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Zinc in PDB 5cgx: Crystal Structure of Fox-4 Cephamycinase Mutant Y150F Complexed with Cefoxitin

Enzymatic activity of Crystal Structure of Fox-4 Cephamycinase Mutant Y150F Complexed with Cefoxitin

All present enzymatic activity of Crystal Structure of Fox-4 Cephamycinase Mutant Y150F Complexed with Cefoxitin:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Fox-4 Cephamycinase Mutant Y150F Complexed with Cefoxitin, PDB code: 5cgx was solved by V.N.Malashkevich, R.Toro, S.Lefurgy, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.64 / 1.21
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.524, 56.588, 55.485, 90.00, 99.23, 90.00
R / Rfree (%) 18.1 / 20.5

Other elements in 5cgx:

The structure of Crystal Structure of Fox-4 Cephamycinase Mutant Y150F Complexed with Cefoxitin also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Fox-4 Cephamycinase Mutant Y150F Complexed with Cefoxitin (pdb code 5cgx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Fox-4 Cephamycinase Mutant Y150F Complexed with Cefoxitin, PDB code: 5cgx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5cgx

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Zinc binding site 1 out of 6 in the Crystal Structure of Fox-4 Cephamycinase Mutant Y150F Complexed with Cefoxitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Fox-4 Cephamycinase Mutant Y150F Complexed with Cefoxitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:11.4
occ:1.00
 ND1 A:HIS39 2.0 14.9 1.0
OE1 A:GLU5 2.0 12.0 1.0
O A:HOH764 2.2 10.8 1.0
OE2 A:GLU5 2.4 20.5 1.0
CD A:GLU5 2.5 12.6 1.0
HB3 A:HIS39 2.8 51.4 1.0
CE1 A:HIS39 2.9 13.1 1.0
CG A:HIS39 3.0 20.1 1.0
HE1 A:HIS39 3.1 15.8 1.0
CB A:HIS39 3.4 42.9 1.0
HD23 A:LEU8 3.7 17.6 1.0
HA A:HIS39 4.0 12.1 1.0
CG A:GLU5 4.0 18.7 1.0
NE2 A:HIS39 4.1 11.4 1.0
HB2 A:HIS39 4.1 51.4 1.0
CD2 A:HIS39 4.1 13.2 1.0
CA A:HIS39 4.3 10.1 1.0
HG3 A:GLU5 4.3 22.4 1.0
HA A:GLU5 4.4 24.8 1.0
O A:HOH702 4.4 11.2 1.0
HG2 A:GLU5 4.5 22.4 1.0
CD2 A:LEU8 4.6 14.7 1.0
HD21 A:LEU8 4.7 17.6 1.0
HZ A:PHE41 4.7 20.1 1.0
HB3 A:GLU5 4.8 22.9 1.0
O A:HOH629 4.8 13.9 1.0
HE2 A:HIS39 4.8 13.7 1.0
CB A:GLU5 4.9 19.1 1.0
O A:HOH617 4.9 32.5 1.0
HD2 A:HIS39 5.0 15.9 1.0
H A:TYR40 5.0 11.5 1.0

Zinc binding site 2 out of 6 in 5cgx

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Zinc binding site 2 out of 6 in the Crystal Structure of Fox-4 Cephamycinase Mutant Y150F Complexed with Cefoxitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Fox-4 Cephamycinase Mutant Y150F Complexed with Cefoxitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:20.0
occ:1.00
 OE2 A:GLU361 1.9 27.1 1.0
ND1 A:HIS1 2.0 16.3 1.0
O A:HOH750 2.1 20.0 1.0
CD A:GLU361 2.6 18.4 1.0
OE1 A:GLU361 2.7 32.4 1.0
CE1 A:HIS1 2.9 22.2 1.0
HE1 A:HIS1 3.0 26.6 1.0
HB3 A:HIS1 3.1 34.1 1.0
CG A:HIS1 3.1 19.7 1.0
HA A:HIS1 3.4 41.1 1.0
CB A:HIS1 3.5 28.4 1.0
CA A:HIS1 4.0 34.3 1.0
NE2 A:HIS1 4.1 24.4 1.0
CG A:GLU361 4.1 19.4 1.0
CD2 A:HIS1 4.1 22.8 1.0
O A:HOH561 4.2 27.9 1.0
HB2 A:HIS1 4.4 34.1 1.0
HG2 A:GLU361 4.4 23.2 1.0
HG3 A:GLU361 4.5 23.2 1.0
HE2 A:HIS1 4.8 29.3 1.0
HA A:GLU361 4.8 24.9 1.0
C A:HIS1 4.9 44.7 1.0
O A:HIS1 5.0 42.7 1.0
N A:HIS1 5.0 34.0 1.0
O A:GLY0 5.0 41.9 1.0

Zinc binding site 3 out of 6 in 5cgx

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Zinc binding site 3 out of 6 in the Crystal Structure of Fox-4 Cephamycinase Mutant Y150F Complexed with Cefoxitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Fox-4 Cephamycinase Mutant Y150F Complexed with Cefoxitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:18.3
occ:1.00
 OD2 A:ASP126 1.9 22.0 1.0
OE1 A:GLU124 2.0 42.0 1.0
O A:HOH786 2.2 18.6 1.0
CG A:ASP126 2.8 20.9 1.0
CD A:GLU124 2.8 36.5 1.0
OD1 A:ASP126 2.9 31.3 1.0
OE2 A:GLU124 3.0 42.2 1.0
HZ2 A:LYS130 3.4 34.9 1.0
HZ3 A:LYS130 3.5 34.9 1.0
NZ A:LYS130 3.7 29.1 1.0
HZ1 A:LYS130 3.8 34.9 1.0
O A:HOH546 4.0 24.1 1.0
CG A:GLU124 4.2 45.5 1.0
HA A:GLU124 4.2 30.3 1.0
CB A:ASP126 4.2 16.2 1.0
HG3 A:GLU124 4.2 54.6 1.0
HB2 A:ASP126 4.4 19.4 1.0
HB3 A:ASP126 4.5 19.4 1.0
HG2 A:GLU124 4.7 54.6 1.0

Zinc binding site 4 out of 6 in 5cgx

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Zinc binding site 4 out of 6 in the Crystal Structure of Fox-4 Cephamycinase Mutant Y150F Complexed with Cefoxitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Fox-4 Cephamycinase Mutant Y150F Complexed with Cefoxitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:22.5
occ:1.00
 O A:HOH563 2.1 18.9 1.0
O A:HOH781 2.1 21.7 1.0
NE2 A:HIS160 2.2 25.6 1.0
O A:HOH778 2.2 15.1 1.0
CD2 A:HIS160 3.0 23.4 1.0
HD2 A:HIS160 3.1 28.0 1.0
CE1 A:HIS160 3.2 22.8 1.0
HE1 A:HIS160 3.5 27.4 1.0
HE21 A:GLN132 3.7 44.4 1.0
HE1 A:TRP95 3.8 24.5 1.0
HZ2 A:TRP95 4.0 20.2 1.0
CG A:HIS160 4.2 14.1 1.0
ND1 A:HIS160 4.3 19.2 1.0
NE2 A:GLN132 4.4 37.0 1.0
HE1 A:MET131 4.4 21.5 1.0
NE1 A:TRP95 4.4 20.4 1.0
HD23 A:LEU161 4.4 14.0 1.0
HE22 A:GLN132 4.4 44.4 1.0
O A:HOH659 4.6 42.1 1.0
CZ2 A:TRP95 4.6 16.9 1.0
OD1 A:ASN128 4.8 55.6 0.5
HD21 A:LEU161 4.8 14.0 1.0
HB2 A:ASN164 4.8 20.5 1.0
CE2 A:TRP95 4.8 15.3 1.0

Zinc binding site 5 out of 6 in 5cgx

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Zinc binding site 5 out of 6 in the Crystal Structure of Fox-4 Cephamycinase Mutant Y150F Complexed with Cefoxitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Fox-4 Cephamycinase Mutant Y150F Complexed with Cefoxitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:18.5
occ:1.00
 ND1 A:HIS185 2.0 26.7 1.0
O A:HOH773 2.1 20.6 1.0
O A:HOH775 2.2 16.3 1.0
CE1 A:HIS185 2.9 30.4 1.0
HA A:HIS185 2.9 14.4 1.0
CG A:HIS185 3.0 18.4 1.0
HE1 A:HIS185 3.0 36.5 1.0
HB3 A:HIS185 3.2 16.3 1.0
CB A:HIS185 3.4 13.6 1.0
CA A:HIS185 3.6 12.0 1.0
O A:HOH774 3.9 23.4 1.0
NE2 A:HIS185 4.0 27.9 1.0
HA A:PRO180 4.1 23.0 1.0
CD2 A:HIS185 4.1 18.6 1.0
HG3 A:PRO180 4.3 22.0 1.0
HB2 A:HIS185 4.4 16.3 1.0
HB3 A:PRO180 4.4 28.9 1.0
O A:HIS185 4.5 13.8 1.0
N A:HIS185 4.6 10.3 1.0
C A:HIS185 4.6 13.3 1.0
HE2 A:HIS185 4.8 33.5 1.0
O A:LEU184 4.8 15.6 1.0
O A:HOH523 4.9 18.8 1.0
CA A:PRO180 4.9 19.2 1.0
O A:HOH530 4.9 33.3 1.0
CB A:PRO180 5.0 24.1 1.0
HD2 A:HIS185 5.0 22.3 1.0
C A:LEU184 5.0 13.1 1.0

Zinc binding site 6 out of 6 in 5cgx

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Zinc binding site 6 out of 6 in the Crystal Structure of Fox-4 Cephamycinase Mutant Y150F Complexed with Cefoxitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Fox-4 Cephamycinase Mutant Y150F Complexed with Cefoxitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:19.3
occ:1.00
 HD1 A:HIS255 1.3 13.9 1.0
ND1 A:HIS255 2.1 11.6 1.0
O A:HOH501 2.3 15.5 1.0
O A:HOH787 2.4 27.0 1.0
O A:HOH761 2.4 15.8 1.0
HB2 A:HIS255 2.9 12.6 1.0
CG A:HIS255 2.9 11.3 1.0
HB3 A:HIS255 3.0 12.6 1.0
CB A:HIS255 3.1 10.5 1.0
CE1 A:HIS255 3.1 13.7 1.0
OE2 A:GLU308 3.2 58.6 1.0
HE1 A:HIS255 3.4 16.5 1.0
HA A:ALA252 3.9 25.9 1.0
HH A:TYR312 3.9 10.3 1.0
OE1 A:GLU308 3.9 59.4 1.0
CD A:GLU308 4.0 60.6 1.0
CD2 A:HIS255 4.1 9.0 1.0
H A:GLY307 4.1 10.7 1.0
NE2 A:HIS255 4.2 9.1 1.0
OH A:TYR312 4.2 8.6 1.0
HA2 A:GLY307 4.2 11.1 1.0
O A:GLY307 4.3 10.7 1.0
C A:GLY307 4.6 8.9 1.0
HG2 A:PRO329 4.7 9.3 1.0
CA A:HIS255 4.7 11.4 1.0
O A:HOH532 4.7 21.0 1.0
CA A:GLY307 4.7 9.2 1.0
N A:GLY307 4.7 8.9 1.0
CZ A:TYR312 4.8 7.7 1.0
CA A:ALA252 4.8 21.6 1.0
HE2 A:TYR312 4.8 9.9 1.0
O A:ALA252 4.9 15.6 1.0
HA A:GLU308 4.9 12.6 1.0
O A:HOH835 4.9 38.6 1.0
HD2 A:HIS255 4.9 10.8 1.0
O A:HOH542 4.9 45.6 1.0
HB1 A:ALA252 5.0 30.4 1.0

Reference:

S.T.Lefurgy, V.N.Malashkevich, J.T.Aguilan, E.Nieves, E.C.Mundorff, B.Biju, M.A.Noel, R.Toro, D.Baiwir, K.M.Papp-Wallace, S.C.Almo, J.M.Frere, G.Bou, R.A.Bonomo. Fox-4 Cephamycinase: An Analysis of Structure and Function. Antimicrob.Agents Chemother. 2015.
ISSN: ESSN 1098-6596
PubMed: 26525784
DOI: 10.1128/AAC.01887-15
Page generated: Sun Oct 27 14:17:41 2024

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