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Zinc in PDB 5lrm: Structure of Di-Zinc Mcr-1 in P41212 Space Group

Protein crystallography data

The structure of Structure of Di-Zinc Mcr-1 in P41212 Space Group, PDB code: 5lrm was solved by P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.09 / 1.75
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 49.044, 49.044, 244.253, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Di-Zinc Mcr-1 in P41212 Space Group (pdb code 5lrm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Di-Zinc Mcr-1 in P41212 Space Group, PDB code: 5lrm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5lrm

Go back to Zinc Binding Sites List in 5lrm
Zinc binding site 1 out of 2 in the Structure of Di-Zinc Mcr-1 in P41212 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Di-Zinc Mcr-1 in P41212 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:35.2
occ:1.00
OD1 A:ASP465 2.0 35.4 1.0
OE2 A:GLU246 2.0 36.3 1.0
OG1 A:THR285 2.1 39.3 1.0
NE2 A:HIS466 2.1 35.7 1.0
OE1 A:GLU246 2.6 35.1 1.0
CD A:GLU246 2.6 33.0 1.0
CG A:ASP465 2.8 33.2 1.0
CD2 A:HIS466 2.9 31.2 1.0
OD2 A:ASP465 3.0 33.0 1.0
CE1 A:HIS466 3.1 32.6 1.0
CB A:THR285 3.1 38.5 1.0
N A:THR285 3.3 33.3 1.0
CA A:THR285 3.3 31.8 1.0
CG2 A:THR285 3.6 33.6 1.0
CG A:HIS466 4.0 32.1 1.0
O A:HOH765 4.1 36.1 1.0
CG A:GLU246 4.1 34.0 1.0
ND1 A:HIS466 4.1 33.1 1.0
C A:SER284 4.1 35.9 1.0
OG1 A:THR247 4.2 34.4 1.0
CB A:ASP465 4.2 31.5 1.0
CD2 A:HIS395 4.3 40.4 1.0
O A:HOH744 4.4 44.3 1.0
ZN A:ZN602 4.5 37.2 1.0
N A:THR247 4.5 27.6 1.0
NE2 A:HIS478 4.6 38.4 1.0
CA A:GLU246 4.7 30.0 1.0
O A:SER284 4.8 33.9 1.0
CA A:SER284 4.8 34.3 1.0
NE2 A:HIS395 4.8 42.2 1.0
CB A:GLU246 4.8 34.0 1.0
C A:THR285 4.8 34.6 1.0
CD2 A:HIS478 5.0 37.1 1.0

Zinc binding site 2 out of 2 in 5lrm

Go back to Zinc Binding Sites List in 5lrm
Zinc binding site 2 out of 2 in the Structure of Di-Zinc Mcr-1 in P41212 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Di-Zinc Mcr-1 in P41212 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:37.2
occ:1.00
NE2 A:HIS395 1.9 42.2 1.0
NE2 A:HIS478 2.0 38.4 1.0
CE1 A:HIS395 2.7 43.6 1.0
CE1 A:HIS478 2.9 34.1 1.0
CD2 A:HIS395 3.0 40.4 1.0
CD2 A:HIS478 3.1 37.1 1.0
ND1 A:HIS395 3.9 49.0 1.0
OG1 A:THR285 3.9 39.3 1.0
CG A:HIS395 4.0 41.9 1.0
ND1 A:HIS478 4.1 36.3 1.0
CG A:HIS478 4.2 36.0 1.0
O A:HOH808 4.4 43.6 1.0
ZN A:ZN601 4.5 35.2 1.0
O A:HOH744 4.5 44.3 1.0
OE2 A:GLU246 4.5 36.3 1.0
NE2 A:HIS466 4.6 35.7 1.0
O A:HOH826 4.7 39.6 1.0
CE1 A:HIS466 4.7 32.6 1.0
N A:THR285 4.8 33.3 1.0
O A:HOH841 4.8 60.4 1.0

Reference:

P.Hinchliffe, Q.E.Yang, E.Portal, T.Young, H.Li, C.L.Tooke, M.J.Carvalho, N.G.Paterson, J.Brem, P.R.Niumsup, U.Tansawai, L.Lei, M.Li, Z.Shen, Y.Wang, C.J.Schofield, A.J.Mulholland, J.Shen, N.Fey, T.R.Walsh, J.Spencer. Insights Into the Mechanistic Basis of Plasmid-Mediated Colistin Resistance From Crystal Structures of the Catalytic Domain of Mcr-1. Sci Rep V. 7 39392 2017.
ISSN: ESSN 2045-2322
PubMed: 28059088
DOI: 10.1038/SREP39392
Page generated: Wed Dec 16 06:30:34 2020

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