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Zinc in PDB 5chj: Crystal Structure of Fox-4 Cephamycinase Complexed with Cephalothin Batsi (SM23)

Enzymatic activity of Crystal Structure of Fox-4 Cephamycinase Complexed with Cephalothin Batsi (SM23)

All present enzymatic activity of Crystal Structure of Fox-4 Cephamycinase Complexed with Cephalothin Batsi (SM23):
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Fox-4 Cephamycinase Complexed with Cephalothin Batsi (SM23), PDB code: 5chj 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) 25.74 / 1.36
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.294, 57.161, 83.229, 90.00, 91.67, 90.00
R / Rfree (%) 16.3 / 19.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Fox-4 Cephamycinase Complexed with Cephalothin Batsi (SM23) (pdb code 5chj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Fox-4 Cephamycinase Complexed with Cephalothin Batsi (SM23), PDB code: 5chj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 5chj

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Zinc binding site 1 out of 10 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Cephalothin Batsi (SM23)


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 Cephalothin Batsi (SM23) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:27.1
occ:1.00
 O A:HOH829 2.1 32.2 1.0
O A:HOH635 2.1 18.9 1.0
NE2 A:HIS160 2.1 19.1 1.0
O A:HOH818 2.1 22.0 1.0
CD2 A:HIS160 3.0 19.7 1.0
HD2 A:HIS160 3.1 23.6 1.0
CE1 A:HIS160 3.2 21.2 1.0
HE1 A:HIS160 3.4 25.4 1.0
HE21 A:GLN132 3.6 28.9 1.0
HE1 A:TRP95 3.8 19.8 1.0
HZ2 A:TRP95 3.9 13.1 1.0
O A:HOH549 4.1 33.2 1.0
O A:HOH794 4.2 37.7 1.0
CG A:HIS160 4.2 15.7 1.0
HE3 A:MET131 4.2 28.8 1.0
NE2 A:GLN132 4.3 24.0 1.0
ND1 A:HIS160 4.3 20.3 1.0
NE1 A:TRP95 4.3 16.5 1.0
HE22 A:GLN132 4.4 28.9 1.0
HD23 A:LEU161 4.5 9.8 1.0
CZ2 A:TRP95 4.5 10.9 1.0
OD1 A:ASN128 4.6 36.9 1.0
CE2 A:TRP95 4.7 12.1 1.0
HD21 A:LEU161 4.9 9.8 1.0
HB2 A:ASN164 5.0 13.3 1.0

Zinc binding site 2 out of 10 in 5chj

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Zinc binding site 2 out of 10 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Cephalothin Batsi (SM23)


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 Cephalothin Batsi (SM23) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:13.2
occ:1.00
 ND1 A:HIS39 2.0 12.1 1.0
O A:HOH540 2.1 14.2 1.0
O A:HOH836 2.1 18.7 1.0
O A:HOH807 2.1 25.1 1.0
CE1 A:HIS39 2.9 12.3 1.0
HE1 A:HIS39 3.0 14.7 1.0
CG A:HIS39 3.1 11.4 1.0
HB3 A:HIS39 3.2 14.1 1.0
HA A:HIS39 3.4 13.2 1.0
CB A:HIS39 3.5 11.8 1.0
CA A:HIS39 4.0 11.0 1.0
O A:ALA38 4.0 11.8 1.0
NE2 A:HIS39 4.1 12.8 1.0
O A:HOH698 4.2 16.4 1.0
CD2 A:HIS39 4.2 11.7 1.0
O A:HOH756 4.3 20.4 1.0
HB2 A:HIS39 4.4 14.1 1.0
O A:HOH847 4.5 29.3 1.0
HD23 A:LEU8 4.5 37.2 1.0
N A:HIS39 4.8 10.7 1.0
C A:ALA38 4.8 11.1 1.0
O A:HOH949 4.8 41.3 1.0
HE2 A:HIS39 4.8 15.4 1.0
H A:TYR40 4.9 13.2 1.0

Zinc binding site 3 out of 10 in 5chj

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Zinc binding site 3 out of 10 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Cephalothin Batsi (SM23)


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 Cephalothin Batsi (SM23) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:15.7
occ:1.00
 OD2 A:ASP126 2.0 15.5 1.0
NE2 B:HIS147 2.0 5.7 1.0
OE1 A:GLU124 2.0 17.9 1.0
O B:HOH776 2.1 28.7 1.0
CD A:GLU124 2.6 10.5 1.0
OE2 A:GLU124 2.6 27.0 1.0
CG A:ASP126 2.7 17.9 1.0
OD1 A:ASP126 2.9 23.6 1.0
CE1 B:HIS147 2.9 8.3 1.0
HE1 B:HIS147 3.0 9.9 1.0
HZ3 A:LYS130 3.0 30.6 1.0
CD2 B:HIS147 3.1 7.5 1.0
HB3 B:PRO296 3.3 9.7 1.0
HD2 B:HIS147 3.3 9.0 1.0
HD3 B:PRO296 3.6 14.6 1.0
HZ1 A:LYS130 3.6 30.6 1.0
HA A:GLU124 3.7 18.9 1.0
NZ A:LYS130 3.7 25.5 1.0
HE1 B:TYR142 4.0 13.3 1.0
HG3 B:PRO296 4.0 11.6 1.0
ND1 B:HIS147 4.1 9.2 1.0
CG A:GLU124 4.1 22.4 1.0
HZ2 A:LYS130 4.1 30.6 1.0
O A:HOH567 4.1 19.9 1.0
CB B:PRO296 4.1 8.1 1.0
CB A:ASP126 4.1 17.3 1.0
CG B:HIS147 4.2 8.1 1.0
CD B:PRO296 4.3 12.2 1.0
CG B:PRO296 4.3 9.7 1.0
HB2 A:ASP126 4.4 20.8 1.0
CE1 B:TYR142 4.4 11.1 1.0
HB3 A:ASP126 4.4 20.8 1.0
HG3 A:GLU124 4.5 26.9 1.0
HD1 B:TYR142 4.5 10.7 1.0
CA A:GLU124 4.5 15.8 1.0
HA B:PRO296 4.5 8.2 1.0
N B:PRO296 4.5 8.9 1.0
HG2 A:GLU124 4.6 26.9 1.0
HB3 A:GLU124 4.6 19.8 1.0
CB A:GLU124 4.7 16.5 1.0
CA B:PRO296 4.7 6.8 1.0
CD1 B:TYR142 4.7 8.9 1.0
HD1 B:HIS147 4.8 11.1 1.0
O A:GLU124 4.8 16.3 1.0
HB2 B:PRO296 4.9 9.7 1.0
HE3 A:LYS130 4.9 26.9 1.0
CE A:LYS130 4.9 22.4 1.0

Zinc binding site 4 out of 10 in 5chj

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Zinc binding site 4 out of 10 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Cephalothin Batsi (SM23)


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 Cephalothin Batsi (SM23) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:40.3
occ:1.00
 ND1 A:HIS185 2.0 26.4 1.0
O A:HOH837 2.1 41.0 1.0
O A:HOH771 2.7 47.5 1.0
CE1 A:HIS185 2.9 26.6 1.0
HE1 A:HIS185 3.0 31.9 1.0
CG A:HIS185 3.1 22.5 1.0
HB3 A:HIS185 3.2 21.3 1.0
HA A:HIS185 3.6 14.8 1.0
CB A:HIS185 3.6 17.7 1.0
HB3 A:PRO180 3.9 16.1 1.0
HG3 A:PRO180 4.0 18.5 1.0
NE2 A:HIS185 4.0 26.4 1.0
CA A:HIS185 4.1 12.3 1.0
CD2 A:HIS185 4.2 24.8 1.0
O A:HOH817 4.2 31.0 1.0
HA A:PRO180 4.3 14.2 1.0
HB2 A:HIS185 4.5 21.3 1.0
O A:HOH611 4.6 24.4 1.0
CB A:PRO180 4.7 13.4 1.0
CG A:PRO180 4.8 15.4 1.0
HE2 A:HIS185 4.8 31.7 1.0
O A:HIS185 5.0 18.0 1.0
CA A:PRO180 5.0 11.8 1.0

Zinc binding site 5 out of 10 in 5chj

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Zinc binding site 5 out of 10 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Cephalothin Batsi (SM23)


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 Cephalothin Batsi (SM23) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:29.8
occ:1.00
 OE2 A:GLU220 2.1 11.8 1.0
ND1 A:HIS160 2.2 20.3 1.0
O A:HOH839 2.3 40.0 1.0
O A:HOH537 2.9 37.6 1.0
O A:HOH741 2.9 36.5 1.0
CE1 A:HIS160 3.1 21.2 1.0
CD A:GLU220 3.2 8.9 1.0
HD23 A:LEU217 3.2 13.0 1.0
HE1 A:HIS160 3.2 25.4 1.0
HD22 A:LEU217 3.2 13.0 1.0
HB2 A:HIS160 3.3 11.3 1.0
CG A:HIS160 3.3 15.7 1.0
HB3 A:PHE170 3.5 11.2 1.0
CD2 A:LEU217 3.5 10.8 1.0
OE1 A:GLU220 3.6 8.1 1.0
HD21 A:LEU217 3.6 13.0 1.0
HB2 A:PHE170 3.7 11.2 1.0
CB A:HIS160 3.7 9.4 1.0
HA A:HIS160 3.8 7.6 1.0
CB A:PHE170 4.1 9.3 1.0
H A:PHE170 4.2 9.0 1.0
NE2 A:HIS160 4.3 19.1 1.0
CA A:HIS160 4.3 6.3 1.0
O A:HOH888 4.4 22.2 1.0
HA A:LEU217 4.4 11.2 1.0
O A:HOH707 4.4 16.0 1.0
CD2 A:HIS160 4.4 19.7 1.0
O A:HOH921 4.5 28.9 1.0
O A:HOH719 4.5 24.7 1.0
CG A:GLU220 4.6 7.6 1.0
HB3 A:HIS160 4.6 11.3 1.0
HG2 A:GLU220 4.6 9.1 1.0
HG3 A:GLU220 4.9 9.1 1.0
CG A:PHE170 4.9 6.1 1.0
N A:PHE170 5.0 7.5 1.0
CG A:LEU217 5.0 9.6 1.0

Zinc binding site 6 out of 10 in 5chj

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Zinc binding site 6 out of 10 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Cephalothin Batsi (SM23)


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 Cephalothin Batsi (SM23) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:26.8
occ:1.00
 O B:HOH808 2.1 27.2 1.0
O B:HOH746 2.1 21.4 1.0
NE2 B:HIS160 2.1 13.2 1.0
O B:ACT408 2.1 31.6 1.0
OXT B:ACT408 2.7 34.6 1.0
C B:ACT408 2.7 25.9 1.0
CE1 B:HIS160 3.1 15.5 1.0
CD2 B:HIS160 3.1 11.5 1.0
HE1 B:HIS160 3.2 18.6 1.0
HD2 B:HIS160 3.3 13.8 1.0
HE21 B:GLN132 3.8 26.5 1.0
O B:HOH799 3.9 39.0 1.0
HE1 B:TRP95 3.9 17.5 1.0
HZ2 B:TRP95 4.0 14.4 1.0
CH3 B:ACT408 4.2 22.2 1.0
ND1 B:HIS160 4.2 17.3 1.0
HE1 B:MET131 4.2 30.7 1.0
CG B:HIS160 4.2 13.4 1.0
O B:HOH693 4.4 27.7 1.0
NE1 B:TRP95 4.5 14.6 1.0
NE2 B:GLN132 4.5 22.1 1.0
OD1 B:ASN128 4.5 35.9 1.0
H1 B:ACT408 4.5 26.6 1.0
HE22 B:GLN132 4.6 26.5 1.0
HD23 B:LEU161 4.6 9.5 1.0
H2 B:ACT408 4.6 26.6 1.0
CZ2 B:TRP95 4.6 12.0 1.0
H3 B:ACT408 4.8 26.6 1.0
CE2 B:TRP95 4.9 12.4 1.0
HB2 B:ASN164 5.0 16.7 1.0
HD1 B:HIS160 5.0 20.8 1.0

Zinc binding site 7 out of 10 in 5chj

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Zinc binding site 7 out of 10 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Cephalothin Batsi (SM23)


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 Cephalothin Batsi (SM23) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:15.3
occ:1.00
 OXT B:ACT409 2.0 20.4 1.0
ND1 B:HIS39 2.0 13.0 1.0
O B:ACT409 2.0 26.5 1.0
O B:HOH557 2.1 15.5 1.0
C B:ACT409 2.4 28.8 1.0
CE1 B:HIS39 2.9 14.4 1.0
HE1 B:HIS39 3.0 17.3 1.0
CG B:HIS39 3.1 12.6 1.0
HB3 B:HIS39 3.2 14.6 1.0
HA B:HIS39 3.4 15.9 1.0
CB B:HIS39 3.6 12.2 1.0
CH3 B:ACT409 3.8 26.8 1.0
CA B:HIS39 4.0 13.2 1.0
NE2 B:HIS39 4.0 15.4 1.0
O B:ALA38 4.1 13.8 1.0
CD2 B:HIS39 4.2 17.2 1.0
O B:HOH561 4.2 22.6 1.0
H2 B:ACT409 4.2 32.1 1.0
H1 B:ACT409 4.4 32.1 1.0
O B:HOH898 4.4 21.9 1.0
H3 B:ACT409 4.4 32.1 1.0
HB2 B:HIS39 4.5 14.6 1.0
HD22 B:LEU8 4.6 36.2 1.0
H B:TYR40 4.8 14.9 1.0
N B:HIS39 4.8 13.0 1.0
HE2 B:HIS39 4.8 18.4 1.0
C B:ALA38 4.8 13.5 1.0

Zinc binding site 8 out of 10 in 5chj

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Zinc binding site 8 out of 10 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Cephalothin Batsi (SM23)


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 Cephalothin Batsi (SM23) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:14.4
occ:1.00
 OE1 B:GLU124 2.0 19.7 1.0
OD2 B:ASP126 2.0 14.2 1.0
O B:ACT406 2.1 38.6 1.0
CD B:GLU124 2.5 14.9 1.0
OE2 B:GLU124 2.5 26.6 1.0
CG B:ASP126 2.7 15.4 1.0
OD1 B:ASP126 2.7 19.5 1.0
H1 B:ACT406 2.8 14.4 1.0
HZ1 B:LYS130 3.0 27.4 1.0
C B:ACT406 3.0 22.0 1.0
CH3 B:ACT406 3.4 12.0 1.0
HZ2 B:LYS130 3.7 27.4 1.0
HA B:GLU124 3.7 20.7 1.0
NZ B:LYS130 3.7 22.9 1.0
O B:HOH513 4.0 20.2 1.0
CG B:GLU124 4.0 19.2 1.0
HZ3 B:LYS130 4.0 27.4 1.0
H2 B:ACT406 4.0 14.4 1.0
H3 B:ACT406 4.1 14.4 1.0
OXT B:ACT406 4.2 15.6 1.0
CB B:ASP126 4.2 16.4 1.0
HB3 B:ASP126 4.5 19.6 1.0
HG3 B:GLU124 4.5 23.0 1.0
HB2 B:ASP126 4.5 19.6 1.0
HG2 B:GLU124 4.5 23.0 1.0
HB3 B:GLU124 4.5 20.6 1.0
CA B:GLU124 4.5 17.2 1.0
CB B:GLU124 4.6 17.2 1.0
O B:GLU124 4.8 14.1 1.0
CE B:LYS130 4.9 21.5 1.0
HE3 B:LYS130 4.9 25.8 1.0

Zinc binding site 9 out of 10 in 5chj

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Zinc binding site 9 out of 10 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Cephalothin Batsi (SM23)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Fox-4 Cephamycinase Complexed with Cephalothin Batsi (SM23) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:26.8
occ:1.00
 ND1 B:HIS185 2.0 20.4 1.0
O B:HOH781 2.1 38.2 1.0
O B:HOH804 2.1 35.9 1.0
CE1 B:HIS185 2.8 22.9 1.0
HE1 B:HIS185 2.9 27.4 1.0
CG B:HIS185 3.1 20.0 1.0
HB3 B:HIS185 3.2 21.9 1.0
CB B:HIS185 3.6 18.3 1.0
O B:HOH689 3.7 33.2 1.0
HA B:HIS185 3.8 17.4 1.0
NE2 B:HIS185 4.0 25.6 1.0
CD2 B:HIS185 4.2 24.6 1.0
HB3 B:PRO180 4.2 19.2 1.0
CA B:HIS185 4.3 14.5 1.0
HB2 B:HIS185 4.5 21.9 1.0
HG3 B:PRO180 4.5 20.4 1.0
HA B:PRO180 4.7 17.5 1.0
HE2 B:HIS185 4.8 30.8 1.0
O B:HIS185 4.9 20.2 1.0

Zinc binding site 10 out of 10 in 5chj

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Zinc binding site 10 out of 10 in the Crystal Structure of Fox-4 Cephamycinase Complexed with Cephalothin Batsi (SM23)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Fox-4 Cephamycinase Complexed with Cephalothin Batsi (SM23) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn405

b:34.2
occ:1.00
 HD1 B:HIS160 1.3 20.8 1.0
OE2 B:GLU220 2.1 11.2 1.0
ND1 B:HIS160 2.2 17.3 1.0
O B:HOH771 2.3 42.7 1.0
O B:HOH774 2.3 37.2 1.0
O B:HOH539 2.5 39.1 1.0
CE1 B:HIS160 3.1 15.5 1.0
CD B:GLU220 3.2 11.4 1.0
HB2 B:HIS160 3.2 11.7 1.0
HE1 B:HIS160 3.3 18.6 1.0
CG B:HIS160 3.3 13.4 1.0
HD23 B:LEU217 3.3 14.1 1.0
HD22 B:LEU217 3.4 14.1 1.0
HB3 B:PHE170 3.5 10.9 1.0
OE1 B:GLU220 3.5 11.2 1.0
HA B:HIS160 3.6 10.3 1.0
HB2 B:PHE170 3.6 10.9 1.0
CB B:HIS160 3.7 9.8 1.0
CD2 B:LEU217 3.7 11.8 1.0
HD21 B:LEU217 3.8 14.1 1.0
CB B:PHE170 4.0 9.1 1.0
H B:PHE170 4.1 14.5 1.0
CA B:HIS160 4.1 8.6 1.0
NE2 B:HIS160 4.3 13.2 1.0
O B:HOH674 4.3 27.6 1.0
CD2 B:HIS160 4.4 11.5 1.0
HA B:LEU217 4.4 11.9 1.0
O B:HOH683 4.4 17.5 1.0
O B:HOH862 4.5 36.9 1.0
O B:HOH904 4.5 29.2 1.0
HB3 B:HIS160 4.5 11.7 1.0
CG B:GLU220 4.5 9.5 1.0
O B:HOH619 4.6 22.9 1.0
HG2 B:GLU220 4.6 11.4 1.0
HG3 B:GLU220 4.9 11.4 1.0
N B:PHE170 4.9 12.1 1.0
CG B:PHE170 4.9 8.7 1.0

Reference:

V.N.Malashkevich, R.Toro, S.Lefurgy, S.C.Almo. Crystal Structure of Fox-4 Cephamycinase Complexed with Batsi (SM23) To Be Published.
Page generated: Sun Oct 27 14:20:37 2024

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