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Zinc in PDB 5mg5: A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg)

Protein crystallography data

The structure of A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg), PDB code: 5mg5 was solved by T.Pavkov-Keller, N.G.Schmidt, W.Kroutil, K.Gruber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.73 / 3.44
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.793, 229.775, 311.129, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 22.1

Zinc Binding Sites:

The binding sites of Zinc atom in the A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg) (pdb code 5mg5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg), PDB code: 5mg5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5mg5

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Zinc binding site 1 out of 8 in the A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn200

b:1.0
occ:1.00
 SG B:CYS48 2.2 62.6 1.0
SG B:CYS37 2.2 77.7 1.0
SG B:CYS51 2.3 73.8 1.0
SG B:CYS34 2.3 85.3 1.0
CB B:CYS34 3.1 69.4 1.0
CB B:CYS48 3.2 55.0 1.0
CB B:CYS37 3.4 81.2 1.0
CB B:CYS51 3.4 62.5 1.0
N B:CYS51 3.9 57.5 1.0
N B:CYS37 4.1 66.3 1.0
CA B:CYS51 4.2 60.3 1.0
CA B:CYS37 4.3 73.2 1.0
CA B:CYS34 4.6 61.5 1.0
CA B:CYS48 4.7 51.6 1.0
CB B:SER53 4.8 65.8 1.0
C B:CYS51 4.8 69.3 1.0
N B:ASN52 4.9 65.0 1.0
N B:SER53 5.0 61.8 1.0
CB B:ALA50 5.0 53.6 1.0

Zinc binding site 2 out of 8 in 5mg5

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Zinc binding site 2 out of 8 in the A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn200

b:96.5
occ:1.00
 SG E:CYS37 2.3 79.1 1.0
SG E:CYS51 2.3 74.6 1.0
SG E:CYS48 2.3 81.7 1.0
SG E:CYS34 2.3 76.8 1.0
CB E:CYS34 2.9 63.6 1.0
CB E:CYS51 3.3 69.0 1.0
CB E:CYS48 3.3 65.2 1.0
CB E:CYS37 3.5 66.4 1.0
N E:CYS51 3.8 68.1 1.0
N E:CYS37 4.0 70.5 1.0
CA E:CYS51 4.1 65.6 1.0
CA E:CYS37 4.3 67.9 1.0
CA E:CYS34 4.4 59.2 1.0
CA E:CYS48 4.7 65.4 1.0
C E:CYS51 4.8 68.4 1.0
C E:CYS37 4.8 68.0 1.0
N E:ASN52 4.8 68.6 1.0
C E:CYS34 4.9 70.4 1.0
N E:ASN38 4.9 68.4 1.0
C E:ALA50 4.9 68.8 1.0
CB E:ALA50 5.0 67.7 1.0
CB E:GLU39 5.0 56.9 1.0

Zinc binding site 3 out of 8 in 5mg5

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Zinc binding site 3 out of 8 in the A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn200

b:81.2
occ:1.00
 SG H:CYS37 2.2 66.7 1.0
SG H:CYS51 2.2 54.4 1.0
SG H:CYS48 2.3 73.5 1.0
SG H:CYS34 2.3 76.7 1.0
CB H:CYS34 2.9 60.1 1.0
CB H:CYS48 3.2 60.7 1.0
CB H:CYS51 3.2 66.2 1.0
CB H:CYS37 3.4 66.3 1.0
N H:CYS51 3.9 58.5 1.0
CA H:CYS51 4.0 63.9 1.0
N H:CYS37 4.2 64.0 1.0
CA H:CYS37 4.3 69.0 1.0
CA H:CYS34 4.4 57.0 1.0
N H:ASN52 4.5 70.9 1.0
C H:CYS51 4.5 65.0 1.0
CA H:CYS48 4.6 61.1 1.0
CB H:GLU39 4.8 54.9 1.0
C H:CYS37 4.8 66.0 1.0
N H:SER53 4.9 63.8 1.0
N H:ASN38 5.0 60.0 1.0
CB H:SER53 5.0 62.8 1.0
C H:CYS34 5.0 61.9 1.0
N H:GLU39 5.0 61.0 1.0

Zinc binding site 4 out of 8 in 5mg5

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Zinc binding site 4 out of 8 in the A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn200

b:0.1
occ:1.00
 SG K:CYS51 2.3 68.9 1.0
SG K:CYS37 2.3 73.1 1.0
SG K:CYS48 2.3 58.9 1.0
SG K:CYS34 2.3 94.7 1.0
CB K:CYS34 3.1 63.6 1.0
CB K:CYS48 3.2 58.6 1.0
CB K:CYS37 3.2 73.5 1.0
CB K:CYS51 3.7 63.6 1.0
N K:CYS37 3.8 69.9 1.0
CA K:CYS37 4.1 72.3 1.0
N K:CYS51 4.1 64.1 1.0
CA K:CYS51 4.5 64.1 1.0
CA K:CYS34 4.6 62.0 1.0
CB K:SER53 4.6 63.4 1.0
CA K:CYS48 4.6 57.8 1.0
C K:CYS37 4.8 70.4 1.0
C K:GLU36 4.8 68.9 1.0
CB K:GLU36 4.9 70.5 1.0
N K:GLU36 5.0 74.2 1.0
N K:ASN38 5.0 70.8 1.0
N K:SER53 5.0 58.2 1.0

Zinc binding site 5 out of 8 in 5mg5

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Zinc binding site 5 out of 8 in the A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn200

b:97.0
occ:1.00
 SG N:CYS51 2.2 74.2 1.0
SG N:CYS34 2.3 82.5 1.0
SG N:CYS37 2.3 85.1 1.0
SG N:CYS48 2.3 69.7 1.0
CB N:CYS34 3.0 67.3 1.0
CB N:CYS48 3.5 62.5 1.0
CB N:CYS51 3.5 76.3 1.0
CB N:CYS37 3.6 73.4 1.0
N N:CYS37 3.8 77.2 1.0
N N:CYS51 3.9 64.7 1.0
CA N:CYS51 4.2 71.8 1.0
CA N:CYS37 4.3 70.0 1.0
CB N:GLU36 4.5 74.5 1.0
CA N:CYS34 4.5 67.6 1.0
C N:CYS51 4.8 68.4 1.0
N N:ASN52 4.8 64.1 1.0
N N:GLU36 4.8 69.2 1.0
C N:GLU36 4.8 75.1 1.0
CB N:SER53 4.8 66.3 1.0
CA N:CYS48 4.9 60.0 1.0
CG N:GLU36 4.9 74.2 1.0
C N:CYS37 4.9 68.0 1.0
CA N:GLU36 4.9 71.3 1.0
C N:CYS34 4.9 68.2 1.0
CB N:ALA50 4.9 57.9 1.0
N N:ASN38 5.0 71.0 1.0

Zinc binding site 6 out of 8 in 5mg5

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Zinc binding site 6 out of 8 in the A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg) within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn200

b:0.3
occ:1.00
 SG Q:CYS37 2.2 68.8 1.0
SG Q:CYS51 2.3 75.9 1.0
SG Q:CYS48 2.3 87.0 1.0
SG Q:CYS34 2.3 80.7 1.0
CB Q:CYS34 3.2 73.4 1.0
CB Q:CYS48 3.2 70.4 1.0
CB Q:CYS51 3.3 77.1 1.0
CB Q:CYS37 3.7 82.5 1.0
N Q:CYS51 3.7 80.7 1.0
CA Q:CYS51 4.1 79.4 1.0
N Q:CYS37 4.3 86.4 1.0
CA Q:CYS37 4.5 89.4 1.0
CA Q:CYS34 4.6 71.4 1.0
CA Q:CYS48 4.7 65.1 1.0
CB Q:ALA50 4.7 68.8 1.0
C Q:CYS51 4.7 79.2 1.0
N Q:ASN52 4.8 71.5 1.0
C Q:ALA50 4.8 70.6 1.0
N Q:ALA50 4.9 68.2 1.0

Zinc binding site 7 out of 8 in 5mg5

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Zinc binding site 7 out of 8 in the A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn200

b:0.6
occ:1.00
 SG T:CYS51 2.2 85.4 1.0
SG T:CYS37 2.3 0.6 1.0
SG T:CYS34 2.3 0.7 1.0
SG T:CYS48 2.3 74.8 1.0
CB T:CYS48 3.0 67.5 1.0
CB T:CYS34 3.1 81.6 1.0
CB T:CYS37 3.5 83.8 1.0
CB T:CYS51 3.8 79.6 1.0
N T:CYS37 4.0 78.5 1.0
N T:CYS51 4.2 70.2 1.0
CB T:SER53 4.3 78.7 1.0
CA T:CYS37 4.3 79.1 1.0
CA T:CYS48 4.4 59.9 1.0
CA T:CYS34 4.5 84.6 1.0
CA T:CYS51 4.5 74.3 1.0
N T:SER53 4.8 72.8 1.0
C T:CYS34 4.9 79.5 1.0
CB T:ALA50 5.0 69.4 1.0
C T:CYS48 5.0 65.5 1.0

Zinc binding site 8 out of 8 in 5mg5

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Zinc binding site 8 out of 8 in the A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of A Multi-Component Acyltransferase Phlabc From Pseudomonas Protegens Soaked with the Monoacetylphloroglucinol (Mapg) within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn200

b:0.3
occ:1.00
 SG W:CYS34 2.2 0.1 1.0
SG W:CYS37 2.2 92.7 1.0
SG W:CYS51 2.3 0.2 1.0
SG W:CYS48 2.3 96.6 1.0
CB W:CYS48 2.9 86.1 1.0
CB W:CYS34 3.0 94.5 1.0
CB W:CYS51 3.5 94.2 1.0
CB W:CYS37 3.5 83.9 1.0
N W:CYS37 3.7 94.5 1.0
N W:CYS51 4.0 84.8 1.0
CA W:CYS37 4.2 91.4 1.0
CA W:CYS51 4.3 90.7 1.0
CA W:CYS34 4.4 84.2 1.0
CA W:CYS48 4.4 77.0 1.0
CB W:GLU36 4.7 91.0 1.0
C W:GLU36 4.7 87.7 1.0
N W:GLU36 4.7 85.0 1.0
C W:CYS34 4.8 88.7 1.0
N W:ASN52 4.9 92.2 1.0
C W:CYS51 4.9 92.6 1.0
C W:CYS37 4.9 83.3 1.0
CA W:GLU36 5.0 84.4 1.0
CB W:SER53 5.0 85.0 1.0
C W:CYS48 5.0 81.9 1.0
N W:SER53 5.0 85.3 1.0

Reference:

T.Pavkov-Keller, N.G.Schmidt, A.Zadlo-Dobrowolska, W.Kroutil, K.Gruber. Structure and Catalytic Mechanism of A Bacterial Friedel-Crafts Acylase. Chembiochem V. 20 88 2019.
ISSN: ESSN 1439-7633
PubMed: 30318713
DOI: 10.1002/CBIC.201800462
Page generated: Sun Oct 27 22:08:30 2024

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