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

Go back to Zinc Binding Sites List in 5hnm
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

Go back to Zinc Binding Sites List in 5hnm
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

Go back to Zinc Binding Sites List in 5hnm
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

Go back to Zinc Binding Sites List in 5hnm
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

Go back to Zinc Binding Sites List in 5hnm
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

Go back to Zinc Binding Sites List in 5hnm
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: Wed Dec 16 06:20:38 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy