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Silver in PDB 7waa: Crystal Structure of Mcr-1-S Treated By AGNO3

Protein crystallography data

The structure of Crystal Structure of Mcr-1-S Treated By AGNO3, PDB code: 7waa was solved by Q.Zhang, M.Wang, H.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.21 / 1.58
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.2, 84.42, 81.76, 90, 98.67, 90
R / Rfree (%) 19.3 / 21.3

Silver Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Silver atom in the Crystal Structure of Mcr-1-S Treated By AGNO3 (pdb code 7waa). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 19 binding sites of Silver where determined in the Crystal Structure of Mcr-1-S Treated By AGNO3, PDB code: 7waa:
Jump to Silver binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Silver binding site 1 out of 19 in 7waa

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Silver binding site 1 out of 19 in the Crystal Structure of Mcr-1-S Treated By AGNO3


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 1 of Crystal Structure of Mcr-1-S Treated By AGNO3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag401

b:27.0
occ:0.74
 OD1 A:ASP249 2.1 25.4 1.0
OE2 A:GLU30 2.1 26.8 1.0
NE2 A:HIS250 2.1 25.3 1.0
OG1 A:TPO69 2.2 34.1 1.0
OE1 A:GLU30 2.5 25.1 1.0
O2P A:TPO69 2.5 34.6 1.0
CD A:GLU30 2.6 25.3 1.0
CG A:ASP249 3.0 25.9 1.0
P A:TPO69 3.0 35.2 1.0
CD2 A:HIS250 3.0 26.3 1.0
CE1 A:HIS250 3.1 25.7 1.0
OD2 A:ASP249 3.2 27.2 1.0
CB A:TPO69 3.3 34.5 1.0
N A:TPO69 3.6 35.5 1.0
CA A:TPO69 3.7 34.8 1.0
O1P A:TPO69 3.8 36.4 1.0
AG A:AG403 3.8 28.4 0.4
CG2 A:TPO69 3.9 33.7 1.0
NE2 A:HIS179 4.1 37.0 1.0
CG A:HIS250 4.1 26.0 1.0
CG A:GLU30 4.1 24.6 1.0
ND1 A:HIS250 4.1 26.3 1.0
O3P A:TPO69 4.2 35.8 1.0
NE2 A:HIS262 4.3 30.8 1.0
OG1 A:THR31 4.3 26.8 1.0
CB A:ASP249 4.4 24.6 1.0
C A:SER68 4.4 29.8 1.0
CD2 A:HIS179 4.6 32.7 1.0
N A:THR31 4.6 24.2 1.0
CA A:GLU30 4.6 23.5 1.0
CE1 A:HIS262 4.7 31.4 1.0
CB A:GLU30 4.8 23.4 1.0
CE1 A:HIS179 4.9 38.7 1.0
CD2 A:HIS262 4.9 32.2 1.0
CA A:SER68 5.0 31.1 1.0

Silver binding site 2 out of 19 in 7waa

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Silver binding site 2 out of 19 in the Crystal Structure of Mcr-1-S Treated By AGNO3


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 2 of Crystal Structure of Mcr-1-S Treated By AGNO3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag402

b:38.0
occ:0.81
 NE2 A:HIS36 2.2 29.5 1.0
O A:HOH553 2.2 30.0 1.0
CD2 A:HIS36 3.1 29.5 1.0
CE1 A:HIS36 3.2 28.6 1.0
NH2 A:ARG33 3.3 31.8 1.0
CZ A:ARG33 3.6 33.3 1.0
NH1 A:ARG33 3.9 32.6 1.0
OE2 A:GLU256 4.1 38.5 1.0
NE A:ARG33 4.2 30.9 1.0
ND1 A:HIS36 4.3 27.9 1.0
CD1 A:ILE212 4.3 37.7 1.0
CG A:HIS36 4.3 27.1 1.0
CD1 A:LEU254 4.3 31.3 1.0
OD2 A:ASP35 4.5 34.8 1.0
OD1 A:ASP35 4.8 31.7 1.0
CE1 A:TYR42 4.8 30.4 1.0
CG A:ASP35 4.9 32.6 1.0

Silver binding site 3 out of 19 in 7waa

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Silver binding site 3 out of 19 in the Crystal Structure of Mcr-1-S Treated By AGNO3


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 3 of Crystal Structure of Mcr-1-S Treated By AGNO3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag403

b:28.4
occ:0.36
 NE2 A:HIS174 2.4 26.5 1.0
OD1 A:ASP249 2.7 25.4 1.0
OE1 A:GLU30 2.7 25.1 1.0
O A:GLY29 3.2 23.2 1.0
CG A:ASP249 3.2 25.9 1.0
CD2 A:HIS174 3.2 25.5 1.0
CE1 A:HIS174 3.4 26.3 1.0
CG2 A:TPO69 3.5 33.7 1.0
ND2 A:ASN113 3.7 26.8 1.0
CD A:GLU30 3.7 25.3 1.0
CB A:ASP249 3.7 24.6 1.0
AG A:AG401 3.8 27.0 0.7
OD2 A:ASP249 3.9 27.2 1.0
CG2 A:VAL73 3.9 26.7 1.0
CB A:GLU30 4.1 23.4 1.0
C A:GLY29 4.2 22.8 1.0
CA A:GLU30 4.2 23.5 1.0
CG A:ASN113 4.2 27.5 1.0
OG1 A:TPO69 4.3 34.1 1.0
CG1 A:VAL28 4.3 24.1 1.0
OE2 A:GLU30 4.4 26.8 1.0
CG A:GLU30 4.4 24.6 1.0
CG A:HIS174 4.4 25.9 1.0
CB A:TPO69 4.5 34.5 1.0
ND1 A:HIS174 4.5 26.5 1.0
OD1 A:ASN113 4.5 27.8 1.0
N A:GLU30 4.7 22.2 1.0
O A:VAL28 4.7 22.9 1.0
O A:GLN175 4.9 25.4 1.0
CA A:TPO69 4.9 34.8 1.0

Silver binding site 4 out of 19 in 7waa

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Silver binding site 4 out of 19 in the Crystal Structure of Mcr-1-S Treated By AGNO3


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 4 of Crystal Structure of Mcr-1-S Treated By AGNO3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag404

b:35.0
occ:0.66
 O A:HOH554 1.9 30.0 1.0
SD A:MET176 2.1 31.7 1.0
ND1 A:HIS179 2.4 38.8 1.0
CG A:HIS179 3.2 33.3 1.0
CG A:MET176 3.2 29.9 1.0
CB A:HIS179 3.3 30.8 1.0
CE1 A:HIS179 3.5 38.7 1.0
CE A:MET176 3.7 33.2 1.0
O A:MET176 3.8 26.6 1.0
CA A:MET176 3.8 25.6 1.0
CB A:MET176 4.0 27.4 1.0
O A:ASN113 4.1 30.7 1.0
C A:MET176 4.3 25.4 1.0
ND2 A:ASN113 4.3 26.8 1.0
CA A:ASN113 4.4 27.5 1.0
CD2 A:HIS179 4.4 32.7 1.0
NE2 A:HIS179 4.5 37.0 1.0
CG A:ASN113 4.6 27.5 1.0
O A:ASN112 4.6 26.8 1.0
C A:ASN113 4.7 29.3 1.0
CA A:HIS179 4.8 30.5 1.0
CB A:ASN113 5.0 26.7 1.0

Silver binding site 5 out of 19 in 7waa

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Silver binding site 5 out of 19 in the Crystal Structure of Mcr-1-S Treated By AGNO3


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 5 of Crystal Structure of Mcr-1-S Treated By AGNO3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag405

b:50.0
occ:0.83
 O A:HOH557 1.9 52.0 1.0
ND1 A:HIS6 2.2 36.3 1.0
CE1 A:HIS6 3.1 36.9 1.0
CG A:HIS6 3.1 36.2 1.0
CB A:HIS6 3.4 35.4 1.0
CA A:HIS6 3.6 35.6 1.0
O A:TYR5 3.7 41.9 1.0
CD A:LYS316 4.2 47.3 1.0
NE2 A:HIS6 4.3 36.2 1.0
CD2 A:HIS6 4.3 35.2 1.0
CE A:LYS316 4.3 48.2 1.0
O A:HIS6 4.4 35.3 1.0
N A:HIS6 4.5 34.3 1.0
C A:TYR5 4.5 41.8 1.0
C A:HIS6 4.5 33.6 1.0
NZ A:LYS316 4.6 51.2 1.0

Silver binding site 6 out of 19 in 7waa

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Silver binding site 6 out of 19 in the Crystal Structure of Mcr-1-S Treated By AGNO3


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 6 of Crystal Structure of Mcr-1-S Treated By AGNO3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag406

b:55.5
occ:0.64
 O A:HOH556 2.1 46.1 1.0
ND1 A:HIS208 2.2 47.0 1.0
CG A:HIS208 3.1 48.5 1.0
CE1 A:HIS208 3.2 48.0 1.0
CB A:HIS208 3.3 47.8 1.0
N A:GLN209 3.8 46.7 1.0
C A:HIS208 3.9 46.4 1.0
NE2 A:GLN209 4.1 50.3 1.0
CA A:GLN209 4.2 45.7 1.0
CA A:HIS208 4.2 47.6 1.0
CD2 A:HIS208 4.2 46.6 1.0
NE2 A:HIS208 4.3 47.7 1.0
O A:HIS208 4.4 44.6 1.0
CB A:GLN209 4.6 47.2 1.0
CG1 A:ILE212 4.7 37.0 1.0
CD A:GLN209 4.8 49.4 1.0

Silver binding site 7 out of 19 in 7waa

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Silver binding site 7 out of 19 in the Crystal Structure of Mcr-1-S Treated By AGNO3


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 7 of Crystal Structure of Mcr-1-S Treated By AGNO3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag407

b:46.8
occ:0.59
 O A:HOH551 2.1 45.2 1.0
SD A:MET291 2.3 38.3 1.0
O A:ILE324 3.3 32.5 1.0
CE A:MET291 3.4 38.7 1.0
CG A:MET291 3.4 35.0 1.0
CA A:ARG325 3.6 43.8 1.0
C A:ILE324 3.9 32.3 1.0
N A:ARG325 4.1 40.6 1.0
NH1 A:ARG325 4.3 49.4 1.0
CZ A:ARG325 4.3 55.4 1.0
OXT A:ARG325 4.4 46.2 1.0
NH2 A:ARG325 4.4 53.5 1.0
C A:ARG325 4.4 44.4 1.0
CB A:ARG325 4.4 45.5 1.0
O A:ALA322 4.5 28.5 1.0
CG A:ARG325 4.6 47.6 1.0
N A:ALA322 4.8 27.8 1.0
NE A:ARG325 4.8 55.3 1.0
CB A:MET291 4.8 35.0 1.0

Silver binding site 8 out of 19 in 7waa

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Silver binding site 8 out of 19 in the Crystal Structure of Mcr-1-S Treated By AGNO3


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 8 of Crystal Structure of Mcr-1-S Treated By AGNO3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag408

b:56.2
occ:0.60
 ND1 A:HIS236 2.1 36.0 1.0
O A:HOH558 2.8 70.0 1.0
CE1 A:HIS236 3.0 36.7 1.0
CG A:HIS236 3.2 35.6 1.0
CB A:HIS236 3.6 34.8 1.0
CA A:HIS236 3.7 34.6 1.0
CE1 A:TYR240 3.9 36.5 1.0
NE2 A:HIS236 4.1 36.4 1.0
CD1 A:TYR240 4.1 35.9 1.0
CD2 A:HIS236 4.2 35.0 1.0
O A:THR235 4.3 36.0 1.0
O A:HIS236 4.6 34.7 1.0
CB A:ALA239 4.6 42.5 1.0
CG1 A:VAL161 4.6 29.8 1.0
C A:HIS236 4.6 33.7 1.0
N A:HIS236 4.7 33.1 1.0
C A:THR235 4.9 34.5 1.0

Silver binding site 9 out of 19 in 7waa

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Silver binding site 9 out of 19 in the Crystal Structure of Mcr-1-S Treated By AGNO3


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 9 of Crystal Structure of Mcr-1-S Treated By AGNO3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag409

b:45.0
occ:0.42
 OD2 A:ASP111 1.9 27.1 1.0
ND1 A:HIS174 1.9 26.5 1.0
O A:ASP115 2.0 29.8 1.0
CE1 A:HIS174 2.6 26.3 1.0
CG A:ASP111 2.6 25.8 1.0
C A:ASP115 2.7 30.7 1.0
OD1 A:ASP111 2.8 27.4 1.0
CG A:HIS174 3.1 25.9 1.0
N A:ASP115 3.3 32.9 1.0
CA A:ASP115 3.3 33.0 1.0
N A:SER116 3.6 29.3 1.0
CB A:HIS174 3.7 25.2 1.0
NE2 A:HIS174 3.8 26.5 1.0
OG A:SER114 3.8 30.0 1.0
NE1 A:TRP109 3.9 23.6 1.0
CA A:SER116 3.9 28.3 1.0
C A:SER114 3.9 30.0 1.0
N A:SER114 4.0 29.3 1.0
CD2 A:HIS174 4.0 25.5 1.0
CZ2 A:TRP109 4.0 22.3 1.0
CB A:ASP111 4.0 25.8 1.0
CB A:ASN113 4.1 26.7 1.0
CE2 A:TRP109 4.3 23.2 1.0
OD1 A:ASN113 4.4 27.8 1.0
CA A:SER114 4.4 30.6 1.0
CG A:ASN113 4.6 27.5 1.0
O A:SER114 4.6 31.7 1.0
CB A:SER114 4.7 30.7 1.0
CB A:ASP115 4.8 33.9 1.0
C A:SER116 4.8 28.8 1.0
CA A:ASP111 4.9 25.3 1.0
C A:ASN113 5.0 29.3 1.0
CA A:ASN113 5.0 27.5 1.0
CB A:SER116 5.0 27.8 1.0

Silver binding site 10 out of 19 in 7waa

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Silver binding site 10 out of 19 in the Crystal Structure of Mcr-1-S Treated By AGNO3


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 10 of Crystal Structure of Mcr-1-S Treated By AGNO3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ag401

b:35.9
occ:0.75
 OE2 B:GLU30 2.1 36.5 1.0
NE2 B:HIS250 2.2 32.1 1.0
OD2 B:ASP249 2.2 36.5 1.0
OG1 B:TPO69 2.2 44.1 1.0
O2P B:TPO69 2.4 44.0 1.0
OE1 B:GLU30 2.5 35.1 1.0
CD B:GLU30 2.6 33.6 1.0
P B:TPO69 2.9 45.3 1.0
CE1 B:HIS250 3.0 33.5 1.0
CG B:ASP249 3.0 33.5 1.0
CD2 B:HIS250 3.1 32.1 1.0
OD1 B:ASP249 3.2 33.7 1.0
CB B:TPO69 3.4 45.1 1.0
N B:TPO69 3.6 45.1 1.0
CA B:TPO69 3.7 44.9 1.0
AG B:AG403 3.8 39.4 0.5
O1P B:TPO69 3.8 46.6 1.0
ND1 B:HIS250 4.0 34.0 1.0
O3P B:TPO69 4.1 46.4 1.0
CG2 B:TPO69 4.1 44.7 1.0
CG B:HIS250 4.1 33.3 1.0
CG B:GLU30 4.1 33.9 1.0
OG1 B:THR31 4.2 36.0 1.0
NE2 B:HIS179 4.2 49.8 1.0
C B:SER68 4.4 38.7 1.0
CB B:ASP249 4.4 32.0 1.0
NE2 B:HIS262 4.5 41.3 1.0
N B:THR31 4.6 32.1 1.0
CD2 B:HIS179 4.7 48.1 1.0
CA B:GLU30 4.7 32.0 1.0
CE1 B:HIS262 4.7 41.5 1.0
CB B:GLU30 4.8 32.1 1.0
CA B:SER68 5.0 40.0 1.0

Reference:

Q.Zhang, R.Wang, M.Wang, C.Liu, M.Koohi-Moghadam, H.Wang, P.L.Ho, H.Li, H.Sun. Re-Sensitization of Mcr Carrying Multidrug Resistant Bacteria to Colistin By Silver. Proc.Natl.Acad.Sci.Usa V. 119 17119 2022.
ISSN: ESSN 1091-6490
PubMed: 35263219
DOI: 10.1073/PNAS.2119417119
Page generated: Wed Jul 10 09:03:06 2024

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