Nickel in PDB 5vb0: Crystal Structure of Fosfomycin Resistance Protein FOSA3

The structure of Crystal Structure of Fosfomycin Resistance Protein FOSA3, PDB code: 5vb0 was solved by E.Klontz, S.Guenther, Z.Silverstein, E.Sundberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.75 / 2.69
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	87.608, 87.608, 357.038, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.9

The structure of Crystal Structure of Fosfomycin Resistance Protein FOSA3 also contains other interesting chemical elements:

Manganese

(Mn)

8 atoms

The binding sites of Nickel atom in the Crystal Structure of Fosfomycin Resistance Protein FOSA3 (pdb code 5vb0). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Crystal Structure of Fosfomycin Resistance Protein FOSA3, PDB code: 5vb0:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the Crystal Structure of Fosfomycin Resistance Protein FOSA3


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 Fosfomycin Resistance Protein FOSA3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:81.1 occ:1.00 NE2 A:HIS139 1.9 66.9 1.0 NE2 F:HIS139 2.1 65.2 1.0 NE2 F:HIS141 2.1 94.7 1.0 NE2 A:HIS141 2.2 91.8 1.0 CD2 F:HIS139 2.8 58.5 1.0 CD2 A:HIS139 2.9 55.7 1.0 CD2 F:HIS141 2.9 76.3 1.0 CE1 A:HIS139 2.9 59.3 1.0 CD2 A:HIS141 3.1 82.8 1.0 CE1 F:HIS141 3.1 87.7 1.0 CE1 F:HIS139 3.2 70.1 1.0 CE1 A:HIS141 3.2 79.3 1.0 ND1 A:HIS139 4.0 56.6 1.0 CG A:HIS139 4.0 54.3 1.0 CG F:HIS141 4.0 76.1 1.0 CG F:HIS139 4.1 59.6 1.0 ND1 F:HIS141 4.1 91.4 1.0 ND1 F:HIS139 4.2 58.8 1.0 CG A:HIS141 4.2 82.0 1.0 ND1 A:HIS141 4.3 84.4 1.0 CD1 G:LEU83 5.0 65.9 1.0

Nickel binding site 2 out of 6 in the Crystal Structure of Fosfomycin Resistance Protein FOSA3


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 Fosfomycin Resistance Protein FOSA3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni203 b:99.1 occ:1.00 OE1 A:GLU128 2.2 77.7 1.0 NE2 A:HIS142 2.6 75.0 1.0 CD A:GLU128 2.8 65.6 1.0 OE2 A:GLU128 2.9 61.3 1.0 CD2 A:HIS142 3.3 78.5 1.0 CE1 A:HIS143 3.4 91.9 1.0 NE2 A:HIS143 3.5 90.1 1.0 CE1 A:HIS142 3.7 68.5 1.0 ND1 A:HIS143 4.1 0.0 1.0 CG A:GLU128 4.3 53.2 1.0 CD2 A:HIS143 4.3 0.5 1.0 O D:GLU75 4.4 72.5 1.0 CA A:GLU128 4.4 62.4 1.0 CB D:GLU75 4.6 63.6 1.0 CG A:HIS142 4.6 80.7 1.0 CG A:HIS143 4.6 0.1 1.0 O A:GLU128 4.6 66.7 1.0 CB A:GLU128 4.7 56.7 1.0 ND1 A:HIS142 4.7 73.2 1.0

Nickel binding site 3 out of 6 in the Crystal Structure of Fosfomycin Resistance Protein FOSA3


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 Fosfomycin Resistance Protein FOSA3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni202 b:87.8 occ:1.00 NE2 C:HIS139 2.0 62.4 1.0 NE2 H:HIS139 2.0 64.7 1.0 NE2 H:HIS141 2.2 96.4 1.0 NE2 C:HIS141 2.2 89.6 1.0 CD2 C:HIS139 2.8 55.8 1.0 CD2 H:HIS139 2.9 55.5 1.0 CD2 C:HIS141 3.0 75.8 1.0 CD2 H:HIS141 3.1 73.6 1.0 CE1 H:HIS141 3.1 85.3 1.0 CE1 H:HIS139 3.1 61.6 1.0 CE1 C:HIS139 3.2 58.1 1.0 CE1 C:HIS141 3.3 75.4 1.0 CG C:HIS139 4.0 55.0 1.0 CG H:HIS139 4.1 52.1 1.0 CG C:HIS141 4.1 79.7 1.0 ND1 H:HIS139 4.1 53.4 1.0 ND1 H:HIS141 4.1 94.1 1.0 CG H:HIS141 4.2 79.3 1.0 ND1 C:HIS139 4.2 54.1 1.0 ND1 C:HIS141 4.2 80.6 1.0 CD1 E:LEU83 4.8 74.8 1.0 CD1 B:LEU83 4.9 69.1 1.0

Nickel binding site 4 out of 6 in the Crystal Structure of Fosfomycin Resistance Protein FOSA3


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 Fosfomycin Resistance Protein FOSA3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni203 b:87.8 occ:1.00 OE1 C:GLU128 2.2 78.3 1.0 NE2 C:HIS142 2.4 73.0 1.0 CD C:GLU128 3.0 66.7 1.0 OE2 C:GLU128 3.2 78.9 1.0 CD2 C:HIS142 3.3 80.5 1.0 CE1 C:HIS142 3.3 66.3 1.0 CD2 C:HIS143 3.9 90.9 1.0 NE2 C:HIS143 4.1 99.7 1.0 CG C:GLU128 4.4 61.5 1.0 CB B:GLU75 4.4 60.6 1.0 ND1 C:HIS142 4.4 66.4 1.0 CA C:GLU128 4.5 57.0 1.0 CG C:HIS142 4.5 80.2 1.0 O B:GLU75 4.5 70.5 1.0 O C:GLU128 4.7 57.7 1.0 CB C:GLU128 4.8 62.5 1.0

Nickel binding site 5 out of 6 in the Crystal Structure of Fosfomycin Resistance Protein FOSA3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Fosfomycin Resistance Protein FOSA3 within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni202 b:86.0 occ:1.00 OE1 F:GLU128 2.4 72.4 1.0 NE2 F:HIS142 2.6 78.2 1.0 CD F:GLU128 3.2 65.5 1.0 OE2 F:GLU128 3.4 57.9 1.0 CD2 F:HIS142 3.5 74.7 1.0 CE1 F:HIS142 3.6 65.7 1.0 NE2 F:HIS143 4.0 94.3 1.0 CD2 F:HIS143 4.1 93.3 1.0 CB G:GLU75 4.3 59.0 1.0 O G:GLU75 4.4 69.1 1.0 CG F:GLU128 4.6 54.2 1.0 ND1 F:HIS142 4.7 70.1 1.0 CG F:HIS142 4.7 68.6 1.0 CA F:GLU128 4.9 59.5 1.0 CG G:GLU75 5.0 64.7 1.0

Nickel binding site 6 out of 6 in the Crystal Structure of Fosfomycin Resistance Protein FOSA3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of Fosfomycin Resistance Protein FOSA3 within 5.0Å range: probe atom residue distance (Å) B Occ H:Ni202 b:89.1 occ:1.00 OE1 H:GLU128 2.5 74.8 1.0 NE2 H:HIS142 2.5 70.3 1.0 CD H:GLU128 3.3 66.2 1.0 CD2 H:HIS142 3.3 69.8 1.0 OE2 H:GLU128 3.5 67.2 1.0 CE1 H:HIS142 3.5 65.4 1.0 CD2 H:HIS143 3.9 97.7 1.0 NE2 H:HIS143 4.2 0.1 1.0 O E:GLU75 4.4 58.9 1.0 CB E:GLU75 4.5 60.5 1.0 CG H:HIS142 4.5 73.8 1.0 ND1 H:HIS142 4.6 66.2 1.0 CA H:GLU128 4.6 56.1 1.0 CG H:GLU128 4.6 65.6 1.0 O H:GLU128 4.9 70.6 1.0 CB H:GLU128 5.0 64.0 1.0

E.H.Klontz, A.D.Tomich, S.Gunther, J.A.Lemkul, D.Deredge, Z.Silverstein, J.F.Shaw, C.Mcelheny, Y.Doi, P.L.Wintrode, A.D.Mackerell, N.Sluis-Cremer, E.J.Sundberg. Structure and Dynamics of Fosa-Mediated Fosfomycin Resistance in Klebsiella Pneumoniae and Escherichia Coli. Antimicrob. Agents V. 61 2017CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 28874374
DOI: 10.1128/AAC.01572-17