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Zinc in PDB 5chu: Crystal Structure of Fox-4 Cephamycinase Complexed with Sulfate

Enzymatic activity of Crystal Structure of Fox-4 Cephamycinase Complexed with Sulfate

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

Protein crystallography data

The structure of Crystal Structure of Fox-4 Cephamycinase Complexed with Sulfate, PDB code: 5chu 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) 19.83 / 1.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.419, 53.922, 116.167, 90.00, 89.87, 90.00
R / Rfree (%) 18.8 / 20.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Fox-4 Cephamycinase Complexed with Sulfate (pdb code 5chu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Fox-4 Cephamycinase Complexed with Sulfate, PDB code: 5chu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5chu

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Zinc binding site 1 out of 8 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Sulfate


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 Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:18.7
occ:1.00
 ND1 A:HIS39 2.0 16.4 1.0
O A:HOH796 2.0 23.5 1.0
O A:HOH816 2.3 25.9 1.0
O A:HOH524 2.4 27.9 1.0
CE1 A:HIS39 2.8 19.6 1.0
HE1 A:HIS39 3.0 23.5 1.0
CG A:HIS39 3.1 14.6 1.0
HB3 A:HIS39 3.1 15.6 1.0
HZ2 A:LYS37 3.5 38.3 1.0
CB A:HIS39 3.5 13.0 1.0
HA A:HIS39 3.8 15.3 1.0
O A:HOH636 3.8 19.6 1.0
NE2 A:HIS39 4.0 23.1 1.0
HD23 A:LEU8 4.1 31.7 1.0
CD2 A:HIS39 4.1 19.2 1.0
CA A:HIS39 4.2 12.7 1.0
HB2 A:HIS39 4.4 15.6 1.0
NZ A:LYS37 4.4 31.9 1.0
O A:ALA38 4.5 15.1 1.0
HD3 A:LYS37 4.6 46.8 1.0
O A:HOH764 4.6 25.3 0.5
HZ3 A:LYS37 4.6 38.3 1.0
O A:HOH894 4.7 27.4 1.0
HE2 A:HIS39 4.8 27.7 1.0
HZ1 A:LYS37 4.8 38.3 1.0
HG3 A:LYS37 4.8 41.1 1.0
HZ A:PHE41 4.9 21.0 1.0
O A:HOH725 4.9 15.3 1.0
HB3 A:LEU8 4.9 29.4 1.0
CD2 A:LEU8 5.0 26.4 1.0

Zinc binding site 2 out of 8 in 5chu

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Zinc binding site 2 out of 8 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Sulfate


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 Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:15.2
occ:1.00
 OD2 B:ASP126 1.9 13.9 1.0
ND1 A:HIS185 2.0 14.6 1.0
O B:HOH563 2.1 18.4 1.0
O A:HOH800 2.2 18.7 1.0
O A:HOH637 2.3 16.7 1.0
CG B:ASP126 2.7 13.8 1.0
OD1 B:ASP126 2.9 14.8 1.0
CE1 A:HIS185 3.0 13.8 1.0
HA A:HIS185 3.0 16.1 1.0
HE1 A:HIS185 3.1 16.6 1.0
CG A:HIS185 3.1 14.3 1.0
HB3 A:HIS185 3.2 17.2 1.0
CB A:HIS185 3.5 14.3 1.0
CA A:HIS185 3.7 13.5 1.0
HG3 A:PRO180 3.9 17.1 1.0
HE3 B:LYS130 3.9 24.3 0.4
O B:HOH543 4.0 31.0 1.0
HE2 B:LYS130 4.1 24.3 0.6
NE2 A:HIS185 4.1 15.4 1.0
O A:HOH575 4.1 16.7 1.0
CB B:ASP126 4.2 14.1 1.0
O B:GLU124 4.2 16.4 1.0
CD2 A:HIS185 4.2 15.3 1.0
HA A:PRO180 4.2 18.2 1.0
HA B:GLU124 4.2 19.8 1.0
HG3 B:LYS130 4.3 21.6 0.4
HG3 B:LYS130 4.3 22.0 0.6
O A:LEU184 4.3 13.0 1.0
O A:HOH555 4.4 17.3 1.0
HB3 B:ASP126 4.4 16.9 1.0
HB2 A:HIS185 4.4 17.2 1.0
HB3 A:PRO180 4.5 19.9 1.0
O B:HOH746 4.5 27.9 1.0
HB2 B:ASP126 4.5 16.9 1.0
O A:HIS185 4.6 16.4 1.0
N A:HIS185 4.7 12.9 1.0
C A:HIS185 4.7 13.9 1.0
CG A:PRO180 4.8 14.3 1.0
C A:LEU184 4.9 12.2 1.0
HE2 A:HIS185 4.9 18.4 1.0
CE B:LYS130 4.9 20.2 0.4
H B:ASP126 4.9 16.4 1.0
C B:GLU124 4.9 14.8 1.0
CB A:PRO180 5.0 16.6 1.0
CA A:PRO180 5.0 15.2 1.0

Zinc binding site 3 out of 8 in 5chu

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Zinc binding site 3 out of 8 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Sulfate


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 Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:14.1
occ:1.00
 O A:HOH798 1.9 17.2 1.0
NE2 A:HIS147 2.0 10.8 1.0
CE1 A:HIS147 3.0 13.7 1.0
CD2 A:HIS147 3.0 10.8 1.0
HE1 A:HIS147 3.2 16.5 1.0
HD2 A:HIS147 3.2 13.0 1.0
HB3 A:PRO296 3.4 16.8 1.0
HD3 A:PRO296 4.0 16.7 1.0
ND1 A:HIS147 4.1 11.9 1.0
CG A:HIS147 4.1 11.4 1.0
HE1 A:TYR142 4.2 16.1 1.0
CB A:PRO296 4.3 14.0 1.0
O A:HOH864 4.3 41.6 1.0
O A:HOH899 4.3 21.6 1.0
HG3 A:PRO296 4.4 18.6 1.0
HD1 A:TYR142 4.4 15.3 1.0
CE1 A:TYR142 4.6 13.4 1.0
HA A:PRO296 4.6 14.9 1.0
CD A:PRO296 4.6 13.9 1.0
CG A:PRO296 4.7 15.5 1.0
CD1 A:TYR142 4.7 12.8 1.0
N A:PRO296 4.8 12.6 1.0
CA A:PRO296 4.8 12.4 1.0
HD1 A:HIS147 4.9 14.3 1.0
HB2 A:PRO296 5.0 16.8 1.0

Zinc binding site 4 out of 8 in 5chu

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Zinc binding site 4 out of 8 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Sulfate


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 Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:18.0
occ:1.00
 NE2 A:HIS186 2.0 18.4 1.0
CE1 A:HIS186 2.9 18.0 1.0
CD2 A:HIS186 3.0 14.6 1.0
HE1 A:HIS186 3.1 21.6 1.0
HD2 A:HIS186 3.3 17.5 1.0
O A:HOH679 3.6 25.2 1.0
ND1 A:HIS186 4.0 17.1 1.0
CG A:HIS186 4.1 13.8 1.0
O A:HOH595 4.2 24.5 1.0
O B:HOH508 4.4 39.9 1.0
HD1 A:HIS186 4.8 20.5 1.0
OE1 A:GLN57 5.0 33.2 1.0

Zinc binding site 5 out of 8 in 5chu

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Zinc binding site 5 out of 8 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Sulfate


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 Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:19.1
occ:1.00
 ND1 B:HIS39 2.0 17.5 1.0
O B:HOH808 2.1 25.6 1.0
O B:HOH818 2.3 22.2 1.0
CE1 B:HIS39 2.9 18.6 1.0
HE1 B:HIS39 3.0 22.3 1.0
HB3 B:HIS39 3.1 16.6 1.0
CG B:HIS39 3.1 14.8 1.0
HZ2 B:LYS37 3.5 36.4 1.0
CB B:HIS39 3.5 13.8 1.0
HA B:HIS39 3.8 15.6 1.0
O B:HOH646 3.9 19.7 1.0
HD23 B:LEU8 4.0 32.8 1.0
NE2 B:HIS39 4.1 21.9 1.0
CD2 B:HIS39 4.2 18.0 1.0
CA B:HIS39 4.2 13.0 1.0
NZ B:LYS37 4.4 30.4 1.0
HB2 B:HIS39 4.4 16.6 1.0
HD3 B:LYS37 4.5 43.7 1.0
O B:ALA38 4.5 15.0 1.0
HZ3 B:LYS37 4.6 36.4 1.0
O B:HOH896 4.6 27.6 1.0
HZ1 B:LYS37 4.8 36.4 1.0
HE2 B:HIS39 4.8 26.3 1.0
HG3 B:LYS37 4.8 32.9 1.0
HZ B:PHE41 4.9 21.6 1.0
O B:HOH734 4.9 15.3 1.0
CD2 B:LEU8 4.9 27.3 1.0
HB3 B:LEU8 4.9 31.3 1.0
O B:HOH816 5.0 18.2 1.0

Zinc binding site 6 out of 8 in 5chu

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Zinc binding site 6 out of 8 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Sulfate


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 Complexed with Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:15.9
occ:1.00
 ND1 B:HIS185 2.0 15.2 1.0
O B:HOH775 2.1 18.2 1.0
O B:HOH802 2.2 19.9 1.0
O B:HOH656 2.3 17.6 1.0
CE1 B:HIS185 3.0 14.2 1.0
HA B:HIS185 3.0 15.6 1.0
HE1 B:HIS185 3.1 17.1 1.0
CG B:HIS185 3.1 15.0 1.0
HB3 B:HIS185 3.2 16.4 1.0
CB B:HIS185 3.5 13.7 1.0
CA B:HIS185 3.7 13.0 1.0
HG3 B:PRO180 3.8 17.1 1.0
O B:HOH577 4.1 17.0 1.0
NE2 B:HIS185 4.1 16.4 1.0
CD2 B:HIS185 4.2 16.5 1.0
HA B:PRO180 4.2 18.0 1.0
O B:LEU184 4.4 13.6 1.0
O B:HOH610 4.4 17.7 1.0
HB3 B:PRO180 4.4 20.0 1.0
HB2 B:HIS185 4.5 16.4 1.0
O B:HIS185 4.7 15.5 1.0
N B:HIS185 4.7 13.5 1.0
C B:HIS185 4.7 13.3 1.0
CG B:PRO180 4.7 14.2 1.0
C B:LEU184 4.9 12.5 1.0
HE2 B:HIS185 4.9 19.7 1.0
CB B:PRO180 4.9 16.7 1.0
CA B:PRO180 5.0 15.0 1.0

Zinc binding site 7 out of 8 in 5chu

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Zinc binding site 7 out of 8 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Sulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Fox-4 Cephamycinase Complexed with Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:14.2
occ:1.00
 O B:HOH782 2.0 17.8 1.0
OXT B:ACT408 2.0 14.9 1.0
NE2 B:HIS147 2.0 11.8 1.0
C B:ACT408 2.7 13.8 1.0
O B:ACT408 2.7 15.7 1.0
CE1 B:HIS147 3.0 12.0 1.0
CD2 B:HIS147 3.0 11.2 1.0
HE1 B:HIS147 3.2 14.3 1.0
HD2 B:HIS147 3.2 13.4 1.0
HB3 B:PRO296 3.4 17.2 1.0
O B:HOH827 4.0 36.9 1.0
HD3 B:PRO296 4.0 16.3 1.0
ND1 B:HIS147 4.1 11.8 1.0
CG B:HIS147 4.1 10.9 1.0
CH3 B:ACT408 4.2 16.1 1.0
HE1 B:TYR142 4.2 16.7 1.0
HG3 B:PRO296 4.3 18.6 1.0
CB B:PRO296 4.3 14.3 1.0
O B:HOH899 4.4 19.8 1.0
H1 B:ACT408 4.5 19.3 1.0
HD1 B:TYR142 4.5 16.9 1.0
CE1 B:TYR142 4.6 13.9 1.0
HA B:PRO296 4.6 15.7 1.0
CG B:PRO296 4.6 15.5 1.0
CD B:PRO296 4.6 13.6 1.0
H2 B:ACT408 4.7 19.3 1.0
CD1 B:TYR142 4.7 14.1 1.0
N B:PRO296 4.8 12.0 1.0
H3 B:ACT408 4.8 19.3 1.0
CA B:PRO296 4.8 13.0 1.0
HD1 B:HIS147 4.9 14.2 1.0
HB2 B:PRO296 5.0 17.2 1.0

Zinc binding site 8 out of 8 in 5chu

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Zinc binding site 8 out of 8 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Sulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Fox-4 Cephamycinase Complexed with Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:19.7
occ:1.00
 OXT B:GLU361 2.0 30.2 1.0
OE2 B:GLU5 2.0 25.4 1.0
N B:SER3 2.1 28.7 1.0
O B:SER3 2.3 24.1 1.0
OE1 B:GLU5 2.6 25.5 1.0
CD B:GLU5 2.6 30.3 1.0
C B:SER3 2.9 22.7 1.0
CA B:SER3 3.0 26.7 1.0
C B:GLU361 3.1 26.4 1.0
HB3 B:GLU361 3.5 34.9 1.0
HA B:SER3 3.5 32.1 1.0
O B:GLU361 3.6 32.1 1.0
HG B:SER3 3.7 42.8 1.0
OG B:SER3 4.1 35.7 1.0
CG B:GLU5 4.1 34.2 1.0
CB B:SER3 4.1 31.6 1.0
O B:HOH653 4.1 39.4 1.0
N B:GLY4 4.2 23.0 1.0
CA B:GLU361 4.2 25.7 1.0
CB B:GLU361 4.2 29.1 1.0
H B:GLU5 4.3 29.4 1.0
HG3 B:GLU5 4.4 41.0 1.0
HA B:GLU361 4.4 30.8 1.0
HG2 B:GLU5 4.5 41.0 1.0
HB2 B:GLU361 4.6 34.9 1.0
HB3 B:SER3 4.6 37.9 1.0
N B:GLU5 4.7 24.5 1.0
H B:GLY4 4.8 27.6 1.0
HB2 B:SER3 4.8 37.9 1.0
HA3 B:GLY4 4.8 31.0 1.0
CA B:GLY4 4.9 25.8 1.0
HB2 B:GLU5 4.9 34.9 1.0

Reference:

V.N.Malashkevich, R.Toro, S.Lefurgy, S.C.Almo. Crystal Structure of Fox-4 Cephamycinase Complexed with Sulfate To Be Published.
Page generated: Sun Oct 27 14:21:27 2024

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