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Platinum in PDB 2fyf: Structure of A Putative Phosphoserine Aminotransferase From Mycobacterium Tuberculosis

Enzymatic activity of Structure of A Putative Phosphoserine Aminotransferase From Mycobacterium Tuberculosis

All present enzymatic activity of Structure of A Putative Phosphoserine Aminotransferase From Mycobacterium Tuberculosis:
2.6.1.52;

Protein crystallography data

The structure of Structure of A Putative Phosphoserine Aminotransferase From Mycobacterium Tuberculosis, PDB code: 2fyf was solved by F.Coulibaly, E.Lassalle, E.N.Baker, Mycobacterium Tuberculosisstructural Proteomics Project (Xmtb), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.93 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.478, 94.056, 101.063, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 16.6

Other elements in 2fyf:

The structure of Structure of A Putative Phosphoserine Aminotransferase From Mycobacterium Tuberculosis also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the Structure of A Putative Phosphoserine Aminotransferase From Mycobacterium Tuberculosis (pdb code 2fyf). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 6 binding sites of Platinum where determined in the Structure of A Putative Phosphoserine Aminotransferase From Mycobacterium Tuberculosis, PDB code: 2fyf:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6;

Platinum binding site 1 out of 6 in 2fyf

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Platinum binding site 1 out of 6 in the Structure of A Putative Phosphoserine Aminotransferase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Structure of A Putative Phosphoserine Aminotransferase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1382

b:36.4
occ:0.10
O A:HOH2827 1.9 32.7 1.0
O A:HOH2830 2.0 18.6 1.0
O A:HOH2829 2.2 28.2 1.0
O A:HOH2828 2.3 21.4 1.0
OE2 A:GLU263 3.1 12.9 0.5
CB A:TRP267 3.6 6.0 1.0
CD1 A:TRP267 3.6 7.2 1.0
CD A:GLU263 3.9 10.5 0.5
CA A:TRP267 3.9 6.9 1.0
O A:HOH2722 3.9 40.0 1.0
CG A:TRP267 3.9 6.0 1.0
O A:GLU263 4.1 6.2 1.0
N A:TRP267 4.2 6.5 1.0
O A:HOH2765 4.3 39.1 1.0
O A:HOH2701 4.4 49.1 1.0
NH1 A:ARG30 4.4 8.0 1.0
NH2 A:ARG30 4.4 7.2 1.0
CG A:GLU263 4.5 8.2 0.5
OE1 A:GLU263 4.5 11.1 0.5
OE1 A:GLU263 4.7 7.4 0.5
O A:HOH2494 4.8 26.7 1.0
NE1 A:TRP267 4.8 7.2 1.0
OE1 A:GLU32 4.8 10.0 0.3
CD A:GLU32 4.9 6.4 0.3
CZ A:ARG30 4.9 6.6 1.0
C A:ASP266 4.9 6.8 1.0

Platinum binding site 2 out of 6 in 2fyf

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Platinum binding site 2 out of 6 in the Structure of A Putative Phosphoserine Aminotransferase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Structure of A Putative Phosphoserine Aminotransferase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1378

b:31.6
occ:0.35
PT A:PC41378 0.0 31.6 0.3
CL2 A:PC41378 1.9 37.1 0.3
ND1 A:HIS8 2.0 25.5 1.0
CL1 A:PC41378 2.2 16.3 0.3
CL3 A:PC41378 2.3 40.9 0.3
CG A:HIS8 2.9 23.1 1.0
CE1 A:HIS8 3.0 25.7 1.0
CB A:HIS8 3.2 21.9 1.0
CA A:HIS8 3.4 20.6 1.0
CB A:ALA332 3.7 5.5 1.0
CD2 A:HIS8 4.1 26.1 1.0
NE2 A:HIS8 4.1 27.2 1.0
N A:HIS8 4.4 21.9 1.0
C A:HIS8 4.4 19.8 1.0
N A:LEU9 4.4 17.7 1.0

Platinum binding site 3 out of 6 in 2fyf

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Platinum binding site 3 out of 6 in the Structure of A Putative Phosphoserine Aminotransferase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Structure of A Putative Phosphoserine Aminotransferase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt2386

b:32.5
occ:0.06
O B:HOH2803 1.8 17.7 1.0
O B:HOH2804 2.1 18.1 1.0
O B:HOH2801 2.1 30.5 1.0
O B:HOH2802 2.4 17.1 1.0
OE1 B:GLU32 3.1 14.7 1.0
OE2 B:GLU32 3.7 19.1 1.0
CD B:GLU32 3.8 14.4 1.0
CB B:ARG30 4.3 8.5 1.0
O B:HOH2482 4.3 15.7 1.0
N B:LEU31 4.4 8.8 1.0
CG B:ARG30 4.5 10.2 1.0
CA B:ARG30 4.6 8.1 1.0
NZ B:LYS28 4.8 5.9 1.0
CE B:LYS28 4.9 6.0 1.0
C B:ARG30 5.0 7.7 1.0

Platinum binding site 4 out of 6 in 2fyf

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Platinum binding site 4 out of 6 in the Structure of A Putative Phosphoserine Aminotransferase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Structure of A Putative Phosphoserine Aminotransferase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt2391

b:31.5
occ:0.10
O B:HOH2680 2.2 33.4 1.0
O B:HOH2659 2.8 34.2 1.0
N B:GLU107 3.6 8.4 1.0
O B:HOH2718 4.0 35.5 1.0
C B:GLY106 4.0 7.3 1.0
CA B:GLU107 4.1 7.5 1.0
CA B:GLY106 4.1 7.6 1.0
OE1 B:GLU107 4.3 17.8 1.0
CB B:GLU107 4.4 8.0 1.0
OG B:SER155 4.5 6.6 1.0
CD1 B:LEU344 4.6 20.1 1.0
O B:GLY106 4.8 7.7 1.0
CB B:SER155 5.0 5.5 1.0

Platinum binding site 5 out of 6 in 2fyf

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Platinum binding site 5 out of 6 in the Structure of A Putative Phosphoserine Aminotransferase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Structure of A Putative Phosphoserine Aminotransferase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt2378

b:17.2
occ:0.22
PT B:PC42378 0.0 17.2 0.2
CL1 B:PC42378 2.1 16.6 0.2
CL2 B:PC42378 2.2 11.1 0.2
CL3 B:PC42378 2.2 12.0 0.2
CL4 B:PC42378 2.3 22.4 0.2
OE1 B:GLU263 2.5 14.1 0.5
CD B:GLU263 3.4 10.4 0.5
CG B:GLU263 3.9 7.9 0.5
CB B:TRP267 4.0 7.5 1.0
CD1 B:TRP267 4.1 7.3 1.0
NH1 B:ARG30 4.1 11.9 1.0
O B:HOH2702 4.2 35.2 1.0
NH2 B:ARG30 4.2 11.2 1.0
O B:HOH2775 4.2 46.6 1.0
O B:GLU263 4.2 7.0 1.0
OE1 B:GLU263 4.3 11.6 0.5
CG B:TRP267 4.4 7.8 1.0
OE2 B:GLU263 4.4 13.2 0.5
CA B:TRP267 4.5 7.0 1.0
CZ B:ARG30 4.7 8.4 1.0
N B:TRP267 4.8 7.3 1.0

Platinum binding site 6 out of 6 in 2fyf

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Platinum binding site 6 out of 6 in the Structure of A Putative Phosphoserine Aminotransferase From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of Structure of A Putative Phosphoserine Aminotransferase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt2383

b:32.3
occ:0.35
PT B:PC42383 0.0 32.3 0.3
CL2 B:PC42383 2.0 37.9 0.3
ND1 B:HIS8 2.0 25.1 1.0
CL1 B:PC42383 2.2 16.2 0.3
CE1 B:HIS8 2.9 26.7 1.0
CG B:HIS8 3.1 24.5 1.0
CB B:HIS8 3.5 22.8 1.0
CA B:HIS8 3.6 21.8 1.0
CB B:ALA332 3.8 6.9 1.0
NE2 B:HIS8 4.1 27.4 1.0
CD2 B:HIS8 4.2 26.4 1.0
N B:LEU9 4.4 18.9 1.0
C B:HIS8 4.5 21.2 1.0
N B:HIS8 4.6 22.9 1.0

Reference:

F.Coulibaly, E.Lassalle, H.M.Baker, E.N.Baker. Structure of Phosphoserine Aminotransferase From Mycobacterium Tuberculosis. Acta Crystallogr.,Sect.D V. 68 553 2012.
ISSN: ISSN 0907-4449
PubMed: 22525753
DOI: 10.1107/S0907444912004829
Page generated: Wed Dec 16 02:03:59 2020

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