Atomistry » Silver » PDB 7sdv-8dx7 » 7waa
Atomistry »
  Silver »
    PDB 7sdv-8dx7 »
      7waa »

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

Go back to Silver Binding Sites List in 7waa
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

Go back to Silver Binding Sites List in 7waa
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

Go back to Silver Binding Sites List in 7waa
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

Go back to Silver Binding Sites List in 7waa
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

Go back to Silver Binding Sites List in 7waa
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

Go back to Silver Binding Sites List in 7waa
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

Go back to Silver Binding Sites List in 7waa
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

Go back to Silver Binding Sites List in 7waa
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

Go back to Silver Binding Sites List in 7waa
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

Go back to Silver Binding Sites List in 7waa
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy