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Silver in PDB 5ku5: Crystal Structure of Cuss Sensor Domain with Silver Bound

Enzymatic activity of Crystal Structure of Cuss Sensor Domain with Silver Bound

All present enzymatic activity of Crystal Structure of Cuss Sensor Domain with Silver Bound:
2.7.13.3;

Protein crystallography data

The structure of Crystal Structure of Cuss Sensor Domain with Silver Bound, PDB code: 5ku5 was solved by T.Affandi, A.V.Issaian, M.M.Mcevoy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.29 / 2.15
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 35.225, 96.289, 203.664, 90.00, 90.00, 90.00
R / Rfree (%) 25 / 28.6

Silver Binding Sites:

The binding sites of Silver atom in the Crystal Structure of Cuss Sensor Domain with Silver Bound (pdb code 5ku5). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 8 binding sites of Silver where determined in the Crystal Structure of Cuss Sensor Domain with Silver Bound, PDB code: 5ku5:
Jump to Silver binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Silver binding site 1 out of 8 in 5ku5

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Silver binding site 1 out of 8 in the Crystal Structure of Cuss Sensor Domain with Silver Bound


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 Cuss Sensor Domain with Silver Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag201

b:24.6
occ:1.00
 ND1 A:HIS145 2.5 25.5 1.0
SD A:MET133 2.5 26.3 1.0
O A:SER84 2.5 26.5 1.0
SD A:MET135 2.6 26.2 1.0
CE A:MET133 3.3 26.2 1.0
CG A:MET133 3.3 26.4 1.0
CG A:HIS145 3.4 26.2 1.0
CE1 A:HIS145 3.4 25.3 1.0
CE A:MET135 3.5 26.4 1.0
CG A:MET135 3.5 27.0 1.0
C A:SER84 3.6 26.3 1.0
CB A:HIS145 3.6 26.8 1.0
CB A:MET133 3.7 26.6 1.0
CA A:ASN85 3.9 25.1 1.0
N A:ASN85 4.2 25.7 1.0
NE2 A:HIS145 4.5 25.3 1.0
CH2 A:TRP148 4.5 23.0 1.0
CD2 A:HIS145 4.6 25.6 1.0
C A:ASN85 4.7 24.4 1.0
CA A:SER84 4.8 27.0 1.0
O A:MET133 4.8 28.6 1.0
O A:MET134 4.9 29.1 1.0
CB A:ASN85 4.9 25.3 1.0
CB A:MET135 5.0 27.4 1.0
CA A:MET133 5.0 27.1 1.0

Silver binding site 2 out of 8 in 5ku5

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Silver binding site 2 out of 8 in the Crystal Structure of Cuss Sensor Domain with Silver Bound


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 Cuss Sensor Domain with Silver Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag202

b:26.0
occ:1.00
 NE2 B:HIS42 2.4 27.8 1.0
ND1 A:HIS176 2.5 24.9 1.0
NE2 B:GLN46 3.0 30.2 1.0
CE1 A:HIS176 3.2 24.7 1.0
CE1 A:PHE43 3.2 26.8 1.0
CD2 B:HIS42 3.3 27.3 1.0
CZ A:PHE43 3.3 26.4 1.0
CE1 B:HIS42 3.4 27.7 1.0
CD1 A:PHE43 3.4 26.8 1.0
CG A:HIS176 3.5 24.8 1.0
CA A:HIS176 3.5 25.6 1.0
CE2 A:PHE43 3.6 26.3 1.0
O B:HOH311 3.6 27.2 1.0
CG A:PHE43 3.8 26.4 1.0
CD B:GLN46 3.9 29.6 1.0
CD2 A:PHE43 3.9 26.4 1.0
CB A:HIS176 3.9 25.2 1.0
N A:HIS176 3.9 25.0 1.0
O A:PHE175 4.3 24.9 1.0
NE2 A:HIS176 4.3 24.7 1.0
C A:PHE175 4.3 24.6 1.0
CG B:HIS42 4.4 27.4 1.0
ND1 B:HIS42 4.4 27.4 1.0
CD2 A:HIS176 4.4 24.9 1.0
CG B:GLN46 4.5 29.1 1.0
OE1 A:GLN46 4.5 29.7 1.0
OE1 B:GLN46 4.6 29.5 1.0
C A:HIS176 4.7 26.4 1.0
CD2 A:PHE175 4.7 25.4 1.0
CB A:PHE43 4.8 26.1 1.0
O A:HIS176 4.8 26.7 1.0
O A:HOH358 4.9 24.4 1.0
CB A:TYR179 5.0 31.6 1.0

Silver binding site 3 out of 8 in 5ku5

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Silver binding site 3 out of 8 in the Crystal Structure of Cuss Sensor Domain with Silver Bound


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 Cuss Sensor Domain with Silver Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ag201

b:29.4
occ:1.00
 SD B:MET133 2.5 29.9 1.0
ND1 B:HIS145 2.6 33.2 1.0
SD B:MET135 2.6 32.9 1.0
O B:SER84 2.8 29.5 1.0
CG B:HIS145 3.3 33.5 1.0
CG B:MET133 3.4 30.4 1.0
CE B:MET133 3.4 29.7 1.0
CE1 B:HIS145 3.5 33.5 1.0
CG B:MET135 3.5 33.5 1.0
CB B:HIS145 3.6 33.7 1.0
CE B:MET135 3.7 33.0 1.0
CB B:MET133 3.7 30.5 1.0
C B:SER84 3.9 29.0 1.0
CA B:ASN85 3.9 27.1 1.0
N B:ASN85 4.3 27.9 1.0
CD2 B:HIS145 4.4 33.1 1.0
NE2 B:HIS145 4.4 32.8 1.0
CH2 B:TRP148 4.4 26.2 1.0
C B:ASN85 4.6 26.2 1.0
O B:MET134 4.8 34.9 1.0
CB B:ASN85 4.8 27.4 1.0
N B:VAL86 4.9 25.7 1.0
O B:MET133 4.9 31.9 1.0
CB B:MET135 4.9 33.9 1.0
CZ3 B:TRP148 5.0 25.9 1.0

Silver binding site 4 out of 8 in 5ku5

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Silver binding site 4 out of 8 in the Crystal Structure of Cuss Sensor Domain with Silver Bound


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 Cuss Sensor Domain with Silver Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ag202

b:25.0
occ:1.00
 NE2 A:HIS42 2.4 25.1 1.0
ND1 B:HIS176 2.5 27.2 1.0
CE1 B:PHE43 3.2 27.1 1.0
NE2 A:GLN46 3.2 28.7 1.0
CE1 B:HIS176 3.2 27.1 1.0
CZ B:PHE43 3.3 26.8 1.0
CD2 A:HIS42 3.3 24.8 1.0
CE1 A:HIS42 3.3 25.0 1.0
CA B:HIS176 3.5 28.0 1.0
CG B:HIS176 3.5 27.5 1.0
CD1 B:PHE43 3.5 27.1 1.0
CE2 B:PHE43 3.7 26.8 1.0
N B:HIS176 3.8 27.2 1.0
CD A:GLN46 3.8 28.6 1.0
CG B:PHE43 3.9 26.7 1.0
CB B:HIS176 3.9 27.8 1.0
CD2 B:PHE43 3.9 26.6 1.0
O A:HOH326 3.9 27.9 1.0
O B:PHE175 4.2 26.9 1.0
C B:PHE175 4.2 26.8 1.0
NE2 B:HIS176 4.3 27.4 1.0
CG A:GLN46 4.4 27.3 1.0
ND1 A:HIS42 4.4 25.1 1.0
CD2 B:HIS176 4.4 27.4 1.0
CG A:HIS42 4.5 24.9 1.0
OE1 A:GLN46 4.5 29.7 1.0
CD2 B:PHE175 4.5 28.5 1.0
OE1 B:GLN46 4.6 29.5 1.0
C B:HIS176 4.7 28.9 1.0
O B:HIS176 4.9 29.2 1.0
CB B:PHE43 4.9 26.6 1.0
O B:HOH339 4.9 23.9 1.0

Silver binding site 5 out of 8 in 5ku5

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Silver binding site 5 out of 8 in the Crystal Structure of Cuss Sensor Domain with Silver Bound


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 Cuss Sensor Domain with Silver Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ag201

b:25.3
occ:1.00
 SD C:MET133 2.3 30.8 1.0
ND1 C:HIS145 2.4 27.5 1.0
O C:SER84 2.5 24.8 1.0
SD C:MET135 2.6 26.9 1.0
CE C:MET133 3.2 30.6 1.0
CG C:MET133 3.3 30.3 1.0
CG C:HIS145 3.3 28.1 1.0
CE1 C:HIS145 3.3 27.5 1.0
CG C:MET135 3.5 27.8 1.0
C C:SER84 3.5 24.8 1.0
CB C:HIS145 3.6 28.8 1.0
CE C:MET135 3.6 27.0 1.0
CB C:MET133 3.7 30.0 1.0
CA C:ASN85 4.0 23.8 1.0
N C:ASN85 4.2 24.2 1.0
NE2 C:HIS145 4.4 27.2 1.0
CD2 C:HIS145 4.4 27.5 1.0
CH2 C:TRP148 4.5 24.5 1.0
CA C:SER84 4.7 25.3 1.0
O C:MET133 4.8 30.5 1.0
O C:MET134 4.8 33.8 1.0
C C:ASN85 4.8 23.5 1.0
CA C:MET133 4.9 29.8 1.0
CB C:MET135 5.0 28.8 1.0
C C:MET133 5.0 30.8 1.0

Silver binding site 6 out of 8 in 5ku5

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Silver binding site 6 out of 8 in the Crystal Structure of Cuss Sensor Domain with Silver Bound


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 Cuss Sensor Domain with Silver Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ag202

b:27.2
occ:1.00
 NE2 D:HIS42 2.3 28.2 1.0
ND1 C:HIS176 2.5 27.5 1.0
CE1 D:HIS42 3.1 28.2 1.0
CE1 C:HIS176 3.2 27.1 1.0
CE1 C:PHE43 3.3 25.7 1.0
CZ C:PHE43 3.4 25.6 1.0
CD2 D:HIS42 3.4 28.4 1.0
CA C:HIS176 3.4 28.4 1.0
CG C:HIS176 3.4 27.3 1.0
CD1 C:PHE43 3.6 25.9 1.0
NE2 D:GLN46 3.6 30.5 1.0
CE2 C:PHE43 3.7 25.3 1.0
CB C:HIS176 3.9 27.8 1.0
N C:HIS176 3.9 27.9 1.0
CG C:PHE43 3.9 25.8 1.0
CD2 C:PHE43 4.0 25.2 1.0
O C:PHE175 4.2 27.7 1.0
O D:HOH308 4.2 34.2 1.0
C C:PHE175 4.3 27.9 1.0
NE2 C:HIS176 4.3 26.7 1.0
ND1 D:HIS42 4.3 28.4 1.0
CD2 C:PHE175 4.3 29.1 1.0
CD2 C:HIS176 4.4 27.1 1.0
CD D:GLN46 4.5 29.9 1.0
CG D:HIS42 4.5 28.6 1.0
OE1 C:GLN46 4.6 29.8 1.0
C C:HIS176 4.6 29.3 1.0
O C:HIS176 4.7 30.2 1.0
OE1 D:GLN46 4.8 30.2 1.0
CE2 C:PHE175 4.9 29.5 1.0
CB C:PHE43 4.9 25.9 1.0

Silver binding site 7 out of 8 in 5ku5

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Silver binding site 7 out of 8 in the Crystal Structure of Cuss Sensor Domain with Silver Bound


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 Cuss Sensor Domain with Silver Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ag201

b:28.0
occ:1.00
 NE2 C:HIS42 2.4 27.2 1.0
ND1 D:HIS176 2.5 32.8 1.0
NE2 C:GLN46 3.0 29.0 1.0
CE1 D:PHE43 3.2 29.7 1.0
CE1 D:HIS176 3.2 32.5 1.0
CZ D:PHE43 3.2 29.8 1.0
CE1 C:HIS42 3.3 27.3 1.0
CD2 C:HIS42 3.4 27.4 1.0
CD1 D:PHE43 3.5 29.8 1.0
CA D:HIS176 3.5 33.2 1.0
CG D:HIS176 3.5 33.0 1.0
CE2 D:PHE43 3.6 29.7 1.0
CD C:GLN46 3.7 29.0 1.0
N D:HIS176 3.8 33.0 1.0
CG D:PHE43 3.9 29.3 1.0
CD2 D:PHE43 3.9 29.4 1.0
CB D:HIS176 4.0 33.3 1.0
O C:HOH339 4.0 29.7 1.0
O D:PHE175 4.2 33.8 1.0
C D:PHE175 4.2 32.5 1.0
CG C:GLN46 4.3 28.3 1.0
NE2 D:HIS176 4.3 32.5 1.0
OE1 C:GLN46 4.4 29.8 1.0
ND1 C:HIS42 4.4 27.3 1.0
CG C:HIS42 4.5 27.2 1.0
CD2 D:HIS176 4.5 32.6 1.0
CD2 D:PHE175 4.5 33.0 1.0
C D:HIS176 4.7 33.8 1.0
OE1 D:GLN46 4.7 30.2 1.0
CB D:PHE43 4.9 29.4 1.0
O D:HOH331 4.9 30.3 1.0
O D:HIS176 4.9 33.5 1.0

Silver binding site 8 out of 8 in 5ku5

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Silver binding site 8 out of 8 in the Crystal Structure of Cuss Sensor Domain with Silver Bound


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 Cuss Sensor Domain with Silver Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ag202

b:33.1
occ:1.00
 SD D:MET133 2.2 31.7 1.0
ND1 D:HIS145 2.4 30.2 1.0
SD D:MET135 2.6 36.1 1.0
O D:SER84 2.8 33.8 1.0
CE D:MET133 3.2 32.0 1.0
CE1 D:HIS145 3.3 30.8 1.0
CG D:MET133 3.3 31.6 1.0
CG D:HIS145 3.3 30.6 1.0
CB D:HIS145 3.6 30.8 1.0
CG D:MET135 3.6 36.5 1.0
CE D:MET135 3.7 35.8 1.0
CB D:MET133 3.7 31.7 1.0
C D:SER84 3.7 34.6 1.0
CA D:ASN85 3.9 31.3 1.0
N D:ASN85 4.2 32.3 1.0
NE2 D:HIS145 4.4 30.2 1.0
CD2 D:HIS145 4.4 30.3 1.0
CH2 D:TRP148 4.5 30.0 1.0
C D:ASN85 4.6 30.5 1.0
O D:MET133 4.8 33.6 1.0
CA D:SER84 4.9 36.8 1.0
N D:VAL86 4.9 29.9 1.0
CB D:ASN85 5.0 31.2 1.0
O D:MET134 5.0 37.4 1.0

Reference:

T.Affandi, A.V.Issaian, M.M.Mcevoy. The Structure of the Periplasmic Sensor Domain of the Histidine Kinase Cuss Shows Unusual Metal Ion Coordination at the Dimeric Interface. Biochemistry V. 55 5296 2016.
ISSN: ISSN 0006-2960
PubMed: 27583660
DOI: 10.1021/ACS.BIOCHEM.6B00707
Page generated: Sat Dec 12 01:22:25 2020

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