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Nickel in PDB 4e2g: Crystal Structure of Cupin Fold Protein STHE2323 From Sphaerobacter Thermophilus

Protein crystallography data

The structure of Crystal Structure of Cupin Fold Protein STHE2323 From Sphaerobacter Thermophilus, PDB code: 4e2g was solved by C.Chang, C.Hatzos-Skintges, R.Jedrzejczak, A.Joachimiak, Midwest Centerfor Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.86
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 193.710, 52.623, 108.818, 90.00, 91.24, 90.00
R / Rfree (%) 15.9 / 21.1

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Cupin Fold Protein STHE2323 From Sphaerobacter Thermophilus (pdb code 4e2g). 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 Cupin Fold Protein STHE2323 From Sphaerobacter Thermophilus, PDB code: 4e2g:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 4e2g

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Nickel binding site 1 out of 4 in the Crystal Structure of Cupin Fold Protein STHE2323 From Sphaerobacter Thermophilus


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 Cupin Fold Protein STHE2323 From Sphaerobacter Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni201

b:44.0
occ:0.50
NE2 B:HIS56 2.1 52.8 1.0
NE2 B:HIS54 2.5 39.7 0.5
OE1 B:GLN60 2.5 33.1 1.0
NE2 B:HIS94 2.6 40.5 1.0
CE1 B:HIS56 3.0 59.6 1.0
CE1 B:HIS94 3.1 40.7 1.0
CD2 B:HIS56 3.2 49.7 1.0
CD2 B:HIS54 3.2 40.5 0.5
CE1 B:HIS54 3.5 40.6 0.5
O B:HOH333 3.6 48.1 1.0
CD B:GLN60 3.7 34.2 1.0
CD2 B:HIS94 3.8 36.3 1.0
NH1 B:ARG113 4.0 44.4 1.0
CE1 B:PHE109 4.1 29.7 1.0
ND1 B:HIS56 4.2 56.6 1.0
NE2 B:GLN60 4.2 41.4 1.0
CG B:HIS56 4.3 48.5 1.0
ND1 B:HIS94 4.4 39.8 1.0
CG B:HIS54 4.4 41.3 0.5
ND1 B:HIS54 4.5 41.2 0.5
CZ B:PHE109 4.5 26.2 1.0
CG B:HIS94 4.7 36.1 1.0
CG B:GLN60 4.9 28.9 1.0

Nickel binding site 2 out of 4 in 4e2g

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Nickel binding site 2 out of 4 in the Crystal Structure of Cupin Fold Protein STHE2323 From Sphaerobacter Thermophilus


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 Cupin Fold Protein STHE2323 From Sphaerobacter Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni201

b:39.2
occ:0.50
O C:HOH340 1.9 47.8 1.0
NE2 C:HIS56 2.0 27.1 0.5
OE1 C:GLN60 2.4 30.7 1.0
NE2 C:HIS94 2.7 31.6 1.0
CD2 C:HIS56 2.8 27.8 0.5
CE1 C:HIS56 3.1 28.5 0.5
CE1 C:HIS94 3.1 30.3 1.0
CD C:GLN60 3.5 29.4 1.0
CD2 C:HIS94 3.9 28.1 1.0
NH1 C:ARG113 4.0 41.6 1.0
NE2 C:GLN60 4.1 34.8 1.0
CG C:HIS56 4.1 28.2 0.5
CD2 C:HIS56 4.1 35.9 0.5
CE1 C:PHE109 4.2 25.7 1.0
ND1 C:HIS56 4.2 29.9 0.5
ND1 C:HIS94 4.4 29.0 1.0
CZ C:PHE109 4.6 26.7 1.0
O C:HOH336 4.8 37.6 1.0
CG C:GLN60 4.8 25.0 1.0
CG C:HIS94 4.8 26.4 1.0
NE2 C:HIS56 4.9 36.0 0.5

Nickel binding site 3 out of 4 in 4e2g

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Nickel binding site 3 out of 4 in the Crystal Structure of Cupin Fold Protein STHE2323 From Sphaerobacter Thermophilus


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 Cupin Fold Protein STHE2323 From Sphaerobacter Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni201

b:73.1
occ:1.00
O C:PHE9 3.9 40.7 1.0
CD F:PRO52 4.0 43.0 1.0
CB C:PHE9 4.2 47.5 1.0
C C:PHE9 4.2 40.8 1.0
CD F:PRO26 4.4 37.0 1.0
CG F:PRO52 4.4 47.5 1.0
CD2 F:LEU25 4.5 41.1 1.0
CB F:LEU25 4.5 35.5 1.0
O F:GLU50 4.5 43.2 1.0
CA C:ALA10 4.6 35.4 1.0
N C:ALA10 4.7 36.0 1.0
O C:HOH352 4.7 34.6 1.0
CD1 F:LEU25 4.7 44.8 1.0
CB C:ALA10 4.8 34.3 1.0
CG F:LEU25 4.8 39.8 1.0
SE F:MSE51 4.8 49.0 0.8
CA C:PHE9 4.9 43.4 1.0
O F:PRO26 5.0 40.7 1.0

Nickel binding site 4 out of 4 in 4e2g

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Nickel binding site 4 out of 4 in the Crystal Structure of Cupin Fold Protein STHE2323 From Sphaerobacter Thermophilus


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 Cupin Fold Protein STHE2323 From Sphaerobacter Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ni201

b:70.2
occ:1.00
NE2 G:HIS94 2.4 25.2 1.0
O G:HOH380 2.4 46.0 1.0
OE1 G:GLN60 2.7 24.0 1.0
O G:HOH308 2.8 43.3 1.0
O G:HOH366 3.1 30.2 1.0
CE1 G:HIS94 3.3 26.5 1.0
CD2 G:HIS56 3.3 26.2 1.0
CD2 G:HIS94 3.5 21.9 1.0
CD G:GLN60 3.7 23.0 1.0
NE2 G:HIS56 3.7 26.8 1.0
O G:HOH330 3.7 39.5 1.0
NH1 G:ARG113 3.8 33.3 1.0
NE2 G:GLN60 4.0 25.6 1.0
CE1 G:PHE109 4.2 24.3 1.0
CZ G:PHE109 4.4 24.6 1.0
ND1 G:HIS94 4.5 23.4 1.0
CG G:HIS56 4.6 24.6 1.0
CG G:HIS94 4.6 22.1 1.0
O G:HOH303 4.8 31.8 1.0
CE1 G:HIS56 5.0 26.6 1.0
CG G:GLN60 5.0 21.7 1.0

Reference:

C.Chang, C.Hatzos-Skintges, R.Jedrzejczak, A.Joachimiak. Crystal Structure of Cupin Fold Protein STHE2323 From Sphaerobacter Thermophilus To Be Published.
Page generated: Fri Sep 25 08:41:18 2020
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