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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: Wed Dec 16 06:34:28 2020

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