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Platinum in PDB 6aqk: Crystal Structure of the C-Terminal Toxin Domain of RHS2 From Yersinia Entomophaga

Protein crystallography data

The structure of Crystal Structure of the C-Terminal Toxin Domain of RHS2 From Yersinia Entomophaga, PDB code: 6aqk was solved by J.N.Busby, M.R.H.Hurst, J.S.Lott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.41 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.510, 54.520, 100.820, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.6

Other elements in 6aqk:

The structure of Crystal Structure of the C-Terminal Toxin Domain of RHS2 From Yersinia Entomophaga also contains other interesting chemical elements:

Bromine (Br) 1 atom
Chlorine (Cl) 9 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the Crystal Structure of the C-Terminal Toxin Domain of RHS2 From Yersinia Entomophaga (pdb code 6aqk). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 6 binding sites of Platinum where determined in the Crystal Structure of the C-Terminal Toxin Domain of RHS2 From Yersinia Entomophaga, PDB code: 6aqk:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6;

Platinum binding site 1 out of 6 in 6aqk

Go back to Platinum Binding Sites List in 6aqk
Platinum binding site 1 out of 6 in the Crystal Structure of the C-Terminal Toxin Domain of RHS2 From Yersinia Entomophaga


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Crystal Structure of the C-Terminal Toxin Domain of RHS2 From Yersinia Entomophaga within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1001

b:64.5
occ:0.96
CL A:CL1007 2.3 62.1 1.0
CL A:CL1009 2.4 78.0 1.0
SD A:MET800 2.4 60.5 1.0
CL A:CL1008 2.6 60.1 1.0
CE A:MET800 2.9 50.9 1.0
CB A:MET800 3.3 49.3 1.0
CG A:MET800 3.4 47.3 1.0
CA A:MET800 3.6 49.2 1.0
O A:HOH1165 3.8 50.5 1.0
N A:LYS801 4.0 51.9 1.0
C A:MET800 4.4 54.4 1.0
O A:LYS801 4.8 59.9 1.0
N A:MET800 4.8 46.9 1.0
O A:ASN799 5.0 48.1 1.0

Platinum binding site 2 out of 6 in 6aqk

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Platinum binding site 2 out of 6 in the Crystal Structure of the C-Terminal Toxin Domain of RHS2 From Yersinia Entomophaga


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 the C-Terminal Toxin Domain of RHS2 From Yersinia Entomophaga within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1002

b:79.9
occ:0.78
SD A:MET870 2.1 54.0 1.0
CL A:CL1010 2.5 55.5 0.8
CE A:MET870 2.5 44.1 1.0
CG A:MET870 3.4 52.4 1.0
CB A:MET870 3.7 44.8 1.0
CA A:MET870 4.2 41.0 1.0
CE A:LYS868 4.4 61.0 1.0
NZ A:LYS868 4.7 69.0 1.0
CB A:LEU872 4.7 36.4 1.0
O A:SER869 4.8 43.2 1.0
N A:ASP871 4.9 36.3 1.0
O A:HOH1127 4.9 42.0 1.0
CB A:TRP851 5.0 36.1 1.0

Platinum binding site 3 out of 6 in 6aqk

Go back to Platinum Binding Sites List in 6aqk
Platinum binding site 3 out of 6 in the Crystal Structure of the C-Terminal Toxin Domain of RHS2 From Yersinia Entomophaga


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 the C-Terminal Toxin Domain of RHS2 From Yersinia Entomophaga within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1003

b:95.4
occ:1.00
SD A:MET786 2.1 54.6 1.0
ND1 A:HIS809 2.4 63.3 1.0
CG A:MET786 2.9 61.3 1.0
CG A:HIS809 3.3 54.8 1.0
CE1 A:HIS809 3.3 66.1 1.0
CB A:HIS809 3.5 48.7 1.0
CB A:MET786 3.9 52.3 1.0
CE A:MET786 3.9 58.9 1.0
CD1 A:ILE790 4.0 52.6 1.0
NE2 A:HIS809 4.4 70.3 1.0
CD2 A:HIS809 4.4 68.1 1.0
CA A:HIS809 4.4 43.6 1.0

Platinum binding site 4 out of 6 in 6aqk

Go back to Platinum Binding Sites List in 6aqk
Platinum binding site 4 out of 6 in the Crystal Structure of the C-Terminal Toxin Domain of RHS2 From Yersinia Entomophaga


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 the C-Terminal Toxin Domain of RHS2 From Yersinia Entomophaga within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1004

b:60.7
occ:0.64
CL A:CL1013 2.3 46.9 0.6
CL A:CL1011 2.4 37.5 0.6
CL A:CL1012 2.4 35.5 0.6
SD A:MET888 2.7 58.8 1.0
CG A:MET888 3.2 45.8 1.0
CE A:MET888 3.4 60.5 1.0
CB A:ASP885 3.5 39.4 1.0
O A:GLU917 3.8 43.7 1.0
N A:ASP885 4.3 32.6 1.0
CG A:ASP885 4.4 44.5 1.0
OD2 A:ASP885 4.5 53.2 1.0
CA A:ASP885 4.5 33.9 1.0
CB A:MET888 4.7 43.0 1.0
C A:GLU917 4.7 40.0 1.0
CA A:GLY918 4.8 34.3 1.0
O A:ASP885 4.8 34.9 1.0

Platinum binding site 5 out of 6 in 6aqk

Go back to Platinum Binding Sites List in 6aqk
Platinum binding site 5 out of 6 in the Crystal Structure of the C-Terminal Toxin Domain of RHS2 From Yersinia Entomophaga


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 the C-Terminal Toxin Domain of RHS2 From Yersinia Entomophaga within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1005

b:95.9
occ:0.45
CE A:MET888 2.9 60.5 1.0
SD A:MET888 3.2 58.8 1.0
N A:GLY889 3.9 41.3 1.0
CA A:MET888 4.1 38.1 1.0
CB A:MET888 4.1 43.0 1.0
CG A:MET888 4.2 45.8 1.0
CE2 A:TYR890 4.5 58.6 1.0
C A:MET888 4.5 43.5 1.0
CD2 A:TYR890 4.5 58.1 1.0
CA A:GLY889 5.0 39.5 1.0

Platinum binding site 6 out of 6 in 6aqk

Go back to Platinum Binding Sites List in 6aqk
Platinum binding site 6 out of 6 in the Crystal Structure of the C-Terminal Toxin Domain of RHS2 From Yersinia Entomophaga


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 the C-Terminal Toxin Domain of RHS2 From Yersinia Entomophaga within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1006

b:0.4
occ:0.92
SD A:MET943 2.1 76.8 1.0
CL A:CL1014 2.7 74.2 0.9
CL A:CL1015 2.8 81.0 0.9
CG A:MET943 3.2 51.9 1.0
CE A:MET943 3.6 68.8 1.0
CB A:MET943 3.6 45.4 1.0
CE2 A:TYR949 4.5 42.5 1.0
OH A:TYR949 4.7 39.7 1.0

Reference:

J.N.Busby, M.R.H.Hurst, J.S.Lott. Crystal Structure of the C-Terminal Toxin Domain of RHS2 From Yersinia Entomophaga To Be Published.
Page generated: Wed Dec 16 02:05:32 2020

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