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Platinum in PDB 1rli: The Structure of Trp Repressor Binding Protein From Bacillus Subtilis

Protein crystallography data

The structure of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis, PDB code: 1rli was solved by Y.Kim, P.Quartey, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.79 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.993, 90.666, 63.446, 90.00, 97.02, 90.00
R / Rfree (%) 19.6 / 23

Platinum Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Platinum atom in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis (pdb code 1rli). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 11 binding sites of Platinum where determined in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis, PDB code: 1rli:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Platinum binding site 1 out of 11 in 1rli

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Platinum binding site 1 out of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt601

b:53.6
occ:0.73
 O A:HOH607 2.1 15.3 1.0
O A:HOH690 2.3 34.2 1.0
O A:HOH689 2.5 35.9 1.0
O A:HOH646 2.5 30.6 1.0
CG A:MET83 2.8 24.5 1.0
CE A:MET83 3.2 28.7 1.0
SD A:MET83 3.5 30.3 1.0
O A:HOH613 3.5 24.5 1.0
N A:MET83 3.7 16.2 1.0
O D:HOH624 3.8 23.2 1.0
CB A:MET83 4.0 19.6 1.0
OE1 A:GLN135 4.0 26.5 1.0
CD A:LYS88 4.1 21.0 1.0
CA A:MET83 4.5 16.8 1.0
CD1 A:LEU132 4.6 19.2 1.0
CB A:LYS88 4.6 17.8 1.0
CA A:GLY82 4.7 16.0 1.0
C A:GLY82 4.7 16.0 1.0
CE A:LYS88 4.7 20.0 1.0
NE2 D:GLN135 4.8 25.5 1.0
CG A:LYS88 4.8 18.3 1.0
CD A:GLN135 4.8 25.9 1.0
CE D:LYS88 4.9 17.7 1.0
NZ A:LYS88 5.0 21.9 1.0

Platinum binding site 2 out of 11 in 1rli

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Platinum binding site 2 out of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt605

b:57.9
occ:0.76
 O A:HOH705 2.4 45.2 1.0
NE2 A:HIS70 2.4 40.1 1.0
O A:HOH707 2.9 49.7 1.0
NZ A:LYS2 3.2 51.0 1.0
CD2 A:HIS70 3.3 38.2 1.0
CE A:LYS2 3.4 50.3 1.0
CE1 A:HIS70 3.5 38.5 1.0
CD A:LYS2 3.5 48.7 1.0
CB A:LYS2 3.8 42.9 1.0
O A:HOH706 4.1 49.2 1.0
CG A:LYS2 4.3 47.5 1.0
CG A:HIS70 4.5 36.4 1.0
ND1 A:HIS70 4.6 39.1 1.0
CG2 A:ILE3 4.7 32.7 1.0

Platinum binding site 3 out of 11 in 1rli

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Platinum binding site 3 out of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt606

b:0.6
occ:0.51
 O A:HOH710 2.2 43.5 1.0
O A:HOH709 2.7 42.9 1.0
O A:HOH672 2.9 39.8 1.0
OG1 A:THR16 3.3 28.3 1.0
N A:THR16 3.3 24.0 1.0
O A:HOH649 3.6 43.0 1.0
N A:ASN15 3.7 27.4 1.0
CB A:ASN15 3.8 22.1 1.0
O A:HOH713 3.8 48.4 1.0
O A:HOH674 3.9 39.6 1.0
CB A:THR16 3.9 28.9 1.0
CA A:ASN15 4.0 24.7 1.0
C A:ASN15 4.1 23.2 1.0
CB A:PRO77 4.2 20.6 1.0
CA A:THR16 4.2 25.3 1.0
C A:GLY14 4.5 29.8 1.0
O A:HOH628 4.7 39.6 1.0
ND2 A:ASN15 4.7 22.8 1.0
CG A:ASN15 4.7 23.6 1.0
CA A:PRO77 4.8 17.6 1.0
CG1 A:VAL120 4.9 19.6 1.0
CA A:GLY14 4.9 32.3 1.0
CB A:VAL120 4.9 18.3 1.0
O A:VAL120 5.0 17.9 1.0

Platinum binding site 4 out of 11 in 1rli

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Platinum binding site 4 out of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt603

b:44.3
occ:0.86
 O C:HOH613 2.3 13.9 1.0
O B:HOH701 2.3 21.3 1.0
O B:HOH702 2.4 22.5 1.0
O C:HOH653 2.4 21.6 1.0
NE2 B:GLN135 2.7 26.4 0.5
CG B:MET83 2.8 17.1 0.5
SD B:MET83 3.4 28.0 0.7
CE B:MET83 3.6 23.2 0.4
O B:HOH642 3.7 26.1 1.0
SD B:MET83 3.8 34.3 0.3
CB B:MET83 3.8 22.8 0.5
CD B:GLN135 3.8 24.6 0.4
N B:MET83 3.9 17.1 0.5
CE B:MET83 3.9 32.6 0.6
N B:MET83 3.9 15.7 0.5
CB B:MET83 4.0 18.0 0.5
O C:HOH621 4.1 23.1 1.0
OE1 B:GLN135 4.1 16.0 0.5
CG B:MET83 4.1 25.5 0.5
CD B:LYS88 4.2 20.4 1.0
OE1 B:GLN135 4.2 25.5 0.5
CA B:MET83 4.4 18.4 0.5
CB B:LYS88 4.5 15.6 1.0
CA B:MET83 4.5 15.9 0.5
CE C:LYS88 4.7 15.4 1.0
CD1 B:LEU132 4.7 21.6 1.0
CG B:LYS88 4.7 18.7 1.0
CE B:LYS88 4.7 22.8 1.0
NE2 C:GLN135 4.9 24.4 1.0
C B:GLY82 4.9 15.3 1.0
CA B:GLY82 4.9 16.5 1.0
CD B:GLN135 4.9 16.7 0.6

Platinum binding site 5 out of 11 in 1rli

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Platinum binding site 5 out of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt608

b:0.2
occ:0.69
 O4 B:PO4614 2.1 35.0 0.9
ND1 B:HIS70 2.4 42.5 1.0
O B:HOH726 2.6 47.7 1.0
CE1 B:HIS70 3.3 44.4 1.0
CG B:HIS70 3.3 38.3 1.0
O B:HOH745 3.4 54.8 1.0
P B:PO4614 3.4 36.0 0.9
CB B:HIS70 3.6 31.9 1.0
O2 B:PO4614 3.7 42.4 0.7
O3 B:PO4614 4.3 41.8 0.9
NE2 B:HIS70 4.4 43.8 1.0
O1 B:PO4614 4.4 41.4 0.9
CD2 B:HIS70 4.4 41.0 1.0
CD1 B:ILE71 4.8 30.1 1.0
CG1 B:ILE71 4.8 27.4 1.0

Platinum binding site 6 out of 11 in 1rli

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Platinum binding site 6 out of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Pt604

b:47.0
occ:0.74
 O B:HOH703 2.2 27.6 1.0
O C:HOH614 2.2 15.8 1.0
O C:HOH636 2.5 25.9 1.0
O C:HOH623 2.5 25.4 1.0
O B:HOH643 3.3 30.6 1.0
O C:HOH703 3.3 41.5 1.0
CD C:LYS36 4.0 36.0 1.0
NZ C:LYS36 4.0 38.7 1.0
CB C:PHE52 4.3 40.1 1.0
N C:GLY85 4.5 16.9 1.0
O C:PHE52 4.6 41.2 1.0
CE2 C:TYR79 4.6 33.6 1.0
N C:GLY50 4.6 43.4 1.0
CE C:LYS36 4.6 36.7 1.0
CA C:GLY85 4.6 17.4 1.0
CD1 C:PHE52 4.7 40.0 1.0
O C:HOH658 4.7 32.5 1.0
C C:PHE52 4.8 41.2 1.0
N C:THR86 4.8 17.1 1.0
N C:PHE52 4.8 40.8 1.0
CA C:PHE52 4.9 40.7 1.0
CG2 C:THR86 4.9 19.0 1.0
CA C:GLY50 4.9 43.4 1.0
CG C:PHE52 5.0 40.7 1.0

Platinum binding site 7 out of 11 in 1rli

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Platinum binding site 7 out of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 7 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Pt609

b:72.5
occ:0.80
 O C:HOH699 2.0 31.4 1.0
O C:HOH697 2.6 26.6 1.0
O C:HOH700 2.6 38.4 1.0
O C:HOH715 3.1 49.7 1.0
O C:HOH711 3.6 62.2 1.0
N C:ASN15 3.7 33.8 1.0
CA C:GLY14 4.1 37.4 1.0
N C:THR16 4.2 31.4 1.0
OG1 C:THR16 4.2 35.2 1.0
C C:GLY14 4.3 34.8 1.0
CB C:ASN15 4.4 31.0 1.0
O C:HOH693 4.5 48.5 1.0
CA C:ASN15 4.5 32.3 1.0
ND2 C:ASN15 4.5 33.0 1.0
CB C:PRO77 4.7 22.3 1.0
CB C:THR16 4.8 34.0 1.0
CG C:ASN15 4.8 32.1 1.0
C C:ASN15 4.9 30.6 1.0
O C:THR10 4.9 54.4 1.0

Platinum binding site 8 out of 11 in 1rli

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Platinum binding site 8 out of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 8 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Pt610

b:83.3
occ:0.79
 O C:HOH695 2.3 54.9 1.0
O C:HOH694 2.4 46.0 1.0
ND1 C:HIS70 2.4 47.6 1.0
NZ C:LYS2 2.9 57.5 1.0
CG C:HIS70 3.2 45.4 1.0
CB C:HIS70 3.4 41.6 1.0
CE1 C:HIS70 3.4 48.6 1.0
CE C:LYS2 3.8 58.0 1.0
CD2 C:HIS70 4.4 47.7 1.0
NE2 C:HIS70 4.5 48.9 1.0
CG C:LYS2 4.6 53.4 1.0
O C:HOH696 4.7 48.3 1.0
CD C:LYS2 4.8 56.6 1.0
CA C:HIS70 4.9 38.2 1.0

Platinum binding site 9 out of 11 in 1rli

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Platinum binding site 9 out of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 9 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Pt602

b:52.1
occ:0.78
 O A:HOH691 2.2 24.6 1.0
O D:HOH711 2.3 30.1 1.0
O D:HOH615 2.4 16.4 1.0
O D:HOH636 2.4 28.3 1.0
O D:HOH692 3.0 40.7 1.0
O A:HOH636 3.4 30.3 1.0
CD D:LYS36 4.2 27.9 1.0
CB D:PHE52 4.2 31.6 1.0
CE2 D:TYR79 4.3 29.8 1.0
N D:GLY50 4.4 41.1 1.0
NZ D:LYS36 4.4 36.2 1.0
O D:HOH626 4.4 27.6 1.0
O D:PHE52 4.5 32.5 1.0
N D:GLY85 4.5 16.0 1.0
CA D:GLY85 4.7 17.5 1.0
C D:PHE52 4.7 32.8 1.0
CA D:GLY50 4.7 42.1 1.0
N D:PHE52 4.8 34.6 1.0
CD1 D:PHE52 4.8 31.3 1.0
N D:THR86 4.8 14.4 1.0
CE D:LYS36 4.8 31.2 1.0
CA D:PHE52 4.8 32.0 1.0
CD2 D:TYR79 4.9 26.6 1.0
CG2 D:THR86 4.9 16.0 1.0
CG D:PHE52 5.0 31.0 1.0

Platinum binding site 10 out of 11 in 1rli

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Platinum binding site 10 out of 11 in the The Structure of Trp Repressor Binding Protein From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 10 of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Pt607

b:74.6
occ:0.75
 O D:HOH736 2.6 36.0 1.0
NZ D:LYS2 2.7 43.4 1.0
ND1 D:HIS70 2.8 35.7 1.0
CE D:LYS2 3.1 43.7 1.0
CG D:HIS70 3.4 31.4 1.0
CE1 D:HIS70 3.6 36.0 1.0
CB D:HIS70 3.6 28.9 1.0
CD2 D:HIS70 4.3 34.6 1.0
O D:HOH764 4.3 44.1 1.0
CD D:LYS2 4.3 42.8 1.0
NE2 D:HIS70 4.3 36.5 1.0

Reference:

Y.Kim, P.Quartey, A.Joachimiak. Crystal Structure Analysis of Trp Repressor Binding Protein From Bacillus Subtilis To Be Published.
Page generated: Wed Dec 16 02:03:47 2020

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