Nickel in PDB 4mgg: Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121

The structure of Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121, PDB code: 4mgg was solved by M.W.Vetting, X.Zhang, S.R.Wasserman, L.L.Morisco, S.Sojitra, J.B.Bonanno, J.A.Gerlt, S.C.Almo, New York Structural Genomics Research Consortium(Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.81 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	110.313, 154.897, 181.983, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 21.6

The structure of Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121 also contains other interesting chemical elements:

Magnesium	(Mg)	17 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Nickel atom in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121 (pdb code 4mgg). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121, PDB code: 4mgg:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121


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 Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:18.1 occ:1.00 O G:HOH502 2.0 19.7 1.0 O A:HOH501 2.0 9.8 1.0 O A:HOH502 2.0 13.5 1.0 NE2 G:HIS98 2.0 16.6 1.0 NE2 A:HIS98 2.2 14.8 1.0 O G:HOH501 2.2 11.3 1.0 CE1 G:HIS98 3.0 16.4 1.0 CD2 G:HIS98 3.0 16.9 1.0 CE1 A:HIS98 3.1 17.6 1.0 CD2 A:HIS98 3.2 14.0 1.0 HE1 G:HIS98 3.2 19.7 1.0 HD2 G:HIS98 3.2 20.2 1.0 HE1 A:HIS98 3.3 21.1 1.0 HD2 A:HIS98 3.3 16.8 1.0 HG G:SER67 3.7 27.1 1.0 HG A:SER67 3.8 29.1 1.0 OG G:SER67 4.0 22.6 1.0 OG A:SER67 4.1 24.3 1.0 OE2 G:GLU71 4.1 31.5 1.0 ND1 G:HIS98 4.1 16.0 1.0 CG G:HIS98 4.2 15.8 1.0 OE2 A:GLU71 4.2 33.6 1.0 ND1 A:HIS98 4.2 14.4 1.0 HD11 G:LEU95 4.3 20.3 1.0 CG A:HIS98 4.3 14.0 1.0 OE1 G:GLU71 4.4 36.5 1.0 OE1 A:GLU71 4.4 31.2 1.0 O G:HOH533 4.5 21.0 1.0 O G:HOH521 4.5 13.9 1.0 HD11 A:LEU95 4.5 26.3 1.0 HA2 A:GLY64 4.6 17.3 1.0 CD G:GLU71 4.7 24.9 1.0 HA2 G:GLY68 4.7 20.3 1.0 CD A:GLU71 4.7 30.6 1.0 HA2 A:GLY68 4.7 17.2 1.0 HA2 G:GLY64 4.8 26.6 1.0 HD1 G:HIS98 4.9 19.2 1.0

Nickel binding site 2 out of 3 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121


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 Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni401 b:29.0 occ:1.00 O E:HOH803 2.1 20.7 1.0 NE2 E:HIS98 2.1 32.3 1.0 O E:HOH802 2.1 22.4 1.0 O C:HOH502 2.2 27.0 1.0 O C:HOH501 2.2 27.7 1.0 NE2 C:HIS98 2.2 28.5 1.0 CE1 E:HIS98 3.0 29.8 1.0 CE1 C:HIS98 3.1 29.8 1.0 HE1 C:HIS98 3.2 35.7 1.0 HE1 E:HIS98 3.2 35.8 1.0 CD2 E:HIS98 3.2 28.4 1.0 CD2 C:HIS98 3.3 23.8 1.0 HD2 E:HIS98 3.4 34.1 1.0 HD2 C:HIS98 3.5 28.6 1.0 OE2 E:GLU71 4.0 57.8 1.0 OE2 C:GLU71 4.1 59.9 1.0 O C:HOH602 4.2 32.7 1.0 O E:HOH881 4.2 29.3 1.0 HG E:SER67 4.2 47.1 1.0 ND1 E:HIS98 4.2 30.5 1.0 ND1 C:HIS98 4.2 26.4 1.0 OG E:SER67 4.3 39.2 1.0 CG E:HIS98 4.3 27.6 1.0 HG C:SER67 4.3 60.3 1.0 CG C:HIS98 4.4 26.9 1.0 HD11 E:LEU95 4.4 56.7 1.0 OE1 E:GLU71 4.5 44.8 1.0 OG C:SER67 4.6 50.2 1.0 HD11 C:LEU95 4.6 44.5 1.0 CD E:GLU71 4.7 50.2 1.0 HA2 E:GLY68 4.8 52.4 1.0 HA2 E:GLY64 4.8 51.1 1.0 HA2 C:GLY68 4.8 30.5 1.0 CD C:GLU71 4.8 59.5 1.0 HD21 E:LEU95 4.9 54.2 1.0 OE1 C:GLU71 4.9 65.4 1.0 HD1 E:HIS98 5.0 36.6 1.0 HD21 C:LEU95 5.0 39.3 1.0 HD1 C:HIS98 5.0 31.7 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121


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 Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni401 b:28.1 occ:1.00 O H:HOH502 1.9 14.0 1.0 O H:HOH503 2.0 22.2 1.0 NE2 D:HIS98 2.0 32.9 1.0 O D:HOH501 2.0 25.8 1.0 NE2 H:HIS98 2.0 28.1 1.0 O H:HOH501 2.1 22.6 1.0 CE1 H:HIS98 2.9 27.6 1.0 CE1 D:HIS98 2.9 27.1 1.0 HE1 H:HIS98 3.0 33.2 1.0 HE1 D:HIS98 3.0 32.5 1.0 CD2 D:HIS98 3.1 30.2 1.0 CD2 H:HIS98 3.1 27.6 1.0 HD2 D:HIS98 3.4 36.2 1.0 HD2 H:HIS98 3.4 33.1 1.0 HG H:SER67 3.7 44.1 1.0 OG H:SER67 3.9 36.8 1.0 OE2 H:GLU71 4.0 45.4 1.0 HG D:SER67 4.0 38.6 1.0 ND1 D:HIS98 4.1 25.9 1.0 ND1 H:HIS98 4.1 26.8 1.0 OG D:SER67 4.1 32.1 1.0 O D:HOH523 4.2 24.2 1.0 CG D:HIS98 4.2 32.9 1.0 CG H:HIS98 4.2 26.8 1.0 OE2 D:GLU71 4.3 47.8 1.0 OE1 D:GLU71 4.3 51.6 1.0 OE1 H:GLU71 4.4 40.2 1.0 O D:HOH565 4.4 34.9 1.0 HD11 H:LEU95 4.4 33.2 1.0 HD11 D:LEU95 4.5 45.1 1.0 CD H:GLU71 4.6 46.4 1.0 HA2 H:GLY68 4.7 34.6 1.0 CD D:GLU71 4.7 48.6 1.0 HA2 H:GLY64 4.8 37.0 1.0 HA2 D:GLY64 4.8 33.9 1.0 HA2 D:GLY68 4.8 39.7 1.0 HD1 H:HIS98 4.8 32.2 1.0 HD1 D:HIS98 4.8 31.1 1.0

M.W.Vetting, X.Zhang, S.R.Wasserman, L.L.Morisco, S.Sojitra, J.B.Bonanno, J.A.Gerlt, S.C.Almo, New York Structural Genomics Research Consortium (Nysgrc). Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121 To Be Published.