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Zinc in PDB 5k4p: Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase

Protein crystallography data

The structure of Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase, PDB code: 5k4p was solved by V.Stojanoski, T.Palzkill, B.V.V.Prasad, B.Sankaran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.92 / 1.32
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 59.080, 59.080, 186.680, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 17.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase (pdb code 5k4p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase, PDB code: 5k4p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 5k4p

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Zinc binding site 1 out of 10 in the Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:8.3
occ:1.00
OE2 A:GLU246 2.0 9.7 1.0
OD2 A:ASP465 2.0 7.8 1.0
O2P A:TPO285 2.0 8.5 1.0
NE2 A:HIS466 2.1 7.1 1.0
OE1 A:GLU246 2.5 9.6 1.0
CD A:GLU246 2.6 9.7 1.0
OG1 A:TPO285 2.6 10.0 1.0
CG A:ASP465 2.9 7.8 1.0
P A:TPO285 2.9 8.7 1.0
CE1 A:HIS466 2.9 6.8 1.0
CD2 A:HIS466 3.0 7.3 1.0
OD1 A:ASP465 3.1 7.8 1.0
O1P A:TPO285 3.8 8.5 1.0
CB A:TPO285 3.9 8.2 1.0
N A:TPO285 4.0 7.7 1.0
ND1 A:HIS466 4.0 7.4 1.0
CG A:HIS466 4.1 6.2 1.0
CG A:GLU246 4.1 8.3 1.0
OG1 A:THR247 4.1 10.3 1.0
O A:HOH766 4.1 10.7 1.0
O3P A:TPO285 4.1 11.6 1.0
CA A:TPO285 4.2 8.2 1.0
CB A:ASP465 4.3 6.6 1.0
O A:HOH705 4.3 18.0 1.0
N A:THR247 4.5 7.3 1.0
CG2 A:TPO285 4.5 11.7 1.0
C A:SER284 4.6 6.6 1.0
NE2 A:HIS478 4.6 8.7 1.0
CA A:GLU246 4.6 6.5 1.0
CE1 A:HIS478 4.8 8.7 1.0
CB A:GLU246 4.8 7.9 1.0
C A:GLU246 5.0 6.8 1.0

Zinc binding site 2 out of 10 in 5k4p

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Zinc binding site 2 out of 10 in the Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:8.6
occ:0.88
O3P A:TPO285 1.9 11.6 1.0
NE2 A:HIS395 2.0 9.0 1.0
O A:HOH960 2.0 12.1 1.0
O A:HOH705 2.3 18.0 1.0
O A:HOH984 2.4 28.6 1.0
CE1 A:HIS395 3.0 10.2 1.0
CD2 A:HIS395 3.0 9.6 1.0
P A:TPO285 3.1 8.7 1.0
ZN A:ZN603 3.3 10.1 0.9
O2P A:TPO285 3.4 8.5 1.0
O A:HOH745 3.7 33.4 1.0
O A:HOH975 3.7 9.3 1.0
ND1 A:HIS395 4.1 10.4 1.0
O A:HOH995 4.1 26.1 1.0
O1P A:TPO285 4.1 8.5 1.0
CG A:HIS395 4.1 8.6 1.0
OG1 A:TPO285 4.2 10.0 1.0
OD1 A:ASN329 4.5 17.7 1.0
OE1 A:GLU246 4.7 9.6 1.0
O A:HOH1063 4.8 22.8 1.0
CB A:TPO285 5.0 8.2 1.0

Zinc binding site 3 out of 10 in 5k4p

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Zinc binding site 3 out of 10 in the Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:10.1
occ:0.93
O A:HOH960 1.7 12.1 1.0
O A:HOH975 1.7 9.3 1.0
O A:HOH995 1.8 26.1 1.0
O A:HOH1063 1.8 22.8 1.0
ZN A:ZN602 3.3 8.6 0.9
O3P A:TPO285 3.5 11.6 1.0
O A:HOH1003 3.8 15.0 1.0
O1P A:TPO285 4.0 8.5 1.0
CE1 A:HIS395 4.2 10.2 1.0
NE2 A:HIS395 4.2 9.0 1.0
P A:TPO285 4.3 8.7 1.0
O A:HOH885 4.5 31.4 1.0
O A:HOH984 4.8 28.6 1.0
NE2 A:HIS478 4.8 8.7 1.0
O A:HOH745 4.8 33.4 1.0
O2P A:TPO285 4.9 8.5 1.0

Zinc binding site 4 out of 10 in 5k4p

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Zinc binding site 4 out of 10 in the Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:8.3
occ:0.96
OE2 A:GLU405 1.9 9.2 1.0
CD A:GLU405 2.8 9.2 1.0
OE1 A:GLU405 3.0 9.3 1.0
O A:HOH918 4.1 11.3 1.0
CG A:GLU405 4.2 8.9 1.0
O A:GLU405 4.8 9.4 1.0

Zinc binding site 5 out of 10 in 5k4p

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Zinc binding site 5 out of 10 in the Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn605

b:9.9
occ:0.38
OE2 A:GLU300 1.9 26.6 1.0
CD A:GLU300 2.8 36.0 1.0
OE1 A:GLU300 3.0 32.4 1.0
O A:HOH704 3.8 31.1 1.0
CG A:GLU300 4.2 19.1 1.0

Zinc binding site 6 out of 10 in 5k4p

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Zinc binding site 6 out of 10 in the Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn606

b:16.2
occ:0.50
O A:HOH956 2.1 30.9 1.0
OD2 A:ASP304 2.2 33.1 1.0
CG A:ASP304 3.2 32.0 1.0
ZN A:ZN610 3.3 14.9 0.5
OD1 A:ASP304 3.4 24.6 1.0
O A:HOH1023 3.5 12.8 1.0
O A:HOH971 4.0 22.9 1.0
OD2 A:ASP302 4.1 25.7 1.0
CB A:ASP304 4.6 17.6 1.0
CG A:ASP302 4.6 30.7 1.0
CB A:ASP302 5.0 19.8 1.0

Zinc binding site 7 out of 10 in 5k4p

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Zinc binding site 7 out of 10 in the Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn607

b:14.9
occ:0.52
OD2 A:ASP261 1.8 14.7 1.0
O A:HOH795 2.1 23.9 1.0
CG A:ASP261 2.8 12.5 1.0
CB A:ASP261 3.2 10.3 1.0
OD1 A:ASP261 4.0 13.9 1.0
O A:HOH816 4.3 20.4 1.0
CB A:PRO264 4.6 10.8 1.0
CA A:ASP261 4.7 8.3 1.0

Zinc binding site 8 out of 10 in 5k4p

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Zinc binding site 8 out of 10 in the Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn608

b:13.5
occ:0.64
O A:HOH987 2.0 28.4 1.0
O A:HOH812 2.1 16.8 1.0
O A:HOH1017 2.1 25.5 1.0
O A:HOH808 2.2 17.2 1.0
O A:HOH930 2.2 28.7 1.0
O A:HOH993 2.2 21.4 1.0
O A:HOH985 3.8 44.5 1.0
O A:HOH961 3.9 42.1 1.0
O A:HOH739 4.1 16.2 1.0
O A:GLY320 4.2 11.7 1.0
NZ A:LYS383 4.2 29.6 1.0
OD1 A:ASP317 4.2 15.5 1.0
OG A:SER322 4.3 14.3 1.0
O A:VAL321 4.3 11.3 1.0
O A:HOH746 4.3 24.5 1.0
O A:HOH976 4.4 41.3 1.0
C A:GLY320 4.5 10.2 1.0
CA A:GLY320 4.6 11.3 1.0
O A:ASP317 4.7 10.3 1.0
CA A:SER322 4.7 11.0 1.0
C A:VAL321 4.7 10.2 1.0
N A:SER322 4.9 9.1 1.0

Zinc binding site 9 out of 10 in 5k4p

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Zinc binding site 9 out of 10 in the Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn609

b:8.7
occ:0.38
O A:HOH962 2.0 32.4 1.0
O A:HOH899 2.1 22.0 1.0
O A:HOH719 2.1 19.4 1.0
OD1 A:ASP302 2.2 21.4 1.0
O A:TYR301 2.2 15.5 1.0
CG A:ASP302 3.3 30.7 1.0
C A:TYR301 3.4 15.7 1.0
O A:ASP299 3.8 13.7 1.0
CA A:ASP302 4.0 16.3 1.0
OH A:TYR287 4.0 15.1 1.0
N A:ASP302 4.1 14.4 1.0
OD2 A:ASP302 4.2 25.7 1.0
O A:HOH967 4.2 21.6 1.0
CB A:ASP302 4.2 19.8 1.0
O A:HOH1048 4.3 38.6 1.0
O A:ALA298 4.4 14.9 1.0
N A:TYR301 4.5 11.7 1.0
CA A:TYR301 4.5 10.1 1.0
C A:GLU300 4.6 11.8 1.0
C A:ASP299 4.7 12.1 1.0
O A:GLU300 4.7 14.7 1.0
O A:HOH716 4.9 24.2 1.0

Zinc binding site 10 out of 10 in 5k4p

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Zinc binding site 10 out of 10 in the Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Catalytic Domain of Mcr-1 Phosphoethanolamine Transferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn610

b:14.9
occ:0.48
ZN A:ZN606 3.3 16.2 0.5
OD2 A:ASP302 3.8 25.7 1.0
OD1 A:ASP302 3.8 21.4 1.0
O A:HOH971 3.9 22.9 1.0
O A:HOH956 4.0 30.9 1.0
CG A:ASP302 4.0 30.7 1.0
O A:HOH1023 4.3 12.8 1.0
O A:HOH1048 4.6 38.6 1.0
OD2 A:ASP304 4.6 33.1 1.0
O A:HOH962 4.6 32.4 1.0
O A:HOH967 4.9 21.6 1.0

Reference:

V.Stojanoski, B.Sankaran, B.V.Prasad, L.Poirel, P.Nordmann, T.Palzkill. Structure of the Catalytic Domain of the Colistin Resistance Enzyme Mcr-1. Bmc Biol. V. 14 81 2016.
ISSN: ESSN 1741-7007
PubMed: 27655155
DOI: 10.1186/S12915-016-0303-0
Page generated: Wed Dec 16 06:26:18 2020

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