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Nickel in PDB 1tgg: RH3 Designed Right-Handed Coiled Coil Trimer

Protein crystallography data

The structure of RH3 Designed Right-Handed Coiled Coil Trimer, PDB code: 1tgg was solved by J.J.Plecs, P.B.Harbury, P.S.Kim, T.Alber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 2.00
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 25.420, 25.420, 141.340, 90.00, 90.00, 120.00
R / Rfree (%) 23.3 / 26.9

Other elements in 1tgg:

The structure of RH3 Designed Right-Handed Coiled Coil Trimer also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the RH3 Designed Right-Handed Coiled Coil Trimer (pdb code 1tgg). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the RH3 Designed Right-Handed Coiled Coil Trimer, PDB code: 1tgg:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 1tgg

Go back to Nickel Binding Sites List in 1tgg
Nickel binding site 1 out of 3 in the RH3 Designed Right-Handed Coiled Coil Trimer


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of RH3 Designed Right-Handed Coiled Coil Trimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni401

b:25.9
occ:1.00
O B:HOH412 1.7 24.6 1.0
OE12 B:CGU119 2.0 29.1 1.0
OE22 B:CGU123 2.0 16.9 1.0
CL B:CL411 2.1 69.3 1.0
OE12 B:CGU123 2.1 16.9 1.0
OE22 B:CGU119 2.7 29.1 1.0
CD1 B:CGU119 2.9 29.1 1.0
CD2 B:CGU123 3.0 16.9 1.0
CD1 B:CGU123 3.0 16.9 1.0
CG B:CGU119 3.1 29.1 1.0
CG B:CGU123 3.2 16.9 1.0
CD2 B:CGU119 3.3 29.1 1.0
HZ2 B:LYS126 3.3 22.0 1.0
HZ1 B:LYS126 3.7 22.0 1.0
HZ3 B:LYS126 3.8 22.0 1.0
NZ B:LYS126 3.8 47.6 1.0
CL B:CL431 4.0 66.4 1.0
OE11 B:CGU119 4.1 29.1 1.0
OE21 B:CGU123 4.1 16.9 1.0
OE11 B:CGU123 4.1 16.9 1.0
CL B:CL432 4.3 45.6 1.0
O B:HOH529 4.3 20.1 1.0
OE21 B:CGU119 4.5 29.1 1.0
CB B:CGU119 4.6 16.1 1.0
CB B:CGU123 4.7 19.3 1.0
O B:CGU119 4.8 16.1 1.0
NI B:NI403 4.9 22.0 1.0

Nickel binding site 2 out of 3 in 1tgg

Go back to Nickel Binding Sites List in 1tgg
Nickel binding site 2 out of 3 in the RH3 Designed Right-Handed Coiled Coil Trimer


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of RH3 Designed Right-Handed Coiled Coil Trimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni402

b:30.4
occ:1.00
CL B:CL421 2.0 80.5 1.0
CL B:CL422 2.0 54.2 1.0
CL B:CL431 4.0 66.4 1.0
HZ1 B:LYS115 4.1 22.0 1.0
O B:HOH520 4.3 20.5 1.0
NI B:NI403 4.9 22.0 1.0
NZ B:LYS115 4.9 48.1 1.0

Nickel binding site 3 out of 3 in 1tgg

Go back to Nickel Binding Sites List in 1tgg
Nickel binding site 3 out of 3 in the RH3 Designed Right-Handed Coiled Coil Trimer


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of RH3 Designed Right-Handed Coiled Coil Trimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni403

b:22.0
occ:1.00
CL B:CL432 2.0 45.6 1.0
CL B:CL431 2.0 66.4 1.0
OE12 B:CGU119 4.2 29.1 1.0
OE22 B:CGU123 4.2 16.9 1.0
O B:HOH412 4.3 24.6 1.0
O B:HOH645 4.4 41.4 1.0
CL B:CL421 4.4 80.5 1.0
CL B:CL422 4.5 54.2 1.0
CD1 B:CGU119 4.8 29.1 1.0
NI B:NI401 4.9 25.9 1.0
NI B:NI402 4.9 30.4 1.0

Reference:

J.J.Plecs, P.B.Harbury, P.S.Kim, T.Alber. Structural Test of the Parameterized-Backbone Method For Protein Design J.Mol.Biol. V. 342 289 2004.
ISSN: ISSN 0022-2836
PubMed: 15313624
DOI: 10.1016/J.JMB.2004.06.051
Page generated: Thu Oct 29 06:15:45 2020
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