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Nickel in PDB 2qjv: Crystal Structure of An Iolb-Like Protein (STM4420) From Salmonella Typhimurium LT2 at 1.90 A Resolution

Protein crystallography data

The structure of Crystal Structure of An Iolb-Like Protein (STM4420) From Salmonella Typhimurium LT2 at 1.90 A Resolution, PDB code: 2qjv was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.51 / 1.90
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 200.140, 200.140, 200.140, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 18.1

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of An Iolb-Like Protein (STM4420) From Salmonella Typhimurium LT2 at 1.90 A Resolution (pdb code 2qjv). 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 An Iolb-Like Protein (STM4420) From Salmonella Typhimurium LT2 at 1.90 A Resolution, PDB code: 2qjv:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 2qjv

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Nickel binding site 1 out of 4 in the Crystal Structure of An Iolb-Like Protein (STM4420) From Salmonella Typhimurium LT2 at 1.90 A Resolution


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 An Iolb-Like Protein (STM4420) From Salmonella Typhimurium LT2 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni270

b:59.2
occ:1.00
NE2 A:HIS91 2.0 28.7 1.0
O A:HOH459 2.1 42.9 1.0
NE2 A:HIS90 2.4 45.1 1.0
O A:HOH484 2.4 44.9 1.0
O A:HOH486 2.6 45.0 1.0
CD2 A:HIS91 2.9 50.2 1.0
CE1 A:HIS91 3.0 51.1 1.0
CD2 A:HIS90 3.2 46.7 1.0
CE1 A:HIS90 3.4 48.3 1.0
O A:HOH642 3.7 65.3 1.0
CG A:HIS91 4.0 48.2 1.0
ND1 A:HIS91 4.0 44.3 1.0
O A:HOH491 4.0 45.8 1.0
OE1 A:GLU47 4.2 70.1 1.0
O A:HOH632 4.3 60.7 1.0
CG A:HIS90 4.4 39.9 1.0
ND1 A:HIS90 4.5 40.9 1.0
O A:PHE112 4.9 41.7 1.0

Nickel binding site 2 out of 4 in 2qjv

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Nickel binding site 2 out of 4 in the Crystal Structure of An Iolb-Like Protein (STM4420) From Salmonella Typhimurium LT2 at 1.90 A Resolution


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 An Iolb-Like Protein (STM4420) From Salmonella Typhimurium LT2 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni271

b:22.2
occ:1.00
OE1 A:GLU185 2.1 38.9 1.0
NE2 A:HIS172 2.2 35.0 1.0
NE2 A:HIS228 2.2 35.9 1.0
O A:HOH296 2.2 23.1 1.0
O A:HOH297 2.2 23.1 1.0
NE2 A:HIS170 2.2 38.8 1.0
CE1 A:HIS172 3.1 35.0 1.0
CD A:GLU185 3.1 44.3 1.0
CE1 A:HIS228 3.1 37.4 1.0
CD2 A:HIS228 3.2 31.8 1.0
CE1 A:HIS170 3.2 44.6 1.0
CD2 A:HIS172 3.2 35.6 1.0
CD2 A:HIS170 3.2 36.2 1.0
OE2 A:GLU185 3.5 49.5 1.0
ND1 A:HIS172 4.2 35.5 1.0
ND1 A:HIS228 4.2 33.3 1.0
CG A:HIS228 4.3 33.5 1.0
CG A:HIS172 4.3 35.6 1.0
OH A:TYR187 4.3 38.4 1.0
ND1 A:HIS170 4.3 39.3 1.0
CG A:HIS170 4.4 36.6 1.0
CG A:GLU185 4.5 36.8 1.0
SE A:MSE244 4.6 45.0 0.8
NE1 A:TRP251 4.7 47.6 1.0
CB A:GLU185 4.8 35.6 1.0

Nickel binding site 3 out of 4 in 2qjv

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Nickel binding site 3 out of 4 in the Crystal Structure of An Iolb-Like Protein (STM4420) From Salmonella Typhimurium LT2 at 1.90 A Resolution


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 An Iolb-Like Protein (STM4420) From Salmonella Typhimurium LT2 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni270

b:58.7
occ:1.00
O B:HOH463 2.1 43.2 1.0
NE2 B:HIS91 2.2 33.2 1.0
NE2 B:HIS90 2.3 44.4 1.0
O B:HOH524 2.5 49.3 1.0
O B:HOH485 2.7 45.3 1.0
CD2 B:HIS91 3.0 54.2 1.0
CE1 B:HIS91 3.2 54.2 1.0
CD2 B:HIS90 3.2 44.2 1.0
CE1 B:HIS90 3.4 46.3 1.0
O B:HOH490 3.9 46.5 1.0
CG B:HIS91 4.1 47.3 1.0
ND1 B:HIS91 4.2 46.2 1.0
OE1 B:GLU47 4.2 69.2 1.0
CG B:HIS90 4.4 35.0 1.0
ND1 B:HIS90 4.4 40.0 1.0
O B:PHE112 5.0 38.4 1.0

Nickel binding site 4 out of 4 in 2qjv

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Nickel binding site 4 out of 4 in the Crystal Structure of An Iolb-Like Protein (STM4420) From Salmonella Typhimurium LT2 at 1.90 A Resolution


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 An Iolb-Like Protein (STM4420) From Salmonella Typhimurium LT2 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni271

b:22.2
occ:1.00
OE1 B:GLU185 2.1 40.0 1.0
NE2 B:HIS228 2.1 34.7 1.0
NE2 B:HIS172 2.1 36.8 1.0
O B:HOH295 2.2 23.0 1.0
O B:HOH307 2.2 25.7 1.0
NE2 B:HIS170 2.3 40.6 1.0
CE1 B:HIS228 3.0 33.1 1.0
CE1 B:HIS172 3.1 35.7 1.0
CD B:GLU185 3.1 41.9 1.0
CD2 B:HIS172 3.2 35.3 1.0
CD2 B:HIS228 3.2 34.4 1.0
CE1 B:HIS170 3.2 44.3 1.0
CD2 B:HIS170 3.2 39.7 1.0
OE2 B:GLU185 3.4 49.8 1.0
ND1 B:HIS228 4.2 33.6 1.0
ND1 B:HIS172 4.2 33.7 1.0
OH B:TYR187 4.2 38.0 1.0
CG B:HIS228 4.3 33.9 1.0
CG B:HIS172 4.3 36.3 1.0
ND1 B:HIS170 4.3 39.6 1.0
CG B:HIS170 4.4 36.9 1.0
CG B:GLU185 4.5 40.9 1.0
SE B:MSE244 4.7 45.7 0.8
NE1 B:TRP251 4.8 47.6 1.0
CB B:GLU185 4.8 39.2 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
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