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Zinc in PDB 5n5h: Crystal Structure of Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor, PDB code: 5n5h 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) 28.58 / 1.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.684, 67.652, 40.217, 90.00, 91.36, 90.00
R / Rfree (%) 15.5 / 16.8

Other elements in 5n5h:

The structure of Crystal Structure of Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor (pdb code 5n5h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor, PDB code: 5n5h:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5n5h

Go back to Zinc Binding Sites List in 5n5h
Zinc binding site 1 out of 2 in the Crystal Structure of Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor


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 Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:9.0
occ:0.94
NE2 A:HIS240 2.1 6.8 1.0
OD2 A:ASP118 2.2 8.1 1.0
SG A:CYS198 2.2 8.1 1.0
O7 A:S3C303 2.4 7.5 0.9
S9 A:S3C303 2.4 9.7 0.9
H3 A:S3C303 2.6 11.6 0.9
CD2 A:HIS240 3.0 5.5 1.0
CE1 A:HIS240 3.1 7.2 1.0
C6 A:S3C303 3.1 16.4 0.9
CG A:ASP118 3.2 6.8 1.0
C5 A:S3C303 3.2 10.5 0.9
HH21 A:ARG119 3.2 15.4 1.0
HD2 A:HIS240 3.2 6.6 1.0
HB3 A:CYS198 3.2 9.7 1.0
HE1 A:HIS240 3.3 8.6 1.0
CB A:CYS198 3.3 8.1 1.0
HE1 A:HIS114 3.4 6.8 1.0
HE A:ARG119 3.5 11.8 1.0
OD1 A:ASP118 3.5 9.7 1.0
HB2 A:CYS198 3.7 9.7 1.0
NH2 A:ARG119 3.8 12.8 1.0
ZN A:ZN302 3.8 7.7 1.0
NE A:ARG119 4.1 9.9 1.0
ND1 A:HIS240 4.2 7.3 1.0
CG A:HIS240 4.2 5.7 1.0
CE1 A:HIS114 4.2 5.6 1.0
O8 A:S3C303 4.3 19.1 0.9
CZ A:ARG119 4.3 14.0 1.0
O A:HOH448 4.4 13.6 1.0
HH22 A:ARG119 4.4 15.4 1.0
CB A:ASP118 4.4 6.7 1.0
HB2 A:ASP118 4.5 8.1 1.0
NE2 A:HIS114 4.5 5.0 1.0
HA3 A:GLY239 4.5 8.8 1.0
HA A:CYS198 4.5 9.8 1.0
CL2 A:S3C303 4.5 19.5 0.9
HB3 A:ASP118 4.6 8.1 1.0
NE2 A:HIS179 4.6 6.2 1.0
CA A:CYS198 4.6 8.1 1.0
C4 A:S3C303 4.7 13.1 0.9
HG2 A:ARG119 4.8 7.2 1.0
HD1 A:HIS240 4.9 8.8 1.0

Zinc binding site 2 out of 2 in 5n5h

Go back to Zinc Binding Sites List in 5n5h
Zinc binding site 2 out of 2 in the Crystal Structure of Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor


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 Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:7.7
occ:1.00
H3 A:S3C303 1.3 11.6 0.9
ND1 A:HIS116 2.0 6.4 1.0
NE2 A:HIS114 2.0 5.0 1.0
NE2 A:HIS179 2.0 6.2 1.0
S9 A:S3C303 2.3 9.7 0.9
HB2 A:HIS116 2.9 6.4 1.0
CE1 A:HIS116 3.0 8.0 1.0
CE1 A:HIS114 3.0 5.6 1.0
CD2 A:HIS179 3.0 6.0 1.0
CD2 A:HIS114 3.0 4.9 1.0
CE1 A:HIS179 3.0 8.3 1.0
CG A:HIS116 3.0 6.8 1.0
HE1 A:HIS116 3.1 9.6 1.0
HE1 A:HIS114 3.2 6.8 1.0
HD2 A:HIS179 3.2 7.2 1.0
HD2 A:HIS114 3.2 5.8 1.0
HE1 A:HIS179 3.2 9.9 1.0
C5 A:S3C303 3.2 10.5 0.9
CB A:HIS116 3.4 5.4 1.0
HB3 A:HIS116 3.6 6.4 1.0
ZN A:ZN301 3.8 9.0 0.9
C4 A:S3C303 3.9 13.1 0.9
C3 A:S3C303 4.0 16.1 0.9
OD1 A:ASP118 4.0 9.7 1.0
HB2 A:CYS198 4.0 9.7 1.0
C6 A:S3C303 4.0 16.4 0.9
O7 A:S3C303 4.1 7.5 0.9
ND1 A:HIS114 4.1 6.2 1.0
NE2 A:HIS116 4.1 10.1 1.0
ND1 A:HIS179 4.1 7.6 1.0
CG A:HIS179 4.1 5.4 1.0
CG A:HIS114 4.1 4.6 1.0
CD2 A:HIS116 4.2 8.9 1.0
HB3 A:CYS198 4.2 9.7 1.0
H A:HIS116 4.4 5.8 1.0
C2 A:S3C303 4.4 17.7 0.9
CB A:CYS198 4.4 8.1 1.0
CL1 A:S3C303 4.5 19.4 0.9
SG A:CYS198 4.5 8.1 1.0
C10 A:S3C303 4.6 13.5 0.9
HB3 A:SER180 4.7 9.3 1.0
OD2 A:ASP118 4.7 8.1 1.0
CG A:ASP118 4.8 6.8 1.0
CA A:HIS116 4.8 5.1 1.0
H2 A:S3C303 4.8 15.7 0.9
HD1 A:HIS114 4.8 7.5 1.0
HE2 A:HIS116 4.9 12.1 1.0
HG2 A:ARG119 4.9 7.2 1.0
HD1 A:HIS179 4.9 9.2 1.0
O8 A:S3C303 4.9 19.1 0.9
N A:HIS116 5.0 4.8 1.0
C15 A:S3C303 5.0 16.4 0.9

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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