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Nickel in PDB 3fwv: Crystal Structure of A Redesigned Tpr Protein, T-Mod(Vmy), in Complex with Meevf Peptide

Protein crystallography data

The structure of Crystal Structure of A Redesigned Tpr Protein, T-Mod(Vmy), in Complex with Meevf Peptide, PDB code: 3fwv was solved by M.E.Jackrel, R.Valverde, L.Regan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.30 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 37.604, 66.599, 48.622, 90.00, 107.21, 90.00
R / Rfree (%) 18.4 / 24.4

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of A Redesigned Tpr Protein, T-Mod(Vmy), in Complex with Meevf Peptide (pdb code 3fwv). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of A Redesigned Tpr Protein, T-Mod(Vmy), in Complex with Meevf Peptide, PDB code: 3fwv:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 3fwv

Go back to Nickel Binding Sites List in 3fwv
Nickel binding site 1 out of 4 in the Crystal Structure of A Redesigned Tpr Protein, T-Mod(Vmy), in Complex with Meevf Peptide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of A Redesigned Tpr Protein, T-Mod(Vmy), in Complex with Meevf Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni3

b:59.2
occ:1.00
NZ A:LYS223 3.8 17.6 1.0
NZ A:LYS227 4.3 17.8 1.0
O A:HOH65 4.6 14.9 1.0
CE A:LYS223 4.9 17.7 1.0

Nickel binding site 2 out of 4 in 3fwv

Go back to Nickel Binding Sites List in 3fwv
Nickel binding site 2 out of 4 in the Crystal Structure of A Redesigned Tpr Protein, T-Mod(Vmy), in Complex with Meevf Peptide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of A Redesigned Tpr Protein, T-Mod(Vmy), in Complex with Meevf Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni5

b:19.9
occ:1.00
NE2 A:HIS321 2.2 11.1 1.0
O A:HOH94 2.3 28.6 1.0
O A:HOH97 2.4 19.0 1.0
NZ A:LYS325 2.4 17.7 1.0
CE A:LYS325 2.9 17.4 1.0
CE1 A:HIS321 3.1 11.0 1.0
CD2 A:HIS321 3.2 12.1 1.0
ND1 A:HIS321 4.2 13.1 1.0
CG A:HIS321 4.3 14.3 1.0
CD A:LYS325 4.4 16.3 1.0
O A:HOH93 4.6 16.1 1.0

Nickel binding site 3 out of 4 in 3fwv

Go back to Nickel Binding Sites List in 3fwv
Nickel binding site 3 out of 4 in the Crystal Structure of A Redesigned Tpr Protein, T-Mod(Vmy), in Complex with Meevf Peptide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of A Redesigned Tpr Protein, T-Mod(Vmy), in Complex with Meevf Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni2

b:27.5
occ:1.00
NH2 B:ARG297 2.0 23.2 1.0
NE2 B:HIS330 2.2 15.1 1.0
CZ B:ARG297 2.7 22.3 1.0
CD2 B:HIS330 2.9 14.5 1.0
NH1 B:ARG297 3.1 22.6 1.0
O B:HOH39 3.2 11.3 1.0
CE1 B:HIS330 3.4 15.2 1.0
NE B:ARG297 3.7 21.8 1.0
CG B:HIS330 4.1 15.9 1.0
O B:HOH111 4.2 5.1 1.0
OD1 B:ASP295 4.3 21.2 1.0
ND1 B:HIS330 4.4 16.1 1.0
OD2 B:ASP295 4.6 23.2 1.0
CB B:ARG297 4.7 16.4 1.0
CG B:ASP295 4.9 20.8 1.0
CD B:ARG297 4.9 19.7 1.0

Nickel binding site 4 out of 4 in 3fwv

Go back to Nickel Binding Sites List in 3fwv
Nickel binding site 4 out of 4 in the Crystal Structure of A Redesigned Tpr Protein, T-Mod(Vmy), in Complex with Meevf Peptide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of A Redesigned Tpr Protein, T-Mod(Vmy), in Complex with Meevf Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni4

b:18.0
occ:1.00
NE2 B:HIS247 2.0 16.5 1.0
O B:HOH25 2.5 18.8 1.0
CE1 B:HIS247 2.8 16.6 1.0
CD2 B:HIS247 3.1 16.9 1.0
O B:HOH116 4.0 30.4 1.0
ND1 B:HIS247 4.0 16.4 1.0
CG B:HIS247 4.1 16.6 1.0
CG2 B:THR243 4.5 16.4 1.0

Reference:

M.E.Jackrel, R.Valverde, L.Regan. Redesign of A Protein-Peptide Interaction: Characterization and Applications Protein Sci. V. 18 762 2009.
ISSN: ISSN 0961-8368
PubMed: 19309728
DOI: 10.1002/PRO.75
Page generated: Fri Sep 25 08:22:06 2020
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