Nickel in PDB 5udw: Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel

The structure of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel, PDB code: 5udw was solved by M.Fellner, B.Desguin, R.P.Hausinger, J.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.58 / 2.70
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	106.800, 106.800, 317.266, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Nickel atom in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel (pdb code 5udw). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 11 binding sites of Nickel where determined in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel, PDB code: 5udw:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 11 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:75.0 occ:1.00 O3 A:SO4306 1.9 95.4 1.0 O4 A:SO4306 1.9 95.3 1.0 NE2 A:HIS190 2.1 0.1 1.0 S A:SO4306 2.2 1.0 1.0 CD2 A:HIS190 2.9 99.5 1.0 CE1 A:HIS190 3.1 96.4 1.0 O1 A:SO4306 3.2 0.2 1.0 O2 A:SO4306 3.4 0.1 1.0 CG A:HIS190 4.0 87.0 1.0 ND1 A:HIS190 4.0 93.3 1.0 OD2 A:ASP82 4.2 85.1 1.0 O3 A:SO4305 4.2 81.2 1.0 O4 A:SO4305 4.6 75.7 1.0 OD1 A:ASP82 4.7 79.7 1.0 O1 A:SO4305 4.7 83.8 1.0 S A:SO4305 4.8 77.6 1.0 CG A:ASP82 4.9 73.4 1.0

Nickel binding site 2 out of 11 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:71.4 occ:1.00 O A:HOH403 1.6 59.2 1.0 OD1 B:ASP231 2.1 0.1 1.0 OD1 A:ASP231 2.1 0.0 1.0 OD2 B:ASP231 2.1 0.8 1.0 OD1 C:ASP231 2.1 0.7 1.0 OD2 A:ASP231 2.1 0.5 1.0 OD2 C:ASP231 2.1 0.2 1.0 CG B:ASP231 2.4 86.6 1.0 CG A:ASP231 2.4 92.4 1.0 CG C:ASP231 2.4 77.1 1.0 CB B:ASP231 3.9 56.8 1.0 CB A:ASP231 4.0 63.4 1.0 CB C:ASP231 4.0 48.0 1.0 O C:ALA227 4.7 51.9 1.0 O B:ALA227 4.8 53.9 1.0 CA B:ASP231 4.8 46.3 1.0 CA A:ASP231 4.8 58.4 1.0 CA C:ASP231 4.8 45.8 1.0 N B:ASP231 4.9 43.7 1.0 N A:ASP231 4.9 54.9 1.0 N C:ASP231 5.0 51.7 1.0

Nickel binding site 3 out of 11 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni302 b:0.1 occ:1.00 NE2 B:HIS88 2.1 1.0 1.0 O3 B:SO4304 2.1 0.1 1.0 O4 B:SO4304 2.2 0.3 1.0 S B:SO4304 2.5 0.3 1.0 CE1 B:HIS88 2.7 92.7 1.0 O2 B:SO4304 3.1 99.5 1.0 CD2 B:HIS88 3.3 86.5 1.0 O1 B:SO4304 3.8 0.1 1.0 OH B:TYR99 3.9 54.7 1.0 ND1 B:HIS88 3.9 81.5 1.0 CG B:HIS88 4.3 75.4 1.0 CZ B:TYR99 4.6 52.2 1.0 CE2 B:TYR99 5.0 46.4 1.0

Nickel binding site 4 out of 11 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni302 b:97.9 occ:1.00 NE2 C:HIS190 2.1 0.6 1.0 CE1 C:HIS190 2.3 0.2 1.0 O C:HOH414 2.4 72.8 1.0 O C:HOH418 2.5 77.2 1.0 CD2 C:HIS190 3.3 0.9 1.0 ND1 C:HIS190 3.4 0.9 1.0 CG C:HIS190 4.0 90.7 1.0 O3 C:SO4305 4.5 93.5 1.0 OD2 C:ASP82 4.7 82.6 1.0 OD1 C:ASP82 4.8 75.5 1.0 O2 C:SO4305 4.8 0.2 1.0

Nickel binding site 5 out of 11 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni303 b:90.9 occ:1.00 NE2 C:HIS88 2.2 0.7 1.0 CE1 C:HIS88 2.8 0.5 1.0 CD2 C:HIS88 3.4 97.3 1.0 ND1 C:HIS88 4.1 95.8 1.0 CG C:HIS88 4.3 80.6 1.0 OH C:TYR99 4.6 67.0 1.0

Nickel binding site 6 out of 11 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni302 b:71.3 occ:1.00 O F:HOH401 1.6 70.6 1.0 OD2 F:ASP231 2.1 0.7 1.0 OD2 E:ASP231 2.1 0.6 1.0 OD1 D:ASP231 2.1 0.8 1.0 OD2 D:ASP231 2.1 95.4 1.0 OD1 E:ASP231 2.1 0.1 1.0 OD1 F:ASP231 2.1 0.6 1.0 CG E:ASP231 2.4 91.4 1.0 CG D:ASP231 2.4 78.7 1.0 CG F:ASP231 2.4 96.5 1.0 O E:HOH402 3.9 38.4 1.0 CB E:ASP231 3.9 57.0 1.0 CB F:ASP231 3.9 70.4 1.0 CB D:ASP231 4.0 47.8 1.0 CA E:ASP231 4.8 51.6 1.0 O D:ALA227 4.8 41.8 1.0 CA D:ASP231 4.8 39.9 1.0 CA F:ASP231 4.9 54.5 1.0 N E:ASP231 4.9 55.8 1.0 N D:ASP231 4.9 46.9 1.0 N F:ASP231 5.0 49.9 1.0

Nickel binding site 7 out of 11 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni303 b:87.9 occ:1.00 NE2 D:HIS88 1.9 0.2 1.0 O D:HOH409 2.0 81.2 1.0 CE1 D:HIS88 2.8 90.9 1.0 CD2 D:HIS88 3.0 90.2 1.0 ND1 D:HIS88 3.9 86.7 1.0 CG D:HIS88 4.0 80.5 1.0 CE1 D:TYR99 4.6 59.2 1.0 OD2 D:ASP87 4.7 89.5 1.0 OD1 D:ASP87 4.8 89.4 1.0

Nickel binding site 8 out of 11 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni304 b:0.8 occ:1.00 NE2 D:HIS190 2.0 0.3 1.0 CE1 D:HIS190 2.8 0.7 1.0 O D:HOH408 2.9 73.4 1.0 CD2 D:HIS190 3.2 0.2 1.0 ND1 D:HIS190 4.0 0.3 1.0 CG D:HIS190 4.2 90.8 1.0 O1 D:SO4306 4.6 0.7 1.0 OD1 D:ASP82 4.7 82.3 1.0 OE2 D:GLU55 4.7 92.7 1.0 OE1 D:GLU55 4.8 78.5 1.0

Nickel binding site 9 out of 11 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni302 b:88.2 occ:0.90 NE2 E:HIS88 2.1 0.3 1.0 O E:HOH406 2.4 67.9 1.0 CE1 E:HIS88 2.8 0.7 1.0 CD2 E:HIS88 3.1 0.5 1.0 ND1 E:HIS88 3.9 0.9 1.0 CG E:HIS88 4.1 0.1 1.0 OH E:TYR99 4.2 0.8 1.0 CZ E:TYR99 4.9 0.8 1.0

Nickel binding site 10 out of 11 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nickel within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni302 b:86.5 occ:1.00 NE2 F:HIS190 1.8 0.7 1.0 O2 F:SO4306 2.0 91.4 1.0 CE1 F:HIS190 2.2 0.5 1.0 O4 F:SO4306 2.2 88.0 1.0 S F:SO4306 2.4 0.3 1.0 O3 F:SO4306 2.7 0.9 1.0 CD2 F:HIS190 3.2 0.7 1.0 ND1 F:HIS190 3.4 0.4 1.0 O1 F:SO4306 3.8 0.3 1.0 CG F:HIS190 3.9 0.6 1.0 O4 F:SO4305 4.3 0.1 1.0

M.Fellner, B.Desguin, R.P.Hausinger, J.Hu. Structural Insights Into the Catalytic Mechanism of A Sacrificial Sulfur Insertase of the N-Type Atp Pyrophosphatase Family, Lare. Proc. Natl. Acad. Sci. V. 114 9074 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28784764
DOI: 10.1073/PNAS.1704967114