Atomistry » Zinc » PDB 5n34-5nek » 5n5i
Atomistry »
  Zinc »
    PDB 5n34-5nek »
      5n5i »

Zinc in PDB 5n5i: Crystal Structure of Vim-1 Metallo-Beta-Lactamase in Complex with Hydrolysed Meropenem

Protein crystallography data

The structure of Crystal Structure of Vim-1 Metallo-Beta-Lactamase in Complex with Hydrolysed Meropenem, PDB code: 5n5i was solved by R.Salimraj, P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.84 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.943, 68.084, 39.817, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 22.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Vim-1 Metallo-Beta-Lactamase in Complex with Hydrolysed Meropenem (pdb code 5n5i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Vim-1 Metallo-Beta-Lactamase in Complex with Hydrolysed Meropenem, PDB code: 5n5i:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5n5i

Go back to Zinc Binding Sites List in 5n5i
Zinc binding site 1 out of 3 in the Crystal Structure of Vim-1 Metallo-Beta-Lactamase in Complex with Hydrolysed Meropenem


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 Vim-1 Metallo-Beta-Lactamase in Complex with Hydrolysed Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:33.7
occ:0.87
OD2 A:ASP118 2.1 23.4 1.0
O A:HOH445 2.3 15.8 1.0
NE2 A:HIS240 2.4 19.0 1.0
SG A:CYS198 2.5 13.4 1.0
O32 A:LMP304 2.6 22.0 1.0
N4 A:LMP304 3.0 30.1 1.0
CG A:ASP118 3.2 17.0 1.0
CD2 A:HIS240 3.3 17.9 1.0
CE1 A:HIS240 3.4 21.5 1.0
C31 A:LMP304 3.5 34.8 1.0
ZN A:ZN302 3.5 13.2 1.0
C3 A:LMP304 3.5 35.4 1.0
OD1 A:ASP118 3.5 10.8 1.0
CB A:CYS198 3.6 9.8 1.0
C5 A:LMP304 4.0 37.5 1.0
NH2 A:ARG119 4.2 22.7 1.0
NE2 A:HIS179 4.2 9.8 1.0
CE1 A:HIS179 4.3 7.5 1.0
NE A:ARG119 4.4 15.5 1.0
C61 A:LMP304 4.4 34.5 1.0
CB A:ASP118 4.5 15.2 1.0
CE1 A:HIS114 4.5 7.1 1.0
CG A:HIS240 4.5 17.1 1.0
ND1 A:HIS240 4.5 24.4 1.0
NE2 A:HIS114 4.5 7.9 1.0
O A:HOH478 4.6 32.5 1.0
O62 A:LMP304 4.7 25.8 1.0
O31 A:LMP304 4.7 33.9 1.0
CZ A:ARG119 4.8 19.3 1.0
C2 A:LMP304 4.8 41.2 1.0
C6 A:LMP304 4.9 41.8 1.0
CA A:CYS198 4.9 17.7 1.0
C1 A:LMP304 5.0 37.5 1.0

Zinc binding site 2 out of 3 in 5n5i

Go back to Zinc Binding Sites List in 5n5i
Zinc binding site 2 out of 3 in the Crystal Structure of Vim-1 Metallo-Beta-Lactamase in Complex with Hydrolysed Meropenem


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 Vim-1 Metallo-Beta-Lactamase in Complex with Hydrolysed Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:13.2
occ:1.00
O A:HOH445 1.8 15.8 1.0
ND1 A:HIS116 1.9 10.6 1.0
NE2 A:HIS179 2.0 9.8 1.0
NE2 A:HIS114 2.1 7.9 1.0
CG A:HIS116 2.9 8.0 1.0
CE1 A:HIS116 2.9 10.2 1.0
CE1 A:HIS179 3.0 7.5 1.0
CD2 A:HIS179 3.0 8.0 1.0
CD2 A:HIS114 3.1 14.1 1.0
CE1 A:HIS114 3.1 7.1 1.0
CB A:HIS116 3.2 7.9 1.0
ZN A:ZN301 3.5 33.7 0.9
OD1 A:ASP118 3.9 10.8 1.0
NE2 A:HIS116 4.0 9.8 1.0
CD2 A:HIS116 4.0 7.5 1.0
O62 A:LMP304 4.1 25.8 1.0
ND1 A:HIS179 4.1 8.7 1.0
CG A:HIS179 4.2 5.2 1.0
ND1 A:HIS114 4.2 10.9 1.0
CG A:HIS114 4.2 9.8 1.0
SG A:CYS198 4.3 13.4 1.0
CB A:CYS198 4.3 9.8 1.0
O32 A:LMP304 4.3 22.0 1.0
OD2 A:ASP118 4.4 23.4 1.0
ND2 A:ASN210 4.5 23.3 1.0
CG A:ASP118 4.6 17.0 1.0
CA A:HIS116 4.7 11.0 1.0
C61 A:LMP304 4.8 34.5 1.0
N4 A:LMP304 4.9 30.1 1.0
N A:HIS116 4.9 11.1 1.0

Zinc binding site 3 out of 3 in 5n5i

Go back to Zinc Binding Sites List in 5n5i
Zinc binding site 3 out of 3 in the Crystal Structure of Vim-1 Metallo-Beta-Lactamase in Complex with Hydrolysed Meropenem


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 Vim-1 Metallo-Beta-Lactamase in Complex with Hydrolysed Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:31.1
occ:0.55
O A:SER154 2.4 19.4 1.0
O A:HOH480 2.5 26.2 1.0
OE1 A:GLU156 2.6 34.8 1.0
OE2 A:GLU156 2.6 27.1 1.0
O A:HOH477 2.8 29.7 1.0
CD A:GLU156 3.0 33.6 1.0
C A:SER154 3.5 13.8 1.0
N A:SER154 4.1 11.3 1.0
CA A:SER154 4.2 13.5 1.0
CB A:SER154 4.3 15.1 1.0
O A:HOH409 4.4 21.6 1.0
CG A:GLU156 4.5 20.7 1.0
N A:LEU155 4.5 15.7 1.0
N A:GLU156 4.7 14.7 1.0
CA A:LEU155 4.8 15.0 1.0

Reference:

R.Salimraj, P.Hinchliffe, M.Kosmopoulou, J.M.Tyrrell, J.Brem, S.S.Van Berkel, A.Verma, R.J.Owens, M.A.Mcdonough, T.R.Walsh, C.J.Schofield, J.Spencer. Crystal Structures of Vim-1 Complexes Explain Active Site Heterogeneity in Vim-Class Metallo-Beta-Lactamases. Febs J. V. 286 169 2019.
ISSN: ISSN 1742-4658
PubMed: 30430727
DOI: 10.1111/FEBS.14695
Page generated: Sun Oct 27 22:34:45 2024

Last articles

Al in 8R1A
Al in 8Q75
Al in 8OIE
Al in 8OX6
Al in 8OX5
Al in 8OP8
Al in 8OP6
Al in 8OP5
Al in 8OOS
Al in 8OO9
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy