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Nickel in PDB 4rt5: The Crystal Structure of A Glyoxalase/Bleomycin Resistance Protein/Dioxygenase Protein From Planctomyces Limnophilus Dsm 3776

Enzymatic activity of The Crystal Structure of A Glyoxalase/Bleomycin Resistance Protein/Dioxygenase Protein From Planctomyces Limnophilus Dsm 3776

All present enzymatic activity of The Crystal Structure of A Glyoxalase/Bleomycin Resistance Protein/Dioxygenase Protein From Planctomyces Limnophilus Dsm 3776:
4.4.1.5;

Protein crystallography data

The structure of The Crystal Structure of A Glyoxalase/Bleomycin Resistance Protein/Dioxygenase Protein From Planctomyces Limnophilus Dsm 3776, PDB code: 4rt5 was solved by R.Wu, J.Bearden, Y.Kim, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.79 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 30.130, 77.496, 45.827, 90.00, 109.19, 90.00
R / Rfree (%) 15.1 / 18

Nickel Binding Sites:

The binding sites of Nickel atom in the The Crystal Structure of A Glyoxalase/Bleomycin Resistance Protein/Dioxygenase Protein From Planctomyces Limnophilus Dsm 3776 (pdb code 4rt5). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the The Crystal Structure of A Glyoxalase/Bleomycin Resistance Protein/Dioxygenase Protein From Planctomyces Limnophilus Dsm 3776, PDB code: 4rt5:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 4rt5

Go back to Nickel Binding Sites List in 4rt5
Nickel binding site 1 out of 2 in the The Crystal Structure of A Glyoxalase/Bleomycin Resistance Protein/Dioxygenase Protein From Planctomyces Limnophilus Dsm 3776


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Crystal Structure of A Glyoxalase/Bleomycin Resistance Protein/Dioxygenase Protein From Planctomyces Limnophilus Dsm 3776 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni201

b:13.0
occ:1.00
NE2 A:HIS69 2.0 11.8 1.0
O2 A:TRS202 2.1 37.8 1.0
OE2 A:GLU104 2.2 14.5 1.0
NE2 A:HIS18 2.2 14.1 1.0
C2 A:TRS202 2.3 32.4 1.0
O3 A:TRS202 2.5 23.1 1.0
O A:HOH360 2.6 9.1 1.0
CE1 A:HIS69 2.9 9.7 1.0
CE1 A:HIS18 3.0 7.9 1.0
CD2 A:HIS69 3.1 9.8 1.0
C3 A:TRS202 3.1 29.8 1.0
CD A:GLU104 3.3 18.9 1.0
C A:TRS202 3.3 34.8 1.0
CD2 A:HIS18 3.3 14.1 1.0
OE1 A:GLU104 3.6 20.8 1.0
ND1 A:HIS69 4.1 10.4 1.0
O A:HOH313 4.2 22.6 1.0
CG A:HIS69 4.2 11.8 1.0
ND1 A:HIS18 4.2 10.0 1.0
N A:TRS202 4.3 33.6 1.0
C1 A:TRS202 4.4 38.5 1.0
CG A:HIS18 4.4 13.4 1.0
NE2 A:HIS66 4.6 12.0 0.4
CG A:GLU104 4.6 15.4 1.0
O A:HOH350 4.6 24.7 1.0
O1 A:TRS202 4.6 37.2 1.0
OH A:TYR94 4.6 34.4 1.0
CE2 A:TYR94 4.6 29.6 1.0
CB A:ALA71 4.7 8.5 1.0
CB A:GLU104 4.8 13.1 1.0
O A:HOH357 5.0 26.6 1.0

Nickel binding site 2 out of 2 in 4rt5

Go back to Nickel Binding Sites List in 4rt5
Nickel binding site 2 out of 2 in the The Crystal Structure of A Glyoxalase/Bleomycin Resistance Protein/Dioxygenase Protein From Planctomyces Limnophilus Dsm 3776


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Crystal Structure of A Glyoxalase/Bleomycin Resistance Protein/Dioxygenase Protein From Planctomyces Limnophilus Dsm 3776 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni201

b:15.0
occ:1.00
O2 B:TRS202 2.0 32.2 1.0
NE2 B:HIS18 2.1 17.8 1.0
NE2 B:HIS69 2.2 13.6 1.0
OE1 B:GLU104 2.3 16.0 1.0
C1 B:TRS202 2.4 21.7 1.0
O1 B:TRS202 2.5 22.1 1.0
CE1 B:HIS18 2.8 16.5 1.0
C2 B:TRS202 2.8 33.5 1.0
CE1 B:HIS69 3.0 12.2 1.0
C B:TRS202 3.2 32.3 1.0
CD2 B:HIS18 3.3 13.0 1.0
CD B:GLU104 3.3 16.8 1.0
CD2 B:HIS69 3.4 10.8 1.0
OE2 B:GLU104 3.6 21.1 1.0
ND1 B:HIS18 4.0 17.0 1.0
ND1 B:HIS69 4.2 10.9 1.0
N B:TRS202 4.2 32.6 1.0
CG B:HIS18 4.3 8.5 1.0
O B:HOH351 4.3 21.2 1.0
C3 B:TRS202 4.3 40.8 1.0
CG B:HIS69 4.4 10.2 1.0
O3 B:TRS202 4.6 45.6 1.0
CG B:GLU104 4.7 12.2 1.0
CB B:ALA71 4.7 9.4 1.0
CE1 B:HIS66 4.8 18.4 0.6
OH B:TYR94 4.9 48.6 1.0
CB B:GLU104 4.9 10.8 1.0
O B:HOH331 4.9 33.4 1.0
O B:HOH347 5.0 30.0 1.0

Reference:

R.Wu, J.Bearden, Y.Kim, A.Joachimiak. The Crystal Structure of A Glyoxalase/Bleomycin Resistance Protein/Dioxygenase Protein From Planctomyces Limnophilus Dsm 3776 To Be Published.
Page generated: Wed Oct 9 19:10:01 2024

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