG2 A:VAL66 4.9 28.6 1.0

Platinum binding site 3 out of 9 in 4lq6

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Platinum binding site 3 out of 9 in the Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt307

b:0.5
occ:0.35
 PT A:PT307 0.0 0.5 0.4
PT A:PT307 2.1 22.4 0.1
PT A:PT307 2.7 50.1 0.1
PT A:PT307 2.9 0.8 0.4
CE A:MET3 3.8 45.3 0.6
CA A:GLY2 3.9 43.2 1.0
N A:GLY2 4.0 44.5 1.0
N A:MET3 4.0 37.5 1.0
CG A:MET3 4.2 43.3 1.0
C A:GLY2 4.3 43.7 1.0
CE A:MET3 4.3 44.6 0.4
SD A:MET3 4.3 48.3 0.6
O A:HOH555 4.3 52.0 1.0
CB A:MET3 4.9 38.3 1.0

Platinum binding site 4 out of 9 in 4lq6

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Platinum binding site 4 out of 9 in the Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt307

b:22.4
occ:0.15
 PT A:PT307 0.0 22.4 0.1
PT A:PT307 1.4 50.1 0.1
PT A:PT307 2.1 0.5 0.4
CG A:MET3 2.2 43.3 1.0
CE A:MET3 2.2 45.3 0.6
SD A:MET3 2.4 48.3 0.6
PT A:PT307 2.5 0.8 0.4
CB A:MET3 3.1 38.3 1.0
N A:MET3 3.3 37.5 1.0
CE A:MET3 3.4 44.6 0.4
SD A:MET3 3.4 46.8 0.4
CA A:MET3 3.7 35.0 1.0
O A:HOH555 4.0 52.0 1.0
C A:GLY2 4.1 43.7 1.0
CA A:GLY2 4.4 43.2 1.0
N A:GLY2 4.6 44.5 1.0
O A:GLY2 5.0 43.4 1.0

Platinum binding site 5 out of 9 in 4lq6

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Platinum binding site 5 out of 9 in the Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt308

b:51.4
occ:0.45
 PT A:PT308 0.0 51.4 0.5
SD A:MET88 2.2 36.9 1.0
OE2 A:GLU84 2.3 21.0 0.5
CG A:MET88 2.6 29.7 1.0
CE A:MET88 2.7 34.5 1.0
PT A:PT308 2.8 74.4 0.2
PT A:PT308 3.1 46.7 0.2
CD A:GLU84 3.2 30.0 0.5
CG A:GLU84 3.3 21.6 0.5
CB A:MET88 3.6 20.8 1.0
O A:GLU84 4.3 16.1 1.0
OE1 A:GLU84 4.4 23.1 0.5
PT A:PT308 4.4 58.9 0.1
CG A:PRO80 4.4 26.8 1.0
CB A:PRO80 4.5 20.4 1.0
O A:HOH526 4.7 37.1 1.0
CB A:GLU84 4.8 15.2 0.5
CA A:MET88 4.8 16.5 1.0
C A:GLU84 4.8 16.6 1.0
CB A:GLU84 4.8 15.6 0.5

Platinum binding site 6 out of 9 in 4lq6

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Platinum binding site 6 out of 9 in the Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt308

b:46.7
occ:0.20
 PT A:PT308 0.0 46.7 0.2
SD A:MET88 2.4 36.9 1.0
PT A:PT308 3.0 58.9 0.1
O A:SER71 3.0 20.6 1.0
PT A:PT308 3.1 51.4 0.5
CG A:MET88 3.3 29.7 1.0
CB A:MET88 3.4 20.8 1.0
CA A:SER71 3.6 14.3 1.0
C A:SER71 3.7 19.7 1.0
CG A:PRO80 3.8 26.8 1.0
CA A:ARG85 3.8 13.8 1.0
CZ A:PHE6 4.0 15.7 1.0
CE A:MET88 4.1 34.5 1.0
CB A:SER71 4.1 14.6 1.0
CG A:ARG85 4.1 14.7 1.0
CB A:PRO80 4.2 20.4 1.0
CB A:ARG85 4.4 13.7 1.0
O A:GLU84 4.4 16.1 1.0
N A:ARG85 4.5 14.2 1.0
CE1 A:PHE6 4.5 17.1 1.0
O A:ARG85 4.6 14.5 1.0
C A:GLU84 4.7 16.6 1.0
O A:LEU70 4.7 18.0 1.0
OE2 A:GLU84 4.7 21.0 0.5
C A:ARG85 4.7 16.9 1.0
CG A:GLU84 4.8 21.6 0.5
N A:SER71 4.9 13.7 1.0
CD A:PRO80 4.9 22.5 1.0
CA A:MET88 5.0 16.5 1.0

Platinum binding site 7 out of 9 in 4lq6

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Platinum binding site 7 out of 9 in the Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 7 of Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt308

b:58.9
occ:0.12
 PT A:PT308 0.0 58.9 0.1
SD A:MET88 2.2 36.9 1.0
O A:HOH533 2.3 31.4 1.0
PT A:PT308 3.0 46.7 0.2
O A:LEU70 3.0 18.0 1.0
CG A:MET88 3.2 29.7 1.0
CE A:MET88 3.2 34.5 1.0
CE1 A:PHE6 3.3 17.1 1.0
CZ A:PHE6 3.7 15.7 1.0
CB A:MET88 3.8 20.8 1.0
O A:HOH496 3.9 40.4 1.0
CA A:SER71 3.9 14.3 1.0
C A:LEU70 4.0 17.4 1.0
O A:SER71 4.3 20.6 1.0
C A:SER71 4.3 19.7 1.0
N A:SER71 4.4 13.7 1.0
PT A:PT308 4.4 51.4 0.5
CD1 A:PHE6 4.5 16.5 1.0
PT A:PT308 4.7 74.4 0.2
O A:HOH559 4.9 52.3 1.0

Platinum binding site 8 out of 9 in 4lq6

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Platinum binding site 8 out of 9 in the Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 8 of Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt308

b:74.4
occ:0.23
 PT A:PT308 0.0 74.4 0.2
O A:HOH526 2.3 37.1 1.0
CE A:MET88 2.3 34.5 1.0
CG A:MET88 2.3 29.7 1.0
PT A:PT308 2.8 51.4 0.5
SD A:MET88 2.9 36.9 1.0
CB A:MET88 3.7 20.8 1.0
O A:HOH559 3.9 52.3 1.0
CA A:MET88 4.3 16.5 1.0
OE2 A:GLU84 4.4 21.0 0.5
PT A:PT308 4.7 58.9 0.1

Platinum binding site 9 out of 9 in 4lq6

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Platinum binding site 9 out of 9 in the Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 9 of Crystal Structure of RV3717 Reveals A Novel Amidase From M. Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt309

b:50.5
occ:0.20
 CL A:CL306 2.0 34.5 1.0
CL A:CL305 2.3 48.0 1.0
O A:HOH524 2.4 54.8 1.0
O A:HOH438 2.7 46.1 1.0
O A:HOH487 3.1 42.0 1.0
CD2 A:LEU162 3.9 20.5 1.0
NZ A:LYS31 4.2 38.2 1.0
O A:HOH420 4.2 25.6 1.0
CG1 A:VAL82 4.2 18.8 1.0
O A:HOH458 4.2 28.7 1.0
O A:HOH457 4.4 30.1 1.0
CB A:LEU162 4.4 13.4 1.0
O A:HOH540 4.4 52.3 1.0
CA A:LEU162 4.5 13.2 1.0
N A:ALA163 4.6 14.5 1.0
CG A:LEU162 4.6 17.2 1.0
O A:HOH525 4.7 40.0 1.0
CB A:VAL82 4.8 17.4 1.0
CE A:LYS31 4.8 39.9 1.0
C A:LEU162 5.0 16.3 1.0

Reference:

A.Kumar, S.Kumar, D.Kumar, A.Mishra, R.P.Dewangan, P.Shrivastava, S.Ramachandran, B.Taneja. The Structure of RV3717 Reveals A Novel Amidase From Mycobacterium Tuberculosis. Acta Crystallogr.,Sect.D V. 69 2543 2013.
ISSN: ISSN 0907-4449
PubMed: 24311595
DOI: 10.1107/S0907444913026371
Page generated: Thu Oct 10 11:03:52 2024

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