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Zinc in PDB 5hnm: Crystal Structure of Vancomycin Resistance D,D-Pentapeptidase Vany E175A Mutant From Vanb-Type Resistance Cassette in Complex with Zn(II)

Enzymatic activity of Crystal Structure of Vancomycin Resistance D,D-Pentapeptidase Vany E175A Mutant From Vanb-Type Resistance Cassette in Complex with Zn(II)

All present enzymatic activity of Crystal Structure of Vancomycin Resistance D,D-Pentapeptidase Vany E175A Mutant From Vanb-Type Resistance Cassette in Complex with Zn(II):
3.4.16.4;

Protein crystallography data

The structure of Crystal Structure of Vancomycin Resistance D,D-Pentapeptidase Vany E175A Mutant From Vanb-Type Resistance Cassette in Complex with Zn(II), PDB code: 5hnm was solved by P.J.Stogios, J.Chun, Z.Wawrzak, E.Evdokimova, R.Di Leo, V.Yim, P.Courvalin, A.Savchenko, W.F.Anderson, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.88 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.709, 77.319, 85.865, 101.34, 108.13, 90.06
R / Rfree (%) 21.9 / 27.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Vancomycin Resistance D,D-Pentapeptidase Vany E175A Mutant From Vanb-Type Resistance Cassette in Complex with Zn(II) (pdb code 5hnm). 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 Vancomycin Resistance D,D-Pentapeptidase Vany E175A Mutant From Vanb-Type Resistance Cassette in Complex with Zn(II), PDB code: 5hnm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5hnm

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Zinc binding site 1 out of 6 in the Crystal Structure of Vancomycin Resistance D,D-Pentapeptidase Vany E175A Mutant From Vanb-Type Resistance Cassette in Complex with Zn(II)


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 Vancomycin Resistance D,D-Pentapeptidase Vany E175A Mutant From Vanb-Type Resistance Cassette in Complex with Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:32.6
occ:0.89
 OD1 A:ASP195 2.0 28.4 1.0
ND1 A:HIS241 2.0 40.6 1.0
NE2 A:HIS188 2.0 24.0 1.0
O4 A:SO4302 2.4 93.0 1.0
CG A:ASP195 2.8 31.8 1.0
CE1 A:HIS241 2.8 44.6 1.0
CE1 A:HIS188 2.9 29.2 1.0
OD2 A:ASP195 2.9 26.0 1.0
CD2 A:HIS188 3.1 24.2 1.0
CG A:HIS241 3.1 40.6 1.0
CB A:HIS241 3.6 41.2 1.0
S A:SO4302 3.6 100.0 1.0
O3 A:SO4302 3.7 0.9 1.0
NH2 A:ARG146 3.9 45.6 1.0
NE2 A:HIS241 4.0 41.1 1.0
ND1 A:HIS188 4.1 29.6 1.0
CD2 A:HIS241 4.2 40.0 1.0
CG A:HIS188 4.2 23.6 1.0
CB A:ASP195 4.2 35.5 1.0
CA A:HIS241 4.3 36.3 1.0
O1 A:SO4302 4.4 0.4 1.0
OE1 A:GLU238 4.4 46.6 1.0
CD1 A:TRP240 4.5 35.1 1.0
NE1 A:TRP240 4.6 35.5 1.0
O2 A:SO4302 4.7 0.6 1.0
CA A:ASP195 4.7 36.9 1.0
CZ A:ARG146 4.8 40.8 1.0
N A:ASP195 4.8 35.4 1.0
O A:HOH447 5.0 28.3 1.0

Zinc binding site 2 out of 6 in 5hnm

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Zinc binding site 2 out of 6 in the Crystal Structure of Vancomycin Resistance D,D-Pentapeptidase Vany E175A Mutant From Vanb-Type Resistance Cassette in Complex with Zn(II)


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 Vancomycin Resistance D,D-Pentapeptidase Vany E175A Mutant From Vanb-Type Resistance Cassette in Complex with Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:49.0
occ:1.00
 OD1 B:ASP195 2.0 44.6 1.0
NE2 B:HIS188 2.0 20.1 1.0
ND1 B:HIS241 2.0 36.0 1.0
OD2 B:ASP195 2.1 44.8 1.0
O3 B:SO4302 2.3 97.5 1.0
CG B:ASP195 2.3 38.1 1.0
O1 B:SO4302 2.6 99.6 1.0
CE1 B:HIS241 2.7 29.2 1.0
S B:SO4302 2.8 98.0 1.0
CE1 B:HIS188 3.0 27.0 1.0
CD2 B:HIS188 3.1 24.6 1.0
CG B:HIS241 3.2 31.6 1.0
O4 B:SO4302 3.2 97.0 1.0
CB B:ASP195 3.8 28.4 1.0
CB B:HIS241 3.8 27.8 1.0
NE2 B:HIS241 4.0 29.5 1.0
NH2 B:ARG146 4.1 39.1 1.0
ND1 B:HIS188 4.1 30.5 1.0
O2 B:SO4302 4.2 99.4 1.0
CG B:HIS188 4.2 28.2 1.0
CD2 B:HIS241 4.2 28.1 1.0
CA B:HIS241 4.4 32.2 1.0
O B:HOH402 4.4 35.4 1.0
CA B:ASP195 4.5 26.0 1.0
NH1 B:ARG146 4.5 33.9 1.0
CD1 B:TRP240 4.5 40.1 1.0
N B:ASP195 4.6 26.8 1.0
NE1 B:TRP240 4.6 44.8 1.0
CZ B:ARG146 4.7 37.5 1.0
O B:HOH415 4.9 44.5 1.0
OE1 B:GLU238 5.0 50.1 1.0

Zinc binding site 3 out of 6 in 5hnm

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Zinc binding site 3 out of 6 in the Crystal Structure of Vancomycin Resistance D,D-Pentapeptidase Vany E175A Mutant From Vanb-Type Resistance Cassette in Complex with Zn(II)


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 Vancomycin Resistance D,D-Pentapeptidase Vany E175A Mutant From Vanb-Type Resistance Cassette in Complex with Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn500

b:64.8
occ:1.00
 OD1 C:ASP195 2.0 69.8 1.0
NE2 C:HIS188 2.0 46.9 1.0
OD2 C:ASP195 2.0 81.2 1.0
ND1 C:HIS241 2.0 47.8 1.0
CG C:ASP195 2.3 70.8 1.0
O C:HOH632 2.8 51.3 1.0
CE1 C:HIS188 2.8 44.2 1.0
CE1 C:HIS241 2.9 45.1 1.0
CG C:HIS241 3.2 37.9 1.0
CD2 C:HIS188 3.2 47.4 1.0
CB C:HIS241 3.6 36.5 1.0
CB C:ASP195 3.8 60.6 1.0
ND1 C:HIS188 4.0 43.4 1.0
NE2 C:HIS241 4.0 41.7 1.0
NH2 C:ARG146 4.1 60.3 1.0
CD2 C:HIS241 4.2 35.1 1.0
CG C:HIS188 4.2 46.3 1.0
CA C:HIS241 4.2 36.1 1.0
CD1 C:TRP240 4.4 52.4 1.0
CA C:ASP195 4.4 47.9 1.0
NE1 C:TRP240 4.5 54.5 1.0
N C:ASP195 4.6 39.5 1.0
OE1 C:GLU238 4.6 62.5 1.0
O C:HOH646 4.6 37.5 1.0
CZ C:ARG146 4.8 56.0 1.0
O C:HOH638 4.8 49.4 1.0
NH1 C:ARG146 5.0 59.2 1.0

Zinc binding site 4 out of 6 in 5hnm

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Zinc binding site 4 out of 6 in the Crystal Structure of Vancomycin Resistance D,D-Pentapeptidase Vany E175A Mutant From Vanb-Type Resistance Cassette in Complex with Zn(II)


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 Vancomycin Resistance D,D-Pentapeptidase Vany E175A Mutant From Vanb-Type Resistance Cassette in Complex with Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn500

b:48.0
occ:1.00
 OD1 D:ASP195 2.0 60.4 1.0
OD2 D:ASP195 2.0 65.2 1.0
NE2 D:HIS188 2.0 44.5 1.0
ND1 D:HIS241 2.0 39.3 1.0
CG D:ASP195 2.3 59.3 1.0
CE1 D:HIS188 2.8 44.7 1.0
O D:HOH667 2.8 49.1 1.0
CE1 D:HIS241 2.8 39.9 1.0
CG D:HIS241 3.2 39.3 1.0
CD2 D:HIS188 3.2 45.9 1.0
CB D:HIS241 3.7 39.1 1.0
CB D:ASP195 3.8 53.3 1.0
ND1 D:HIS188 4.0 48.8 1.0
NE2 D:HIS241 4.0 42.0 1.0
CD2 D:HIS241 4.2 42.2 1.0
CG D:HIS188 4.2 50.2 1.0
NH2 D:ARG146 4.2 63.4 1.0
OE1 D:GLU238 4.3 72.8 1.0
CA D:HIS241 4.4 44.7 1.0
O D:HOH677 4.4 64.6 1.0
CD1 D:TRP240 4.4 39.2 1.0
CA D:ASP195 4.5 50.7 1.0
NE1 D:TRP240 4.5 42.2 1.0
N D:ASP195 4.6 42.8 1.0
NH1 D:ARG146 4.7 68.4 1.0
CZ D:ARG146 4.7 64.4 1.0

Zinc binding site 5 out of 6 in 5hnm

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Zinc binding site 5 out of 6 in the Crystal Structure of Vancomycin Resistance D,D-Pentapeptidase Vany E175A Mutant From Vanb-Type Resistance Cassette in Complex with Zn(II)


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 Vancomycin Resistance D,D-Pentapeptidase Vany E175A Mutant From Vanb-Type Resistance Cassette in Complex with Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:31.0
occ:0.89
 OD1 E:ASP195 2.0 43.8 1.0
ND1 E:HIS241 2.0 29.5 1.0
NE2 E:HIS188 2.0 31.0 1.0
OD2 E:ASP195 2.0 32.7 1.0
O2 E:SO4302 2.2 0.5 1.0
CG E:ASP195 2.3 33.7 1.0
O1 E:SO4302 2.7 0.4 1.0
CE1 E:HIS241 2.8 34.4 1.0
S E:SO4302 2.8 0.9 1.0
CE1 E:HIS188 3.0 31.7 1.0
CD2 E:HIS188 3.0 31.6 1.0
CG E:HIS241 3.2 33.7 1.0
O4 E:SO4302 3.3 1.0 1.0
NH2 E:ARG146 3.7 60.5 1.0
CB E:HIS241 3.7 26.2 1.0
CB E:ASP195 3.8 29.0 1.0
NE2 E:HIS241 4.0 31.2 1.0
ND1 E:HIS188 4.1 30.3 1.0
CG E:HIS188 4.2 30.9 1.0
O3 E:SO4302 4.2 98.8 1.0
CD2 E:HIS241 4.2 31.4 1.0
CA E:HIS241 4.3 27.4 1.0
CD1 E:TRP240 4.4 36.3 1.0
CZ E:ARG146 4.4 52.3 1.0
CA E:ASP195 4.5 28.3 1.0
NE1 E:TRP240 4.5 35.6 1.0
N E:ASP195 4.7 29.1 1.0
NH1 E:ARG146 4.7 43.0 1.0
OG E:SER143 4.8 30.5 0.3
O E:HOH401 4.8 44.2 1.0

Zinc binding site 6 out of 6 in 5hnm

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Zinc binding site 6 out of 6 in the Crystal Structure of Vancomycin Resistance D,D-Pentapeptidase Vany E175A Mutant From Vanb-Type Resistance Cassette in Complex with Zn(II)


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 Vancomycin Resistance D,D-Pentapeptidase Vany E175A Mutant From Vanb-Type Resistance Cassette in Complex with Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:37.5
occ:1.00
 OD1 F:ASP195 2.0 54.4 1.0
NE2 F:HIS188 2.0 36.2 1.0
OD2 F:ASP195 2.0 45.1 1.0
ND1 F:HIS241 2.0 34.8 1.0
CG F:ASP195 2.3 43.2 1.0
O F:HOH443 2.3 35.3 1.0
CE1 F:HIS241 2.8 45.3 1.0
CE1 F:HIS188 2.8 33.5 1.0
CD2 F:HIS188 3.1 41.9 1.0
CG F:HIS241 3.2 34.8 1.0
CB F:HIS241 3.8 28.8 1.0
CB F:ASP195 3.8 33.2 1.0
NH2 F:ARG146 3.8 38.0 1.0
NE2 F:HIS241 4.0 35.3 1.0
ND1 F:HIS188 4.0 35.9 1.0
CG F:HIS188 4.2 40.7 1.0
CD2 F:HIS241 4.2 32.9 1.0
CD1 F:TRP240 4.3 41.5 1.0
NE1 F:TRP240 4.3 44.4 1.0
CA F:HIS241 4.4 32.6 1.0
O F:HOH458 4.5 49.5 1.0
OE1 F:GLU238 4.5 58.7 1.0
CA F:ASP195 4.5 31.8 1.0
CZ F:ARG146 4.7 37.7 1.0
N F:ASP195 4.7 26.0 1.0
O F:HOH470 4.9 36.9 1.0

Reference:

P.J.Stogios, P.J.Stogios, J.Chun, Z.Wawrzak, E.Evdokimova, R.Di Leo, V.Yim, P.Courvalin, A.Savchenko, W.F.Anderson, Center For Structural Genomics Ofinfectious Diseases (Csgid). N/A N/A.
Page generated: Sun Oct 27 17:35:38 2024

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