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Zinc in PDB 6reg: Crystal Structure of PIZZA6-S with ZN2+

Protein crystallography data

The structure of Crystal Structure of PIZZA6-S with ZN2+, PDB code: 6reg was solved by H.Noguchi, D.E.Clarke, J.L.Gryspeerdt, S.D.Feyter, A.R.D.Voet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.78 / 1.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 72.135, 72.135, 166.957, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 17.6

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of PIZZA6-S with ZN2+ (pdb code 6reg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of PIZZA6-S with ZN2+, PDB code: 6reg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 6reg

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Zinc binding site 1 out of 12 in the Crystal Structure of PIZZA6-S with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of PIZZA6-S with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:23.5
occ:0.61
O B:HOH538 2.0 27.9 1.0
NE2 B:HIS31 2.1 22.2 1.0
ZN A:ZN302 2.1 26.7 0.6
NE2 A:HIS241 2.3 21.0 1.0
O B:HOH315 2.5 21.8 1.0
CE1 B:HIS31 2.8 21.1 1.0
CD2 A:HIS241 2.9 20.4 1.0
CD2 B:HIS31 3.3 21.6 1.0
ZN A:ZN312 3.3 24.2 0.6
CE1 A:HIS241 3.5 21.3 1.0
O A:HOH647 3.5 25.6 1.0
ND1 B:HIS31 4.0 18.9 1.0
CG A:HIS241 4.1 16.8 1.0
CG B:HIS31 4.3 17.4 1.0
CB B:THR56 4.3 20.1 1.0
ND1 A:HIS241 4.4 20.2 1.0
OG1 B:THR56 4.4 22.3 1.0
O A:HOH405 4.4 23.3 1.0
CG2 B:THR56 4.6 19.9 1.0
CE1 A:HIS199 4.6 27.1 1.0
NE2 A:HIS199 4.7 28.5 1.0
OG1 A:THR224 4.7 21.2 1.0

Zinc binding site 2 out of 12 in 6reg

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Zinc binding site 2 out of 12 in the Crystal Structure of PIZZA6-S with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of PIZZA6-S with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:26.7
occ:0.58
O A:HOH647 2.0 25.6 1.0
ZN A:ZN301 2.1 23.5 0.6
NE2 A:HIS241 2.2 21.0 1.0
O A:HOH405 2.4 23.3 1.0
NE2 B:HIS31 2.5 22.2 1.0
CE1 A:HIS241 2.7 21.3 1.0
CD2 B:HIS31 2.9 21.6 1.0
ZN A:ZN303 3.2 27.3 0.6
O B:HOH538 3.4 27.9 1.0
CD2 A:HIS241 3.4 20.4 1.0
CE1 B:HIS31 3.7 21.1 1.0
ND1 A:HIS241 4.0 20.2 1.0
CG B:HIS31 4.2 17.4 1.0
OG1 A:THR14 4.3 20.1 1.0
CG A:HIS241 4.3 16.8 1.0
CB A:THR14 4.4 18.6 1.0
ND1 B:HIS31 4.5 18.9 1.0
O B:HOH315 4.6 21.8 1.0
CG2 A:THR14 4.7 18.9 1.0
CE1 B:HIS241 4.7 21.4 1.0
OG1 B:THR14 4.8 20.6 1.0

Zinc binding site 3 out of 12 in 6reg

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Zinc binding site 3 out of 12 in the Crystal Structure of PIZZA6-S with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of PIZZA6-S with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:27.3
occ:0.56
O A:HOH647 1.9 25.6 1.0
NE2 B:HIS241 2.2 21.4 1.0
ZN A:ZN304 2.2 18.7 0.6
O A:HOH405 2.5 23.3 1.0
CE1 B:HIS241 2.5 21.4 1.0
NE2 A:HIS31 2.7 20.6 1.0
CD2 A:HIS31 3.1 18.5 1.0
ZN A:ZN302 3.2 26.7 0.6
O B:HOH529 3.5 22.7 1.0
CD2 B:HIS241 3.5 19.3 1.0
ND1 B:HIS241 3.9 19.8 1.0
CE1 A:HIS31 3.9 19.9 1.0
CG A:HIS31 4.3 16.2 1.0
CG B:HIS241 4.3 16.6 1.0
O B:HOH434 4.4 42.0 1.0
OG1 A:THR14 4.5 20.1 1.0
CB B:THR14 4.5 17.8 1.0
CE1 A:HIS241 4.6 21.3 1.0
O B:HOH349 4.7 18.8 1.0
ND1 A:HIS31 4.7 18.4 1.0
OG1 B:THR14 4.7 20.6 1.0
CG2 B:THR14 4.8 18.1 1.0
NE2 A:HIS241 4.9 21.0 1.0

Zinc binding site 4 out of 12 in 6reg

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Zinc binding site 4 out of 12 in the Crystal Structure of PIZZA6-S with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of PIZZA6-S with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:18.7
occ:0.56
O B:HOH529 1.9 22.7 1.0
NE2 A:HIS31 2.0 20.6 1.0
NE2 B:HIS241 2.2 21.4 1.0
ZN A:ZN303 2.2 27.3 0.6
O B:HOH349 2.5 18.8 1.0
CE1 A:HIS31 2.8 19.9 1.0
CD2 B:HIS241 2.9 19.3 1.0
CD2 A:HIS31 3.2 18.5 1.0
CE1 B:HIS241 3.4 21.4 1.0
ZN A:ZN305 3.4 20.8 0.7
O A:HOH647 3.6 25.6 1.0
ND1 A:HIS31 4.0 18.4 1.0
O B:HOH434 4.1 42.0 1.0
CG B:HIS241 4.1 16.6 1.0
CG A:HIS31 4.2 16.2 1.0
O A:HOH636 4.3 43.1 1.0
ND1 B:HIS241 4.3 19.8 1.0
CB A:THR56 4.5 17.4 1.0
CE1 B:HIS199 4.6 20.0 1.0
NE2 B:HIS199 4.6 20.6 1.0
OG1 A:THR56 4.6 19.5 1.0
O A:HOH405 4.6 23.3 1.0
OG1 B:THR224 4.7 20.0 1.0
CG2 A:THR56 4.8 17.0 1.0
NE2 A:HIS73 4.9 24.4 1.0

Zinc binding site 5 out of 12 in 6reg

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Zinc binding site 5 out of 12 in the Crystal Structure of PIZZA6-S with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of PIZZA6-S with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:20.8
occ:0.65
O B:HOH529 2.0 22.7 1.0
NE2 B:HIS199 2.1 20.6 1.0
NE2 A:HIS73 2.2 24.4 1.0
ZN A:ZN306 2.3 21.8 0.4
O B:HOH349 2.5 18.8 1.0
CD2 A:HIS73 3.0 22.4 1.0
CE1 B:HIS199 3.0 20.0 1.0
CD2 B:HIS199 3.1 19.1 1.0
CE1 A:HIS73 3.3 24.7 1.0
ZN A:ZN304 3.4 18.7 0.6
O B:HOH554 3.5 23.4 1.0
O A:HOH636 3.8 43.1 1.0
ND1 B:HIS199 4.1 18.6 1.0
CG A:HIS73 4.1 18.7 1.0
CG B:HIS199 4.2 17.0 1.0
ND1 A:HIS73 4.3 21.2 1.0
O B:HOH550 4.4 46.0 1.0
O B:HOH434 4.5 42.0 1.0
O A:HOH403 4.5 29.0 1.0
CE1 A:HIS31 4.6 19.9 1.0
CB B:THR224 4.6 16.1 1.0
OG1 B:THR224 4.6 20.0 1.0
NE2 A:HIS31 4.7 20.6 1.0
OG1 A:THR56 4.8 19.5 1.0
CG2 B:THR224 4.9 17.8 1.0
NE2 B:HIS241 5.0 21.4 1.0

Zinc binding site 6 out of 12 in 6reg

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Zinc binding site 6 out of 12 in the Crystal Structure of PIZZA6-S with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of PIZZA6-S with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:21.8
occ:0.43
O B:HOH554 2.0 23.4 1.0
ZN A:ZN305 2.3 20.8 0.7
O A:HOH403 2.4 29.0 1.0
NE2 A:HIS73 2.4 24.4 1.0
CE1 A:HIS73 2.7 24.7 1.0
NE2 B:HIS199 2.8 20.6 1.0
CD2 B:HIS199 2.9 19.1 1.0
ZN A:ZN307 3.2 24.5 0.4
O B:HOH529 3.7 22.7 1.0
CD2 A:HIS73 3.7 22.4 1.0
O B:HOH550 3.9 46.0 1.0
ND1 A:HIS73 4.0 21.2 1.0
CE1 B:HIS199 4.0 20.0 1.0
CG B:HIS199 4.1 17.0 1.0
OG1 A:THR98 4.3 23.7 1.0
CB A:THR98 4.3 22.8 1.0
O A:HOH636 4.3 43.1 1.0
OG1 B:THR182 4.5 24.3 1.0
CG A:HIS73 4.5 18.7 1.0
CG2 A:THR98 4.7 24.2 1.0
ND1 B:HIS199 4.7 18.6 1.0
CE1 B:HIS157 4.7 21.9 1.0
O B:HOH349 4.7 18.8 1.0

Zinc binding site 7 out of 12 in 6reg

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Zinc binding site 7 out of 12 in the Crystal Structure of PIZZA6-S with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of PIZZA6-S with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn307

b:24.5
occ:0.39
O B:HOH554 2.0 23.4 1.0
ZN A:ZN308 2.1 24.2 0.7
NE2 B:HIS157 2.3 21.5 1.0
CE1 B:HIS157 2.6 21.9 1.0
O A:HOH403 2.6 29.0 1.0
NE2 A:HIS115 2.7 19.1 1.0
CD2 A:HIS115 2.9 18.9 1.0
ZN A:ZN306 3.2 21.8 0.4
O B:HOH530 3.6 23.4 1.0
CD2 B:HIS157 3.7 19.4 1.0
ND1 B:HIS157 3.9 19.9 1.0
CE1 A:HIS115 3.9 18.9 1.0
O B:HOH550 4.2 46.0 1.0
CG A:HIS115 4.2 16.3 1.0
CG B:HIS157 4.4 17.3 1.0
OG1 A:THR98 4.4 23.7 1.0
CB B:THR182 4.5 21.3 1.0
OG1 B:THR182 4.6 24.3 1.0
ND1 A:HIS115 4.6 17.2 1.0
O B:HOH309 4.8 18.7 1.0
CE1 A:HIS73 4.8 24.7 1.0
CG2 B:THR182 4.9 22.0 1.0

Zinc binding site 8 out of 12 in 6reg

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Zinc binding site 8 out of 12 in the Crystal Structure of PIZZA6-S with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of PIZZA6-S with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn308

b:24.2
occ:0.73
O B:HOH530 1.9 23.4 1.0
NE2 A:HIS115 2.0 19.1 1.0
NE2 B:HIS157 2.1 21.5 1.0
ZN A:ZN307 2.1 24.5 0.4
O B:HOH309 2.7 18.7 1.0
CE1 A:HIS115 2.9 18.9 1.0
CD2 B:HIS157 2.9 19.4 1.0
CD2 A:HIS115 3.1 18.9 1.0
CE1 B:HIS157 3.2 21.9 1.0
ZN A:ZN309 3.4 19.1 0.6
O B:HOH554 3.5 23.4 1.0
ND1 A:HIS115 4.1 17.2 1.0
CG B:HIS157 4.1 17.3 1.0
CG A:HIS115 4.2 16.3 1.0
ND1 B:HIS157 4.2 19.9 1.0
O A:HOH579 4.5 38.7 1.0
CE1 B:HIS115 4.6 18.5 1.0
OG1 B:THR140 4.7 19.1 1.0
CB A:THR140 4.7 15.2 1.0
O A:HOH403 4.7 29.0 1.0
NE2 B:HIS115 4.7 20.0 1.0
OG1 A:THR140 4.8 18.8 1.0
NE2 A:HIS157 4.9 20.8 1.0
CG2 A:THR140 5.0 15.5 1.0

Zinc binding site 9 out of 12 in 6reg

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Zinc binding site 9 out of 12 in the Crystal Structure of PIZZA6-S with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of PIZZA6-S with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn309

b:19.1
occ:0.59
O B:HOH530 1.9 23.4 1.0
ZN A:ZN310 2.0 27.2 0.5
NE2 B:HIS115 2.1 20.0 1.0
NE2 A:HIS157 2.2 20.8 1.0
O B:HOH309 2.5 18.7 1.0
CE1 B:HIS115 2.9 18.5 1.0
CD2 A:HIS157 3.0 19.1 1.0
CD2 B:HIS115 3.2 19.4 1.0
O A:HOH643 3.3 28.5 1.0
CE1 A:HIS157 3.3 20.2 1.0
ZN A:ZN308 3.4 24.2 0.7
ND1 B:HIS115 4.1 18.8 1.0
CG A:HIS157 4.2 16.6 1.0
CG B:HIS115 4.2 16.6 1.0
ND1 A:HIS157 4.3 18.6 1.0
OG1 B:THR140 4.3 19.1 1.0
O A:HOH579 4.4 38.7 1.0
CB B:THR140 4.4 16.6 1.0
CE1 A:HIS115 4.6 18.9 1.0
O B:HOH318 4.6 23.2 1.0
NE2 A:HIS115 4.6 19.1 1.0
CG2 B:THR140 4.7 16.0 1.0
NE2 B:HIS157 4.8 21.5 1.0
OG1 A:THR140 4.8 18.8 1.0
CD2 B:HIS157 4.9 19.4 1.0
O B:HOH442 5.0 41.0 1.0

Zinc binding site 10 out of 12 in 6reg

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Zinc binding site 10 out of 12 in the Crystal Structure of PIZZA6-S with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of PIZZA6-S with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn310

b:27.2
occ:0.52
O A:HOH643 1.9 28.5 1.0
ZN A:ZN309 2.0 19.1 0.6
NE2 A:HIS157 2.1 20.8 1.0
CE1 A:HIS157 2.6 20.2 1.0
NE2 B:HIS115 2.6 20.0 1.0
O B:HOH318 2.7 23.2 1.0
CD2 B:HIS115 2.9 19.4 1.0
ZN A:ZN311 3.3 27.1 0.5
O B:HOH530 3.3 23.4 1.0
CD2 A:HIS157 3.5 19.1 1.0
CE1 B:HIS115 3.8 18.5 1.0
ND1 A:HIS157 3.9 18.6 1.0
CG B:HIS115 4.2 16.6 1.0
CG A:HIS157 4.3 16.6 1.0
O B:HOH309 4.4 18.7 1.0
CB A:THR182 4.4 20.7 1.0
ND1 B:HIS115 4.6 18.8 1.0
CG2 A:THR182 4.6 21.6 1.0
OG1 B:THR98 4.7 22.0 1.0
O A:HOH579 4.7 38.7 1.0
OG1 A:THR182 4.7 21.7 1.0
CE1 B:HIS73 4.8 28.3 1.0

Reference:

D.E.Clarke, H.Noguchi, J.A.G.Gryspeerdt, S.De Feyter, A.R.D.Voet. Artificial Beta-Propeller Protein-Based Hydrolases. Chem.Commun.(Camb.) V. 55 8880 2019.
ISSN: ESSN 1364-548X
PubMed: 31321399
DOI: 10.1039/C9CC04388H
Page generated: Wed Dec 16 12:39:38 2020

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