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Zinc in PDB 5chm: Crystal Structure of Fox-4 Cephamycinase Complexed with Ceftazidime Batsi (LP06)

Enzymatic activity of Crystal Structure of Fox-4 Cephamycinase Complexed with Ceftazidime Batsi (LP06)

All present enzymatic activity of Crystal Structure of Fox-4 Cephamycinase Complexed with Ceftazidime Batsi (LP06):
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Fox-4 Cephamycinase Complexed with Ceftazidime Batsi (LP06), PDB code: 5chm 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) 25.96 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.803, 57.144, 56.123, 90.00, 95.98, 90.00
R / Rfree (%) 17 / 22.9

Other elements in 5chm:

The structure of Crystal Structure of Fox-4 Cephamycinase Complexed with Ceftazidime Batsi (LP06) 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 Complexed with Ceftazidime Batsi (LP06) (pdb code 5chm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Fox-4 Cephamycinase Complexed with Ceftazidime Batsi (LP06), PDB code: 5chm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 5chm

Go back to Zinc Binding Sites List in 5chm
Zinc binding site 1 out of 5 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Ceftazidime Batsi (LP06)


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 Complexed with Ceftazidime Batsi (LP06) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:54.0
occ:1.00
 NE2 A:HIS160 2.1 41.0 1.0
O A:HOH569 2.4 49.8 1.0
O A:HOH671 2.7 38.5 1.0
CD2 A:HIS160 3.0 30.6 1.0
CE1 A:HIS160 3.1 42.3 1.0
O A:HOH677 3.3 43.6 1.0
CG A:HIS160 4.2 31.5 1.0
ND1 A:HIS160 4.2 38.5 1.0
NE2 A:GLN132 4.2 50.3 1.0
NE1 A:TRP95 4.3 33.7 1.0
OD1 A:ASN128 4.7 39.2 1.0
CZ2 A:TRP95 4.7 32.2 1.0
CE2 A:TRP95 4.8 33.5 1.0

Zinc binding site 2 out of 5 in 5chm

Go back to Zinc Binding Sites List in 5chm
Zinc binding site 2 out of 5 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Ceftazidime Batsi (LP06)


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 Complexed with Ceftazidime Batsi (LP06) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:35.5
occ:1.00
 ND1 A:HIS39 2.1 36.5 1.0
CE1 A:HIS39 3.0 32.0 1.0
CG A:HIS39 3.1 37.5 1.0
CB A:HIS39 3.5 36.4 1.0
O A:HOH610 3.8 39.9 1.0
CA A:HIS39 4.0 31.8 1.0
O A:ALA38 4.1 33.3 1.0
NE2 A:HIS39 4.1 36.2 1.0
CD2 A:HIS39 4.2 38.6 1.0
N A:HIS39 4.8 27.1 1.0
C A:ALA38 4.8 30.5 1.0
CD2 A:LEU8 4.9 56.6 1.0

Zinc binding site 3 out of 5 in 5chm

Go back to Zinc Binding Sites List in 5chm
Zinc binding site 3 out of 5 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Ceftazidime Batsi (LP06)


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 Complexed with Ceftazidime Batsi (LP06) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:28.4
occ:1.00
 OE1 A:GLU124 2.0 35.4 1.0
OD2 A:ASP126 2.1 31.2 1.0
OXT A:ACT407 2.2 27.7 1.0
CG A:ASP126 2.8 30.1 1.0
O A:ACT407 2.8 33.1 1.0
OD1 A:ASP126 2.8 30.9 1.0
C A:ACT407 2.9 30.8 1.0
CD A:GLU124 2.9 46.3 1.0
OE2 A:GLU124 3.1 45.5 1.0
NZ A:LYS130 3.8 34.6 1.0
O A:HOH513 3.9 29.4 1.0
CB A:ASP126 4.2 31.5 1.0
CG A:GLU124 4.3 44.9 1.0
CH3 A:ACT407 4.3 27.1 1.0
CA A:GLU124 4.6 31.5 1.0
CB A:GLU124 4.6 33.9 1.0
O A:GLU124 4.8 33.8 1.0
CE A:LYS130 4.9 39.2 1.0

Zinc binding site 4 out of 5 in 5chm

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Zinc binding site 4 out of 5 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Ceftazidime Batsi (LP06)


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 Complexed with Ceftazidime Batsi (LP06) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:55.1
occ:1.00
 ND1 A:HIS185 2.4 48.8 1.0
CG A:HIS185 3.3 47.5 1.0
CE1 A:HIS185 3.4 48.7 1.0
CB A:HIS185 3.5 37.5 1.0
CA A:HIS185 4.1 32.8 1.0
CD2 A:HIS185 4.5 47.8 1.0
NE2 A:HIS185 4.5 49.9 1.0
O A:HIS185 4.7 32.9 1.0
C A:HIS185 4.9 30.1 1.0
CG A:PRO180 5.0 33.6 1.0
O A:HOH579 5.0 37.1 1.0

Zinc binding site 5 out of 5 in 5chm

Go back to Zinc Binding Sites List in 5chm
Zinc binding site 5 out of 5 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Ceftazidime Batsi (LP06)


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 Complexed with Ceftazidime Batsi (LP06) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:52.8
occ:1.00
 ND1 A:HIS255 2.2 28.5 1.0
O A:HOH681 2.7 36.1 1.0
O A:HOH524 2.7 37.2 1.0
CE1 A:HIS255 3.2 22.7 1.0
CG A:HIS255 3.2 25.1 1.0
CB A:HIS255 3.5 16.9 1.0
O A:HOH645 3.5 26.0 1.0
OE2 A:GLU308 3.7 59.8 1.0
OE1 A:GLU308 4.2 61.8 1.0
O A:HOH729 4.3 33.6 1.0
NE2 A:HIS255 4.3 19.9 1.0
CD2 A:HIS255 4.3 21.7 1.0
CD A:GLU308 4.4 56.1 1.0
CA A:ALA252 4.7 27.8 1.0
O A:ASN238 4.7 28.6 1.0
OH A:TYR312 4.7 23.4 1.0
O A:GLY307 4.8 26.5 1.0
O A:HOH531 5.0 30.7 1.0
CA A:HIS255 5.0 14.9 1.0

Reference:

V.N.Malashkevich, R.Toro, S.Lefurgy, S.C.Almo. Crystal Structure of Fox-4 Cephamycinase Complexed with Ceftazidime Batsi (LP06) To Be Published.
Page generated: Sun Oct 27 14:20:37 2024

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