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Copper in PDB 1xtm: Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis.

Protein crystallography data

The structure of Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis., PDB code: 1xtm was solved by V.Calderone, S.Mangani, L.Banci, M.Benvenuti, I.Bertini, A.Fantoni, M.S.Viezzoli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.60 / 1.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 52.462, 104.350, 58.756, 90.00, 90.00, 90.00
R / Rfree (%) 25.3 / 26.6

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis. (pdb code 1xtm). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis., PDB code: 1xtm:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 1xtm

Go back to Copper Binding Sites List in 1xtm
Copper binding site 1 out of 2 in the Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu500

b:23.3
occ:1.00
NE2 B:HIS166 2.0 15.8 1.0
ND1 B:HIS86 2.1 14.7 1.0
NE2 B:HIS88 2.1 16.3 1.0
O B:HOH508 2.8 21.3 1.0
CE1 B:HIS88 2.9 13.1 1.0
CE1 B:HIS166 3.0 15.2 1.0
CE1 B:HIS86 3.0 19.1 1.0
CD2 B:HIS166 3.0 12.3 1.0
CG B:HIS86 3.1 13.9 1.0
NE2 B:HIS104 3.2 18.5 1.0
CD2 B:HIS88 3.2 11.0 1.0
CB B:HIS86 3.4 11.3 1.0
CD2 B:HIS104 3.6 15.6 1.0
ND1 B:HIS88 4.0 12.6 1.0
ND1 B:HIS166 4.1 12.4 1.0
CG B:HIS166 4.1 9.3 1.0
NE2 B:HIS86 4.1 17.0 1.0
CD2 B:HIS86 4.2 16.1 1.0
CE1 B:HIS104 4.2 19.3 1.0
CG B:HIS88 4.2 11.2 1.0
CG2 B:ILE164 4.4 13.1 1.0
CB B:ILE164 4.5 9.2 1.0
CA B:HIS86 4.6 9.4 1.0
N B:HIS86 4.7 8.9 1.0
CG B:HIS104 4.8 15.5 1.0
O B:ILE164 4.8 11.9 1.0
O B:HIS86 5.0 10.0 1.0

Copper binding site 2 out of 2 in 1xtm

Go back to Copper Binding Sites List in 1xtm
Copper binding site 2 out of 2 in the Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu503

b:42.0
occ:1.00
NE2 A:HIS166 1.9 19.3 1.0
NE2 A:HIS88 2.2 33.8 1.0
ND1 A:HIS86 2.4 28.9 1.0
NE2 A:HIS104 2.5 33.5 1.0
CE1 A:HIS166 2.8 25.6 1.0
CD2 A:HIS166 2.9 26.4 1.0
CE1 A:HIS88 3.0 35.0 1.0
CG A:HIS86 3.2 27.1 1.0
CD2 A:HIS104 3.2 33.6 1.0
O A:HOH531 3.2 44.7 1.0
CE1 A:HIS86 3.2 27.9 1.0
CD2 A:HIS88 3.4 34.3 1.0
CE1 A:HIS104 3.4 31.6 1.0
CB A:HIS86 3.5 26.1 1.0
ND1 A:HIS166 3.9 25.2 1.0
CG A:HIS166 4.0 26.0 1.0
ND1 A:HIS88 4.2 35.0 1.0
CD2 A:HIS86 4.2 27.9 1.0
NE2 A:HIS86 4.2 28.0 1.0
CG A:HIS104 4.3 34.8 1.0
ND1 A:HIS104 4.4 32.1 1.0
CG A:HIS88 4.4 33.3 1.0
N A:HIS86 4.4 24.8 1.0
CA A:HIS86 4.5 25.4 1.0
CB A:ILE164 4.6 27.9 1.0
CG2 A:ILE164 4.6 28.3 1.0
O A:HOH541 4.7 43.6 1.0
O A:ILE164 4.9 27.0 1.0
O A:HIS86 4.9 26.7 1.0
C A:HIS86 5.0 25.5 1.0

Reference:

L.Banci, M.Benvenuti, I.Bertini, D.E.Cabelli, V.Calderone, A.Fantoni, S.Mangani, M.Migliardi, M.S.Viezzoli. From An Inactive Prokaryotic Sod Homologue to An Active Protein Through Site-Directed Mutagenesis. J.Am.Chem.Soc. V. 127 13287 2005.
ISSN: ISSN 0002-7863
PubMed: 16173759
DOI: 10.1021/JA052790O
Page generated: Thu Sep 3 16:25:58 2020
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