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Zinc in PDB 5n5g: Crystal Structure of Di-Zinc Metallo-Beta-Lactamase Vim-1

Protein crystallography data

The structure of Crystal Structure of Di-Zinc Metallo-Beta-Lactamase Vim-1, PDB code: 5n5g 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) 34.25 / 1.29
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.760, 67.940, 40.360, 90.00, 94.01, 90.00
R / Rfree (%) 14.5 / 15.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Di-Zinc Metallo-Beta-Lactamase Vim-1 (pdb code 5n5g). 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 Di-Zinc Metallo-Beta-Lactamase Vim-1, PDB code: 5n5g:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5n5g

Go back to Zinc Binding Sites List in 5n5g
Zinc binding site 1 out of 3 in the Crystal Structure of Di-Zinc Metallo-Beta-Lactamase Vim-1


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 Di-Zinc Metallo-Beta-Lactamase Vim-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:13.3
occ:0.94
O A:HOH533 1.9 14.7 1.0
NE2 A:HIS179 2.0 10.3 1.0
ND1 A:HIS116 2.1 12.6 1.0
NE2 A:HIS114 2.1 10.5 1.0
HB2 A:HIS116 2.9 11.2 1.0
CD2 A:HIS179 2.9 8.6 1.0
CE1 A:HIS114 3.0 11.7 1.0
CE1 A:HIS179 3.0 11.6 1.0
CE1 A:HIS116 3.0 12.3 1.0
CD2 A:HIS114 3.1 8.5 1.0
CG A:HIS116 3.1 11.0 1.0
HD2 A:HIS179 3.1 10.3 1.0
HE1 A:HIS114 3.2 14.1 1.0
HE1 A:HIS116 3.2 14.8 1.0
HE1 A:HIS179 3.2 13.9 1.0
HD2 A:HIS114 3.3 10.2 1.0
CB A:HIS116 3.4 9.3 1.0
HB3 A:HIS116 3.6 11.2 1.0
ZN A:ZN302 3.6 24.6 0.7
OD1 A:ASP118 3.9 13.8 1.0
O A:HOH555 4.1 21.7 1.0
CG A:HIS179 4.1 8.6 1.0
ND1 A:HIS179 4.1 11.0 1.0
ND1 A:HIS114 4.1 9.5 1.0
NE2 A:HIS116 4.1 11.9 1.0
CG A:HIS114 4.2 8.8 1.0
CD2 A:HIS116 4.2 9.9 1.0
CB A:CYS198 4.3 10.7 1.0
SG A:CYS198 4.4 15.3 1.0
OD2 A:ASP118 4.5 17.5 1.0
H A:HIS116 4.5 10.2 1.0
CG A:ASP118 4.6 10.9 1.0
HD22 A:ASN210 4.7 49.5 1.0
HB3 A:SER180 4.7 10.6 1.0
HE A:ARG119 4.8 13.3 1.0
HG2 A:ARG119 4.8 12.1 1.0
CA A:HIS116 4.8 7.8 1.0
HD1 A:HIS114 4.9 11.4 1.0
HD1 A:HIS179 4.9 13.2 1.0
HG3 A:ARG119 4.9 12.1 1.0
HE2 A:HIS116 4.9 14.3 1.0

Zinc binding site 2 out of 3 in 5n5g

Go back to Zinc Binding Sites List in 5n5g
Zinc binding site 2 out of 3 in the Crystal Structure of Di-Zinc Metallo-Beta-Lactamase Vim-1


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 Di-Zinc Metallo-Beta-Lactamase Vim-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:24.6
occ:0.73
O A:HOH555 2.1 21.7 1.0
OD2 A:ASP118 2.2 17.5 1.0
O A:HOH533 2.2 14.7 1.0
NE2 A:HIS240 2.2 13.2 1.0
SG A:CYS198 2.5 15.3 1.0
HH21 A:ARG119 3.0 24.5 1.0
CE1 A:HIS240 3.2 12.9 1.0
CD2 A:HIS240 3.2 14.2 1.0
CG A:ASP118 3.3 10.9 1.0
HE1 A:HIS240 3.3 15.5 1.0
HD2 A:HIS240 3.3 17.1 1.0
HE A:ARG119 3.4 13.3 1.0
CB A:CYS198 3.5 10.7 1.0
ZN A:ZN301 3.6 13.3 0.9
OD1 A:ASP118 3.6 13.8 1.0
HE1 A:HIS114 3.7 14.1 1.0
NH2 A:ARG119 3.9 20.4 1.0
NE A:ARG119 4.2 11.1 1.0
NE2 A:HIS179 4.2 10.3 1.0
ND1 A:HIS240 4.3 13.0 1.0
CG A:HIS240 4.3 12.2 1.0
HE1 A:HIS179 4.3 13.9 1.0
CE1 A:HIS114 4.4 11.7 1.0
HH22 A:ARG119 4.5 24.5 1.0
CE1 A:HIS179 4.5 11.6 1.0
O A:HOH595 4.5 24.8 1.0
NE2 A:HIS114 4.5 10.5 1.0
CZ A:ARG119 4.5 11.4 1.0
CB A:ASP118 4.6 9.6 1.0
HB2 A:ASP118 4.6 11.5 1.0
CA A:CYS198 4.8 10.3 1.0
HB3 A:ASP118 4.8 11.5 1.0
O A:HOH598 4.8 33.5 1.0
HA3 A:GLY239 4.8 11.4 1.0
HG2 A:ARG119 4.9 12.1 1.0

Zinc binding site 3 out of 3 in 5n5g

Go back to Zinc Binding Sites List in 5n5g
Zinc binding site 3 out of 3 in the Crystal Structure of Di-Zinc Metallo-Beta-Lactamase Vim-1


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 Di-Zinc Metallo-Beta-Lactamase Vim-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:10.5
occ:0.54
O A:HOH417 2.2 28.4 1.0
O A:HOH467 2.3 16.7 1.0
O22 A:BCN304 2.4 10.5 1.0
O A:HOH551 2.4 17.8 1.0
O4 A:BCN304 2.5 14.7 1.0
O A:HOH405 2.5 41.1 1.0
O6 A:BCN304 2.5 20.4 1.0
O A:HOH549 2.6 21.0 1.0
N1 A:BCN304 2.7 15.0 1.0
C2 A:BCN304 3.3 12.2 1.0
C1 A:BCN304 3.4 14.0 1.0
C3 A:BCN304 3.4 16.1 1.0
C6 A:BCN304 3.4 19.0 1.0
C4 A:BCN304 3.5 15.6 1.0
C5 A:BCN304 3.5 17.5 1.0
HA2 A:GLY88 3.6 11.3 1.0
H A:ALA89 3.8 10.6 1.0
HA3 A:GLY88 4.3 11.3 1.0
OE2 A:GLU149 4.3 17.8 1.0
OD2 A:ASP117 4.4 12.1 1.0
CA A:GLY88 4.4 9.4 1.0
O21 A:BCN304 4.5 12.9 1.0
O A:HOH671 4.5 22.8 1.0
OD1 A:ASP117 4.5 10.9 1.0
N A:ALA89 4.6 8.8 1.0
O A:HOH594 4.6 46.7 1.0
HB2 A:ALA89 4.8 13.2 1.0
CG A:ASP117 4.9 9.1 1.0
HB3 A:ALA89 5.0 13.2 1.0
HA3 A:GLY121 5.0 9.0 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 06:34:26 2020

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