Nickel in PDB 1rxq: Yfit From Bacillus Subtilis Is A Probable Metal-Dependent Hydrolase with An Unusual Four-Helix Bundle Topology

The structure of Yfit From Bacillus Subtilis Is A Probable Metal-Dependent Hydrolase with An Unusual Four-Helix Bundle Topology, PDB code: 1rxq was solved by S.S.Rajan, X.Yang, W.F.Anderson, Midwest Center For Structural Genomics(Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.370, 50.420, 89.410, 104.38, 90.61, 112.05
R / Rfree (%)	18.6 / 21.7

The binding sites of Nickel atom in the Yfit From Bacillus Subtilis Is A Probable Metal-Dependent Hydrolase with An Unusual Four-Helix Bundle Topology (pdb code 1rxq). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Yfit From Bacillus Subtilis Is A Probable Metal-Dependent Hydrolase with An Unusual Four-Helix Bundle Topology, PDB code: 1rxq:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Yfit From Bacillus Subtilis Is A Probable Metal-Dependent Hydrolase with An Unusual Four-Helix Bundle Topology


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Yfit From Bacillus Subtilis Is A Probable Metal-Dependent Hydrolase with An Unusual Four-Helix Bundle Topology within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni300 b:23.3 occ:1.00 CE1 A:HIS160 2.1 16.3 1.0 O A:HOH310 2.1 23.4 1.0 NE2 A:HIS164 2.1 19.1 1.0 O A:HOH312 2.1 25.4 1.0 O A:HOH311 2.1 21.4 1.0 NE2 A:HIS67 2.2 13.3 1.0 NE2 A:HIS160 3.0 21.5 1.0 CE1 A:HIS164 3.1 20.9 1.0 CE1 A:HIS67 3.1 17.2 1.0 ND1 A:HIS160 3.1 20.1 1.0 CD2 A:HIS164 3.1 19.1 1.0 CD2 A:HIS67 3.1 15.8 1.0 OE2 A:GLU95 4.2 32.7 1.0 ND1 A:HIS164 4.2 18.6 1.0 ND1 A:HIS67 4.2 15.6 1.0 CD2 A:HIS160 4.2 16.0 1.0 O A:HOH329 4.2 39.1 1.0 CG A:HIS164 4.2 16.2 1.0 CG A:HIS67 4.2 14.1 1.0 CG A:HIS160 4.2 18.1 1.0 OE1 A:GLU95 4.3 30.2 1.0 CD A:GLU95 4.6 26.7 1.0 O A:HOH355 4.8 45.6 1.0 CZ3 A:TRP59 4.8 23.2 1.0 CD2 A:HIS163 4.9 26.7 1.0 O A:HOH308 5.0 31.4 1.0

Nickel binding site 2 out of 4 in the Yfit From Bacillus Subtilis Is A Probable Metal-Dependent Hydrolase with An Unusual Four-Helix Bundle Topology


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Yfit From Bacillus Subtilis Is A Probable Metal-Dependent Hydrolase with An Unusual Four-Helix Bundle Topology within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni300 b:22.1 occ:1.00 O B:HOH312 1.9 24.4 1.0 NE2 B:HIS160 2.1 17.1 1.0 O B:HOH311 2.1 24.6 1.0 NE2 B:HIS67 2.2 13.6 1.0 NE2 B:HIS164 2.2 16.6 1.0 O B:HOH313 2.2 23.5 1.0 CD2 B:HIS160 3.0 19.9 1.0 CD2 B:HIS67 3.1 13.0 1.0 CE1 B:HIS67 3.1 19.5 1.0 CE1 B:HIS160 3.1 17.8 1.0 CD2 B:HIS164 3.2 18.0 1.0 CE1 B:HIS164 3.2 16.4 1.0 O B:HOH330 4.1 36.3 1.0 ND1 B:HIS67 4.2 14.9 1.0 CG B:HIS67 4.2 14.2 1.0 CG B:HIS160 4.2 16.2 1.0 ND1 B:HIS160 4.2 15.4 1.0 ND1 B:HIS164 4.3 17.9 1.0 OE1 B:GLU95 4.3 31.1 1.0 CG B:HIS164 4.3 15.3 1.0 OE2 B:GLU95 4.4 28.2 1.0 CD B:GLU95 4.7 26.2 1.0 CZ3 B:TRP59 4.8 18.8 1.0 CD2 B:HIS163 4.9 22.3 1.0 O B:HOH309 5.0 29.1 1.0

Nickel binding site 3 out of 4 in the Yfit From Bacillus Subtilis Is A Probable Metal-Dependent Hydrolase with An Unusual Four-Helix Bundle Topology


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Yfit From Bacillus Subtilis Is A Probable Metal-Dependent Hydrolase with An Unusual Four-Helix Bundle Topology within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni300 b:19.7 occ:1.00 NE2 C:HIS164 2.1 12.3 1.0 NE2 C:HIS67 2.1 12.0 1.0 NE2 C:HIS160 2.1 12.4 1.0 O C:HOH346 2.2 19.2 1.0 O C:HOH303 2.2 21.4 1.0 O C:HOH302 2.2 19.7 1.0 CD2 C:HIS160 3.0 14.0 1.0 CE1 C:HIS67 3.1 17.6 1.0 CD2 C:HIS164 3.1 13.5 1.0 CD2 C:HIS67 3.1 13.1 1.0 CE1 C:HIS164 3.1 15.9 1.0 CE1 C:HIS160 3.1 16.3 1.0 O C:HOH301 4.0 39.3 1.0 O C:HOH304 4.1 24.5 0.5 ND1 C:HIS67 4.2 12.8 1.0 CG C:HIS160 4.2 12.4 1.0 ND1 C:HIS164 4.2 14.6 1.0 CG C:HIS67 4.2 13.6 1.0 CG C:HIS164 4.2 11.6 1.0 ND1 C:HIS160 4.2 11.6 1.0 OE1 C:GLU95 4.2 30.6 1.0 OE2 C:GLU95 4.3 36.3 1.0 O C:HOH341 4.3 32.1 1.0 CD C:GLU95 4.3 28.7 1.0 CZ3 C:TRP59 4.8 19.6 1.0 O C:HOH412 5.0 43.1 1.0

Nickel binding site 4 out of 4 in the Yfit From Bacillus Subtilis Is A Probable Metal-Dependent Hydrolase with An Unusual Four-Helix Bundle Topology


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Yfit From Bacillus Subtilis Is A Probable Metal-Dependent Hydrolase with An Unusual Four-Helix Bundle Topology within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni300 b:26.0 occ:1.00 OE1 D:GLU501 1.4 23.3 0.6 NE2 D:HIS164 2.0 21.6 1.0 CD D:GLU501 2.1 24.9 0.6 NE2 D:HIS67 2.2 13.1 1.0 NE2 D:HIS160 2.2 19.4 1.0 O D:HOH624 2.2 26.9 1.0 O D:HOH623 2.2 16.8 0.4 OE2 D:GLU501 2.3 28.6 0.6 O D:HOH625 2.5 25.8 0.4 CE1 D:HIS164 3.0 18.6 1.0 CD2 D:HIS164 3.0 20.1 1.0 CE1 D:HIS67 3.1 17.4 1.0 CD2 D:HIS160 3.1 21.8 1.0 CD2 D:HIS67 3.1 16.4 1.0 CE1 D:HIS160 3.2 22.2 1.0 CG D:GLU501 3.5 32.4 0.6 ND1 D:HIS164 4.1 23.6 1.0 CG D:HIS164 4.2 20.4 1.0 ND1 D:HIS67 4.2 12.4 1.0 CG D:HIS67 4.2 10.7 1.0 ND1 D:HIS160 4.2 18.0 1.0 CG D:HIS160 4.2 18.6 1.0 CB D:GLU501 4.3 42.1 0.6 O D:HOH626 4.5 45.9 1.0 CZ3 D:TRP59 4.6 26.6 1.0 N D:SER502 4.7 34.4 0.6 OE1 D:GLU95 4.7 40.4 1.0 C D:GLU501 4.7 36.7 0.6 O D:GLU501 4.9 28.8 0.6

S.S.Rajan, X.Yang, L.Shuvalova, F.Collart, W.F.Anderson. Yfit From Bacillus Subtilis Is A Probable Metal-Dependent Hydrolase with An Unusual Four-Helix Bundle Topology Biochemistry V. 43 15472 2004.
ISSN: ISSN 0006-2960
PubMed: 15581359
DOI: 10.1021/BI048665R