Zinc in PDB 7dbu: Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form)

Protein crystallography data

The structure of Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form), PDB code: 7dbu was solved by Y.Yoshida, T.Satoh, C.Ota, S.Tanaka, D.D.Horikawa, M.Tomita, K.Kato, K.Arakawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 41.293, 48.537, 49.034, 73.25, 68.61, 89.95
R / Rfree (%) 19.2 / 24.5

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form) (pdb code 7dbu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form), PDB code: 7dbu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 7dbu

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Zinc binding site 1 out of 11 in the Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form)


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 Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:18.4
occ:1.00
 OD2 A:ASP163 1.9 19.0 1.0
OD2 A:ASP98 2.0 19.7 1.0
OD1 A:ASP161 2.0 18.3 1.0
OD2 A:ASP92 2.0 20.1 1.0
CG A:ASP161 2.7 17.2 1.0
CG A:ASP92 2.7 19.3 1.0
OD2 A:ASP161 2.8 18.5 1.0
OD1 A:ASP92 2.9 18.6 1.0
CG A:ASP163 3.0 18.6 1.0
CG A:ASP98 3.1 13.7 1.0
CB A:ASP163 3.4 18.1 1.0
O A:HOH412 3.5 22.7 1.0
CB A:ASP98 3.5 13.9 1.0
N A:ASP163 4.0 17.3 1.0
OD1 A:ASP163 4.1 33.8 1.0
OD1 A:ASP98 4.2 16.1 1.0
CB A:ASP161 4.2 16.9 1.0
CB A:ASP92 4.2 17.8 1.0
N A:ASP98 4.2 10.9 1.0
CA A:ASP163 4.3 16.8 1.0
O A:HOH515 4.4 44.7 1.0
O A:ALA96 4.4 23.6 1.0
CA A:ASP98 4.5 10.6 1.0
OE1 A:GLN168 4.5 24.4 0.5
N A:ALA162 4.6 18.4 1.0
O A:HOH405 4.6 43.7 1.0
NE2 A:GLN168 4.8 12.1 0.5
C A:CYS97 4.9 12.3 1.0
CA A:ASP161 5.0 15.7 1.0
C A:ALA162 5.0 16.7 1.0
C A:ASP161 5.0 16.2 1.0

Zinc binding site 2 out of 11 in 7dbu

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Zinc binding site 2 out of 11 in the Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form)


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 Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:31.6
occ:1.00
 OD2 A:ASP67 2.1 36.6 1.0
OD1 A:ASP67 2.7 29.6 1.0
CG A:ASP67 2.7 25.4 1.0
CB A:ASP67 4.2 18.6 1.0
O A:HOH408 4.6 32.8 1.0

Zinc binding site 3 out of 11 in 7dbu

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Zinc binding site 3 out of 11 in the Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form)


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 Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:36.0
occ:1.00
 OE2 A:GLU74 2.0 20.8 1.0
CD A:GLU74 2.7 21.2 1.0
OE1 A:GLU74 2.8 24.0 1.0
O A:HOH525 2.9 43.6 1.0
NH2 A:ARG214 3.8 19.9 1.0
CG A:GLU74 4.1 17.2 1.0
CA A:GLY138 4.3 12.1 1.0
NE A:ARG214 4.4 15.3 1.0
CZ A:ARG214 4.4 15.3 1.0
OE1 A:GLN76 4.5 15.4 1.0
CG A:GLN76 4.5 12.6 1.0
CD A:GLN76 5.0 12.9 1.0

Zinc binding site 4 out of 11 in 7dbu

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Zinc binding site 4 out of 11 in the Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form)


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 Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:37.3
occ:1.00
 OD1 A:ASP169 2.1 26.5 1.0
OE2 A:GLU170 2.1 19.8 1.0
CD A:GLU170 2.8 17.1 1.0
OE1 A:GLU170 2.8 20.1 1.0
O A:HOH442 2.8 32.1 1.0
O A:HOH507 3.1 54.7 1.0
CG A:ASP169 3.1 24.4 1.0
O A:HOH441 3.4 30.9 1.0
OD2 A:ASP169 3.4 31.8 1.0
O A:HOH419 4.0 23.6 1.0
CG A:GLU170 4.2 14.7 1.0
O A:HOH541 4.4 31.2 1.0
CB A:ASP169 4.4 21.4 1.0
CB A:ALA86 4.5 13.8 1.0
N A:GLU170 4.6 15.3 1.0
NZ A:LYS173 4.8 20.1 1.0
CA A:ASP169 4.8 20.0 1.0
CE A:LYS173 5.0 15.6 1.0

Zinc binding site 5 out of 11 in 7dbu

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Zinc binding site 5 out of 11 in the Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form)


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 Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:23.4
occ:0.50
 OD1 A:ASP79 1.8 23.9 1.0
O A:HOH521 2.3 47.4 1.0
CG A:ASP79 2.5 17.3 1.0
O A:HOH447 2.6 52.1 1.0
OD2 A:ASP79 2.7 23.6 1.0
O B:HOH487 3.6 38.0 1.0
O A:HOH497 3.7 31.3 1.0
CG2 B:THR201 3.7 15.8 1.0
OG A:SER134 3.8 14.0 1.0
CB A:ASP79 3.9 14.1 1.0
CD A:PRO81 4.2 10.0 1.0
CB B:THR201 4.2 17.2 1.0
CB A:PRO81 4.3 12.6 1.0
CB A:SER134 4.3 19.1 1.0
OG1 B:THR201 4.4 23.4 1.0
CG A:PRO81 4.5 12.2 1.0
O A:HOH483 4.5 27.1 1.0
CA A:ASP79 4.6 11.8 1.0
N A:PRO81 4.8 11.1 1.0
CA A:PRO81 4.8 12.6 1.0
O B:HOH429 5.0 21.1 1.0
N A:ASN80 5.0 13.6 1.0

Zinc binding site 6 out of 11 in 7dbu

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Zinc binding site 6 out of 11 in the Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form)


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 Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:13.9
occ:1.00
 OE2 B:GLU72 1.9 15.4 1.0
O B:HOH483 2.0 26.7 1.0
O B:HOH491 2.1 26.7 1.0
CD B:GLU72 2.8 14.7 1.0
OE1 B:GLU72 3.1 16.7 1.0
NH1 B:ARG216 4.1 19.5 1.0
CG B:GLU72 4.2 14.5 1.0
CZ B:PHE218 4.3 10.6 1.0
CD1 B:ILE142 4.4 19.0 1.0
CD B:ARG70 4.7 12.2 1.0
CE2 B:PHE218 4.9 12.1 1.0

Zinc binding site 7 out of 11 in 7dbu

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Zinc binding site 7 out of 11 in the Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form)


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 Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:19.0
occ:1.00
 OD2 B:ASP98 1.9 20.1 1.0
OD2 B:ASP92 1.9 17.9 1.0
OD2 B:ASP163 1.9 22.2 1.0
OD1 B:ASP161 2.0 15.1 1.0
CG B:ASP92 2.7 19.9 1.0
CG B:ASP161 2.8 14.6 1.0
OD1 B:ASP92 2.9 18.9 1.0
OD2 B:ASP161 2.9 14.4 1.0
CG B:ASP98 3.0 13.4 1.0
CG B:ASP163 3.0 20.0 1.0
CB B:ASP163 3.4 23.1 1.0
CB B:ASP98 3.5 15.1 1.0
O B:HOH414 3.8 21.7 1.0
N B:ASP163 3.9 16.3 1.0
OD1 B:ASP98 4.0 18.0 1.0
CB B:ASP92 4.2 16.2 1.0
N B:ASP98 4.2 11.3 1.0
OD1 B:ASP163 4.2 25.4 1.0
CB B:ASP161 4.2 16.8 1.0
O B:HOH488 4.4 28.8 1.0
CA B:ASP163 4.4 21.3 1.0
CA B:ASP98 4.4 11.7 1.0
O B:ALA96 4.5 22.0 1.0
N B:ALA162 4.6 18.0 1.0
O B:HOH405 4.9 28.2 1.0
C B:ALA162 4.9 18.5 1.0
C B:CYS97 4.9 11.9 1.0
C B:ASP161 5.0 17.2 1.0

Zinc binding site 8 out of 11 in 7dbu

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Zinc binding site 8 out of 11 in the Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form)


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 Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:13.8
occ:1.00
 O B:HOH480 1.9 23.1 1.0
OE2 B:GLU108 1.9 14.3 1.0
O B:HOH484 2.1 25.4 1.0
CD B:GLU108 2.7 12.5 1.0
OE1 B:GLU108 2.9 12.1 1.0
CG B:GLU108 4.1 12.2 1.0
O B:HOH482 4.2 30.6 1.0

Zinc binding site 9 out of 11 in 7dbu

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Zinc binding site 9 out of 11 in the Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form)


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 Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:38.2
occ:1.00
 OD2 B:ASP67 2.2 37.7 1.0
OD1 B:ASP67 2.6 23.5 1.0
CG B:ASP67 2.7 24.9 1.0
CB B:ASP67 4.2 19.5 1.0

Zinc binding site 10 out of 11 in 7dbu

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Zinc binding site 10 out of 11 in the Crystal Structure of Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form)


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 Catalytic Domain of Anhydrobiosis-Related Mn- Dependent Peroxidase (Amnp) From Ramazzottius Varieornatus (ZN2+- Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn305

b:36.0
occ:1.00
 OE2 B:GLU74 2.0 22.9 1.0
O B:HOH457 2.2 57.9 1.0
O B:HOH485 2.7 28.3 1.0
CD B:GLU74 2.8 20.5 1.0
OE1 B:GLU74 3.0 22.7 1.0
NH2 B:ARG214 3.9 25.7 1.0
O B:HOH495 4.0 28.5 1.0
O B:HOH422 4.0 27.9 1.0
CG B:GLU74 4.2 14.3 1.0
CA B:GLY138 4.3 17.0 1.0
CZ B:ARG214 4.6 20.1 1.0
NE B:ARG214 4.6 16.8 1.0
NE2 B:GLN76 4.6 24.5 1.0
CG B:GLN76 4.7 13.4 1.0

Reference:

Y.Yoshida, T.Satoh, C.Ota, S.Tanaka, D.D.Horikawa, M.Tomita, K.Kato, K.Arakawa. A Novel Mn-Dependent Peroxidase Contributes to Tardigrade Anhydrobiosis To Be Published.
Page generated: Fri Nov 5 16:49:55 2021

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