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Copper in PDB 1xtl: Crystal Structure of P104H Mutant of Sod-Like Protein From Bacillus Subtilis.

Protein crystallography data

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

Resolution Low / High (Å) 38.92 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 52.147, 56.586, 59.118, 78.24, 89.91, 85.47
R / Rfree (%) 23.2 / 29.9

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of P104H Mutant of Sod-Like Protein From Bacillus Subtilis. (pdb code 1xtl). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Crystal Structure of P104H Mutant of Sod-Like Protein From Bacillus Subtilis., PDB code: 1xtl:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 1xtl

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Copper binding site 1 out of 4 in the Crystal Structure of P104H Mutant of 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 P104H Mutant of Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1171

b:27.7
occ:1.00
NE2 B:HIS104 2.0 7.5 1.0
NE2 B:HIS166 2.2 6.0 1.0
CD2 B:HIS86 2.5 22.2 1.0
OH B:TYR88 2.7 22.2 1.0
CE1 B:HIS104 2.9 20.2 1.0
CD2 B:HIS166 2.9 14.2 1.0
CD2 B:HIS104 3.1 17.5 1.0
NE2 B:HIS86 3.2 20.8 1.0
CG B:HIS86 3.3 20.5 1.0
CE1 B:HIS166 3.4 17.5 1.0
CZ B:TYR88 3.4 23.0 1.0
CE1 B:TYR88 3.5 27.6 1.0
CB B:HIS86 3.9 19.2 1.0
CB B:SER177 3.9 23.2 1.0
ND1 B:HIS104 4.0 20.1 1.0
CE1 B:HIS86 4.1 22.2 1.0
CG B:HIS166 4.2 16.4 1.0
ND1 B:HIS86 4.2 21.1 1.0
CG B:HIS104 4.2 13.3 1.0
ND1 B:HIS166 4.3 10.4 1.0
CE2 B:TYR88 4.6 23.6 1.0
CD1 B:TYR88 4.7 25.1 1.0
O B:SER177 4.8 23.7 1.0
CA B:SER177 4.8 24.0 1.0
OG B:SER177 4.8 28.2 1.0

Copper binding site 2 out of 4 in 1xtl

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Copper binding site 2 out of 4 in the Crystal Structure of P104H Mutant of 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 P104H Mutant of Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1173

b:27.9
occ:1.00
NE2 A:HIS166 2.1 3.9 1.0
NE2 A:HIS104 2.1 11.5 1.0
ND1 A:HIS86 2.2 26.0 1.0
OH A:TYR88 2.7 24.4 1.0
CD2 A:HIS166 2.9 17.0 1.0
CE1 A:HIS86 3.0 24.1 1.0
CG A:HIS86 3.1 20.4 1.0
CD2 A:HIS104 3.1 16.5 1.0
CE1 A:HIS166 3.1 13.3 1.0
CE1 A:HIS104 3.1 17.1 1.0
CE2 A:TYR88 3.2 24.6 1.0
CZ A:TYR88 3.4 20.3 1.0
CB A:HIS86 3.5 19.6 1.0
CB A:SER177 3.8 24.2 1.0
NE2 A:HIS86 4.0 22.8 1.0
CD2 A:HIS86 4.0 22.0 1.0
CG A:HIS166 4.1 14.0 1.0
ND1 A:HIS166 4.2 6.8 1.0
CG A:HIS104 4.2 19.5 1.0
ND1 A:HIS104 4.2 20.9 1.0
CD2 A:TYR88 4.5 20.6 1.0
CE1 A:TYR88 4.6 20.8 1.0
O A:SER177 4.7 25.5 1.0
CA A:SER177 4.7 24.6 1.0
OG A:SER177 4.9 28.3 1.0
CA A:HIS86 4.9 19.7 1.0
O A:HOH1397 4.9 28.9 1.0

Copper binding site 3 out of 4 in 1xtl

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Copper binding site 3 out of 4 in the Crystal Structure of P104H Mutant of 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 3 of Crystal Structure of P104H Mutant of Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu1175

b:34.5
occ:1.00
NE2 C:HIS104 1.9 11.6 1.0
NE2 C:HIS166 2.2 16.5 1.0
OH C:TYR88 2.3 21.1 1.0
ND1 C:HIS86 2.5 25.6 1.0
CE1 C:HIS104 2.8 11.2 1.0
CE1 C:HIS166 2.9 21.1 1.0
CD2 C:HIS104 3.0 15.2 1.0
CE1 C:HIS86 3.0 16.6 1.0
CZ C:TYR88 3.1 18.9 1.0
CD2 C:HIS166 3.1 19.6 1.0
CE1 C:TYR88 3.2 17.3 1.0
CG C:HIS86 3.3 19.4 1.0
O C:HOH1361 3.7 22.6 1.0
NE2 C:HIS86 3.9 19.7 1.0
ND1 C:HIS104 3.9 6.9 1.0
CB C:HIS86 3.9 20.4 1.0
ND1 C:HIS166 4.0 21.0 1.0
CB C:SER177 4.0 27.6 1.0
CG C:HIS104 4.0 13.7 1.0
CD2 C:HIS86 4.0 18.1 1.0
CG C:HIS166 4.1 22.3 1.0
CE2 C:TYR88 4.3 11.4 1.0
CD1 C:TYR88 4.5 17.1 1.0
O C:SER177 4.8 27.0 1.0
OG C:SER180 4.8 25.3 1.0
CA C:SER177 4.9 26.8 1.0
OG C:SER177 5.0 32.8 1.0

Copper binding site 4 out of 4 in 1xtl

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Copper binding site 4 out of 4 in the Crystal Structure of P104H Mutant of 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 4 of Crystal Structure of P104H Mutant of Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu1177

b:29.0
occ:1.00
NE2 D:HIS104 2.0 2.0 1.0
NE2 D:HIS166 2.1 5.3 1.0
OH D:TYR88 2.2 20.5 1.0
ND1 D:HIS86 2.4 28.4 1.0
CE1 D:HIS166 2.7 7.0 1.0
CD2 D:HIS166 2.7 16.4 1.0
CD2 D:HIS104 2.9 14.9 1.0
CZ D:TYR88 3.0 16.0 1.0
CE1 D:TYR88 3.1 7.4 1.0
CE1 D:HIS104 3.1 20.6 1.0
CE1 D:HIS86 3.2 29.1 1.0
ND1 D:HIS166 3.5 21.3 1.0
CG D:HIS86 3.6 20.4 1.0
CG D:HIS166 3.6 17.6 1.0
O D:HOH1383 4.0 21.7 1.0
CB D:HIS86 4.0 17.0 1.0
CB D:SER177 4.0 27.9 1.0
CG D:HIS104 4.1 4.3 1.0
ND1 D:HIS104 4.2 2.0 1.0
CE2 D:TYR88 4.3 15.2 1.0
NE2 D:HIS86 4.4 24.1 1.0
CD1 D:TYR88 4.5 10.8 1.0
CD2 D:HIS86 4.6 26.5 1.0
O D:HOH1370 4.6 20.1 1.0
OG D:SER180 4.8 23.5 1.0
CG2 D:ILE164 4.9 17.2 1.0
O D:SER177 4.9 28.2 1.0
OG D:SER177 5.0 26.6 1.0
CB D:HIS166 5.0 23.2 1.0
CA D:SER177 5.0 27.1 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 16:25:59 2020
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