Zinc in PDB 6agq: Acetyl Xylan Esterase From Paenibacillus Sp. R4

Protein crystallography data

The structure of Acetyl Xylan Esterase From Paenibacillus Sp. R4, PDB code: 6agq was solved by S.Park, C.W.Lee, J.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.39 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 153.797, 141.659, 105.369, 90.00, 104.49, 90.00
R / Rfree (%) 19.8 / 25.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Acetyl Xylan Esterase From Paenibacillus Sp. R4 (pdb code 6agq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Acetyl Xylan Esterase From Paenibacillus Sp. R4, PDB code: 6agq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6agq

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Zinc binding site 1 out of 6 in the Acetyl Xylan Esterase From Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Acetyl Xylan Esterase From Paenibacillus Sp. R4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:63.8
occ:1.00
 O A:HOH558 3.6 36.6 1.0
O A:HOH504 3.7 37.7 1.0
O A:TYR247 3.7 28.0 1.0
OD2 A:ASP254 3.7 31.4 1.0
OG1 A:THR19 4.0 30.0 1.0
CB A:PHE214 4.1 30.7 1.0
O A:HOH619 4.1 31.7 1.0
CA A:SER251 4.2 23.8 1.0
N A:SER251 4.2 24.9 1.0
CB A:SER251 4.3 23.7 1.0
N A:ARG215 4.3 29.7 1.0
CB A:THR19 4.4 36.3 1.0
CB A:TYR247 4.4 30.8 1.0
CG2 A:THR19 4.4 38.4 1.0
N A:PHE214 4.5 31.2 1.0
C A:TYR247 4.6 29.6 1.0
CD1 A:TYR247 4.6 33.3 1.0
C A:LEU250 4.7 27.1 1.0
CB A:ARG215 4.7 32.9 1.0
CA A:PHE214 4.7 30.1 1.0
CD2 A:PHE214 4.7 30.5 1.0
CA A:TYR247 4.7 29.4 1.0
CG A:ASP254 4.7 28.3 1.0
CB A:LEU250 4.8 24.1 1.0
CG A:TYR247 4.9 33.2 1.0
CG A:PHE214 4.9 32.0 1.0
CB A:ASP254 5.0 25.9 1.0

Zinc binding site 2 out of 6 in 6agq

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Zinc binding site 2 out of 6 in the Acetyl Xylan Esterase From Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Acetyl Xylan Esterase From Paenibacillus Sp. R4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:67.5
occ:1.00
 O B:TYR247 3.4 37.0 1.0
O B:HOH555 3.7 41.1 1.0
OG1 B:THR19 3.7 32.5 1.0
OD2 B:ASP254 3.8 31.9 1.0
CA B:SER251 4.1 27.0 1.0
CB B:SER251 4.2 31.1 1.0
CG2 B:THR19 4.2 38.6 1.0
CB B:THR19 4.2 40.0 1.0
N B:SER251 4.2 29.1 1.0
CB B:PHE214 4.3 31.0 1.0
CB B:TYR247 4.3 32.7 1.0
N B:ARG215 4.3 31.5 1.0
C B:TYR247 4.4 33.5 1.0
CD1 B:TYR247 4.5 36.2 1.0
N B:PHE214 4.5 32.5 1.0
CA B:TYR247 4.5 30.8 1.0
C B:LEU250 4.7 27.9 1.0
CD2 B:PHE214 4.7 36.3 1.0
CB B:ARG215 4.7 37.5 1.0
CG B:TYR247 4.8 36.7 1.0
CG B:ASP254 4.8 31.7 1.0
CA B:PHE214 4.8 33.3 1.0
CB B:LEU250 4.9 27.3 1.0
CG B:PHE214 5.0 34.1 1.0

Zinc binding site 3 out of 6 in 6agq

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Zinc binding site 3 out of 6 in the Acetyl Xylan Esterase From Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Acetyl Xylan Esterase From Paenibacillus Sp. R4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:70.5
occ:1.00
 O C:HOH529 3.6 48.5 1.0
O C:HOH611 3.6 43.4 1.0
O C:TYR247 3.7 24.8 1.0
OD2 C:ASP254 3.8 29.5 1.0
OG1 C:THR19 3.8 25.9 1.0
O C:HOH584 4.1 37.4 1.0
CA C:SER251 4.1 22.0 1.0
CB C:THR19 4.1 30.9 1.0
CG2 C:THR19 4.2 32.6 1.0
CB C:SER251 4.2 24.8 1.0
N C:SER251 4.3 21.4 1.0
CB C:PHE214 4.3 29.4 1.0
N C:ARG215 4.3 34.2 1.0
CB C:TYR247 4.5 27.6 1.0
C C:TYR247 4.6 25.4 1.0
N C:PHE214 4.6 33.1 1.0
CD1 C:TYR247 4.6 30.9 1.0
CB C:ARG215 4.7 34.4 1.0
C C:LEU250 4.7 24.0 1.0
CA C:TYR247 4.8 27.1 1.0
CG C:ASP254 4.8 26.7 1.0
CD2 C:PHE214 4.8 29.1 1.0
O C:HOH633 4.9 40.1 1.0
CA C:PHE214 4.9 32.1 1.0
CB C:LEU250 4.9 22.0 1.0
CG C:TYR247 5.0 28.6 1.0
CB C:ASP254 5.0 23.0 1.0

Zinc binding site 4 out of 6 in 6agq

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Zinc binding site 4 out of 6 in the Acetyl Xylan Esterase From Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Acetyl Xylan Esterase From Paenibacillus Sp. R4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:71.7
occ:1.00
 O D:HOH540 3.5 47.4 1.0
O D:TYR247 3.7 27.1 1.0
OG1 D:THR19 3.7 27.3 1.0
OD2 D:ASP254 3.8 39.4 1.0
CA D:SER251 4.0 23.6 1.0
CG2 D:THR19 4.1 32.3 1.0
CB D:THR19 4.1 33.4 1.0
CB D:SER251 4.1 24.7 1.0
N D:SER251 4.2 23.3 1.0
CB D:PHE214 4.2 32.9 1.0
O D:HOH627 4.2 34.7 1.0
N D:ARG215 4.4 36.2 1.0
C D:TYR247 4.5 28.7 1.0
N D:PHE214 4.5 31.3 1.0
CB D:TYR247 4.5 33.5 1.0
CB D:ARG215 4.6 40.5 1.0
C D:LEU250 4.6 27.9 1.0
CD1 D:TYR247 4.7 37.6 1.0
CA D:TYR247 4.7 31.5 1.0
CA D:PHE214 4.8 32.1 1.0
CG D:ASP254 4.8 28.6 1.0
CD2 D:PHE214 4.9 32.2 1.0
O D:LEU250 4.9 25.2 1.0

Zinc binding site 5 out of 6 in 6agq

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Zinc binding site 5 out of 6 in the Acetyl Xylan Esterase From Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Acetyl Xylan Esterase From Paenibacillus Sp. R4 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:67.4
occ:1.00
 O E:HOH508 3.5 40.7 1.0
OD2 E:ASP254 3.7 28.3 1.0
OG1 E:THR19 3.7 31.3 1.0
O E:TYR247 3.8 25.3 1.0
O E:HOH541 3.8 35.9 1.0
CA E:SER251 4.1 22.1 1.0
CB E:THR19 4.1 31.6 1.0
N E:SER251 4.2 20.4 1.0
CB E:SER251 4.2 21.6 1.0
CG2 E:THR19 4.2 34.5 1.0
CB E:PHE214 4.3 31.1 1.0
N E:ARG215 4.3 34.3 1.0
CB E:TYR247 4.4 28.7 1.0
N E:PHE214 4.4 30.7 1.0
CD1 E:TYR247 4.6 28.6 1.0
CB E:ARG215 4.6 40.0 1.0
C E:TYR247 4.6 26.0 1.0
CD2 E:PHE214 4.7 28.6 1.0
CG E:ASP254 4.8 27.1 1.0
C E:LEU250 4.8 21.3 1.0
CA E:PHE214 4.8 31.5 1.0
CA E:TYR247 4.8 27.1 1.0
O E:HOH622 4.8 36.6 1.0
CB E:LEU250 4.9 21.9 1.0
CG E:TYR247 5.0 31.6 1.0

Zinc binding site 6 out of 6 in 6agq

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Zinc binding site 6 out of 6 in the Acetyl Xylan Esterase From Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Acetyl Xylan Esterase From Paenibacillus Sp. R4 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:71.8
occ:1.00
 O F:HOH515 3.2 58.4 1.0
O F:TYR247 3.5 35.7 1.0
OD2 F:ASP254 3.6 39.9 1.0
OG1 F:THR19 3.8 39.0 1.0
CB F:PHE214 4.1 36.7 1.0
CG2 F:THR19 4.1 47.4 1.0
CA F:SER251 4.1 30.6 1.0
N F:SER251 4.1 27.5 1.0
CB F:THR19 4.2 45.1 1.0
CB F:SER251 4.2 32.7 1.0
N F:PHE214 4.2 36.4 1.0
N F:ARG215 4.3 38.3 1.0
C F:TYR247 4.5 31.2 1.0
CB F:TYR247 4.5 33.8 1.0
CD1 F:TYR247 4.6 35.7 1.0
CD2 F:PHE214 4.6 40.2 1.0
C F:LEU250 4.6 28.8 1.0
CA F:PHE214 4.6 39.5 1.0
CG F:ASP254 4.7 36.9 1.0
CA F:TYR247 4.7 32.2 1.0
CB F:LEU250 4.8 26.9 1.0
CB F:ARG215 4.8 45.3 1.0
CG F:PHE214 4.9 38.4 1.0
O F:LEU250 4.9 27.5 1.0
C F:PHE214 4.9 36.6 1.0
CB F:ASP254 5.0 34.6 1.0

Reference:

S.H.Park, W.Yoo, C.W.Lee, C.S.Jeong, S.C.Shin, H.W.Kim, H.Park, K.K.Kim, T.D.Kim, J.H.Lee. Crystal Structure and Functional Characterization of A Cold-Active Acetyl Xylan Esterase (Pbace) From Psychrophilic Soil Microbe Paenibacillus Sp. Plos One V. 13 06260 2018.
ISSN: ESSN 1932-6203
PubMed: 30379876
DOI: 10.1371/JOURNAL.PONE.0206260
Page generated: Wed Dec 16 11:29:42 2020

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