Zinc in PDB 6mn5: Crystal Structure of Aminoglycoside Acetyltransferase Aac(3)-Iva, H154A Mutant, in Complex with Gentamicin C1A

Enzymatic activity of Crystal Structure of Aminoglycoside Acetyltransferase Aac(3)-Iva, H154A Mutant, in Complex with Gentamicin C1A

All present enzymatic activity of Crystal Structure of Aminoglycoside Acetyltransferase Aac(3)-Iva, H154A Mutant, in Complex with Gentamicin C1A:
2.3.1.81;

Protein crystallography data

The structure of Crystal Structure of Aminoglycoside Acetyltransferase Aac(3)-Iva, H154A Mutant, in Complex with Gentamicin C1A, PDB code: 6mn5 was solved by P.J.Stogios, E.Evdokimova, Y.Kim, R.Di Leo, A.Savchenko, A.Joachimiak, K.J.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.40 / 2.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.609, 131.881, 266.872, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Aminoglycoside Acetyltransferase Aac(3)-Iva, H154A Mutant, in Complex with Gentamicin C1A (pdb code 6mn5). 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 Aminoglycoside Acetyltransferase Aac(3)-Iva, H154A Mutant, in Complex with Gentamicin C1A, PDB code: 6mn5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6mn5

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Zinc binding site 1 out of 6 in the Crystal Structure of Aminoglycoside Acetyltransferase Aac(3)-Iva, H154A Mutant, in Complex with Gentamicin C1A


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 Aminoglycoside Acetyltransferase Aac(3)-Iva, H154A Mutant, in Complex with Gentamicin C1A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:94.4
occ:0.90
 ND1 A:HIS241 2.1 89.7 1.0
SG A:CYS247 2.3 77.5 1.0
SG A:CYS189 2.3 70.3 1.0
SG A:CYS250 2.4 78.2 1.0
CE1 A:HIS241 3.0 74.9 1.0
CB A:CYS247 3.0 69.8 1.0
CB A:CYS189 3.1 64.0 1.0
CG A:HIS241 3.2 75.0 1.0
CB A:CYS250 3.4 71.1 1.0
CB A:HIS241 3.6 52.9 1.0
NE2 A:HIS241 4.1 77.5 1.0
N A:CYS250 4.2 63.1 1.0
N A:HIS241 4.2 56.8 1.0
CD2 A:HIS241 4.2 79.7 1.0
N A:CYS189 4.3 76.4 1.0
CA A:CYS189 4.3 69.8 1.0
CA A:CYS250 4.4 63.8 1.0
O A:HOH425 4.5 47.6 1.0
CA A:CYS247 4.5 69.3 1.0
CA A:HIS241 4.6 61.1 1.0

Zinc binding site 2 out of 6 in 6mn5

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Zinc binding site 2 out of 6 in the Crystal Structure of Aminoglycoside Acetyltransferase Aac(3)-Iva, H154A Mutant, in Complex with Gentamicin C1A


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 Aminoglycoside Acetyltransferase Aac(3)-Iva, H154A Mutant, in Complex with Gentamicin C1A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:80.0
occ:0.90
 SG B:CYS247 2.2 94.4 1.0
ND1 B:HIS241 2.2 92.2 1.0
SG B:CYS250 2.3 76.6 1.0
SG B:CYS189 2.4 78.5 1.0
CB B:CYS247 3.0 93.1 1.0
CG B:HIS241 3.1 90.6 1.0
CB B:CYS250 3.1 71.4 1.0
CB B:CYS189 3.2 82.8 1.0
CE1 B:HIS241 3.2 92.8 1.0
CB B:HIS241 3.3 88.3 1.0
N B:HIS241 4.2 85.1 1.0
N B:CYS250 4.2 91.1 1.0
O B:HOH437 4.2 62.9 1.0
CA B:CYS250 4.2 75.7 1.0
N B:CYS189 4.3 74.8 1.0
CD2 B:HIS241 4.3 91.8 1.0
CA B:CYS189 4.3 78.3 1.0
O B:HOH515 4.3 86.2 1.0
NE2 B:HIS241 4.3 91.9 1.0
CA B:HIS241 4.4 83.1 1.0
CA B:CYS247 4.5 0.1 1.0
CG B:GLU249 4.9 0.1 1.0

Zinc binding site 3 out of 6 in 6mn5

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Zinc binding site 3 out of 6 in the Crystal Structure of Aminoglycoside Acetyltransferase Aac(3)-Iva, H154A Mutant, in Complex with Gentamicin C1A


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 Aminoglycoside Acetyltransferase Aac(3)-Iva, H154A Mutant, in Complex with Gentamicin C1A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:57.5
occ:0.67
 ND1 C:HIS241 2.2 0.0 1.0
SG C:CYS247 2.3 90.5 1.0
SG C:CYS250 2.3 77.6 1.0
SG C:CYS189 2.4 81.3 1.0
CB C:CYS247 3.1 94.8 1.0
CG C:HIS241 3.1 95.2 1.0
CE1 C:HIS241 3.1 98.3 1.0
CB C:CYS189 3.2 89.2 1.0
CB C:CYS250 3.2 86.6 1.0
CB C:HIS241 3.4 88.4 1.0
N C:CYS250 4.1 89.2 1.0
CA C:CYS250 4.2 92.2 1.0
N C:HIS241 4.2 94.8 1.0
NE2 C:HIS241 4.2 98.7 1.0
CD2 C:HIS241 4.3 99.9 1.0
N C:CYS189 4.3 0.6 1.0
CA C:CYS189 4.3 95.3 1.0
CA C:HIS241 4.4 92.2 1.0
CA C:CYS247 4.6 0.1 1.0
O C:HOH481 4.8 94.6 1.0

Zinc binding site 4 out of 6 in 6mn5

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Zinc binding site 4 out of 6 in the Crystal Structure of Aminoglycoside Acetyltransferase Aac(3)-Iva, H154A Mutant, in Complex with Gentamicin C1A


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 Aminoglycoside Acetyltransferase Aac(3)-Iva, H154A Mutant, in Complex with Gentamicin C1A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:86.7
occ:0.72
 ND1 D:HIS241 2.2 0.1 1.0
SG D:CYS250 2.3 90.2 1.0
SG D:CYS247 2.4 95.5 1.0
SG D:CYS189 2.4 0.7 1.0
CG D:HIS241 3.0 0.8 1.0
CB D:CYS250 3.1 93.2 1.0
CE1 D:HIS241 3.2 0.5 1.0
CB D:CYS247 3.2 0.4 1.0
CB D:CYS189 3.2 0.2 1.0
CB D:HIS241 3.3 0.8 1.0
N D:HIS241 4.0 0.3 1.0
CD2 D:HIS241 4.2 0.6 1.0
CA D:CYS250 4.2 0.8 1.0
NE2 D:HIS241 4.2 0.5 1.0
N D:CYS250 4.2 0.7 1.0
CA D:HIS241 4.2 0.5 1.0
CA D:CYS189 4.4 0.0 1.0
N D:CYS189 4.4 0.4 1.0
CA D:CYS247 4.6 0.6 1.0
O D:CYS247 4.9 0.9 1.0
C D:CYS247 5.0 0.4 1.0

Zinc binding site 5 out of 6 in 6mn5

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Zinc binding site 5 out of 6 in the Crystal Structure of Aminoglycoside Acetyltransferase Aac(3)-Iva, H154A Mutant, in Complex with Gentamicin C1A


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 Aminoglycoside Acetyltransferase Aac(3)-Iva, H154A Mutant, in Complex with Gentamicin C1A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn302

b:0.5
occ:0.83
 SG E:CYS250 1.7 0.3 1.0
SG E:CYS189 2.4 1.0 1.0
ND1 E:HIS241 2.7 0.7 1.0
SG E:CYS247 2.7 0.7 1.0
CB E:CYS247 3.0 0.9 1.0
CG E:HIS241 3.3 0.9 1.0
CB E:CYS250 3.3 0.3 1.0
CE1 E:HIS241 3.5 0.4 1.0
CB E:HIS241 3.5 0.8 1.0
OE1 E:GLU191 3.9 0.7 1.0
CB E:CYS189 3.9 0.1 1.0
CD2 E:HIS241 4.2 0.5 1.0
CA E:CYS250 4.3 1.0 1.0
NE2 E:HIS241 4.3 0.8 1.0
N E:CYS250 4.4 0.6 1.0
CA E:CYS247 4.5 0.2 1.0
N E:HIS241 4.6 0.0 1.0
CA E:HIS241 4.7 0.1 1.0
N E:CYS189 4.9 0.4 1.0
CD E:GLU191 4.9 0.8 1.0
CD1 E:LEU240 4.9 0.6 1.0
CA E:CYS189 5.0 0.6 1.0

Zinc binding site 6 out of 6 in 6mn5

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Zinc binding site 6 out of 6 in the Crystal Structure of Aminoglycoside Acetyltransferase Aac(3)-Iva, H154A Mutant, in Complex with Gentamicin C1A


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 Aminoglycoside Acetyltransferase Aac(3)-Iva, H154A Mutant, in Complex with Gentamicin C1A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn302

b:0.8
occ:0.80
 SG F:CYS250 2.3 0.8 1.0
ND1 F:HIS241 2.5 0.2 1.0
SG F:CYS189 2.7 0.7 1.0
SG F:CYS247 2.8 0.1 1.0
CE1 F:HIS241 2.9 0.9 1.0
CB F:CYS247 3.1 0.9 1.0
CB F:CYS250 3.2 0.8 1.0
CG F:HIS241 3.7 0.8 1.0
NE2 F:HIS241 4.1 1.0 1.0
N F:CYS250 4.1 0.5 1.0
OE2 F:GLU191 4.1 0.8 1.0
CB F:CYS189 4.2 0.6 1.0
CA F:CYS250 4.2 0.6 1.0
CB F:HIS241 4.4 0.1 1.0
N F:HIS241 4.4 0.1 1.0
CD2 F:HIS241 4.5 0.9 1.0
CA F:CYS247 4.6 0.6 1.0
N F:CYS189 4.8 0.3 1.0

Reference:

P.J.Stogios, P.J.Stogios, E.Evdokimova, Y.Kim, R.Di Leo, A.Savchenko, A.Joachimiak, K.J.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid). N/A N/A.
Page generated: Wed Dec 16 12:20:09 2020

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