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Zinc in PDB 3m4c: A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase

Protein crystallography data

The structure of A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase, PDB code: 3m4c was solved by F.A.Tezcan, T.W.Ni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.66 / 1.90
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 126.892, 126.892, 167.944, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 22.3

Other elements in 3m4c:

The structure of A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase also contains other interesting chemical elements:

Iron (Fe) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase (pdb code 3m4c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase, PDB code: 3m4c:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 3m4c

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Zinc binding site 1 out of 10 in the A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn107

b:21.2
occ:1.00
 OD2 A:ASP39 2.0 24.8 1.0
O A:HOH228 2.0 24.6 1.0
N A:ALA1 2.2 21.7 1.0
O A:ALA1 2.3 20.2 1.0
CG A:ASP39 2.8 24.2 1.0
OD1 A:ASP39 3.0 25.2 1.0
C A:ALA1 3.0 21.0 1.0
CA A:ALA1 3.1 21.4 1.0
CB A:ALA1 3.7 20.0 1.0
CB A:ASP39 4.2 22.4 1.0
O A:HOH208 4.3 26.6 1.0
N A:ASP2 4.3 21.3 1.0
ND2 A:ASN6 4.4 20.9 1.0
O A:HOH301 4.5 36.1 1.0
OD1 A:ASN6 5.0 20.1 1.0

Zinc binding site 2 out of 10 in 3m4c

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Zinc binding site 2 out of 10 in the A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn108

b:13.9
occ:1.00
 OE2 A:GLU8 1.9 15.5 1.0
OD2 A:ASP12 1.9 16.1 1.0
CG A:ASP12 2.8 14.7 1.0
CD A:GLU8 2.9 15.6 1.0
OD1 A:ASP12 2.9 13.4 1.0
CG A:GLU8 3.2 14.9 1.0
OE1 A:GLU8 4.0 15.8 1.0
O A:HOH222 4.1 30.1 1.0
CB A:ASP12 4.2 13.8 1.0
O A:HOH232 4.3 17.8 1.0
O A:HOH312 4.6 39.8 1.0
O A:GLU8 4.6 12.8 1.0
O A:HOH249 4.6 41.8 1.0
CB A:GLU8 4.7 15.3 1.0

Zinc binding site 3 out of 10 in 3m4c

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Zinc binding site 3 out of 10 in the A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn109

b:26.2
occ:1.00
 NE2 A:HIS59 2.0 23.9 1.0
CE1 A:HIS59 2.9 26.0 1.0
CD2 A:HIS59 3.1 23.8 1.0
ND1 A:HIS59 4.1 25.7 1.0
CG A:HIS59 4.2 23.5 1.0
CB A:ASP54 4.3 29.6 1.0
CA A:ASP54 4.4 28.8 1.0
O A:ASP54 4.8 28.8 1.0
NH2 A:ARG62 4.9 27.7 1.0
C A:ASP54 5.0 28.2 1.0

Zinc binding site 4 out of 10 in 3m4c

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Zinc binding site 4 out of 10 in the A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn107

b:23.0
occ:1.00
 OD2 B:ASP39 2.0 23.9 1.0
N B:ALA1 2.2 22.0 1.0
O B:HOH220 2.2 26.1 1.0
O B:ALA1 2.3 21.1 1.0
CG B:ASP39 2.8 24.1 1.0
C B:ALA1 2.9 21.7 1.0
CA B:ALA1 2.9 21.5 1.0
OD1 B:ASP39 3.0 25.6 1.0
CB B:ALA1 3.5 20.5 1.0
N B:ASP2 4.2 22.1 1.0
CB B:ASP39 4.3 22.8 1.0
O B:HOH209 4.4 28.6 1.0
ND2 B:ASN6 4.4 20.6 1.0
CA B:ASP2 5.0 22.5 1.0

Zinc binding site 5 out of 10 in 3m4c

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Zinc binding site 5 out of 10 in the A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn108

b:16.3
occ:1.00
 OD2 D:ASP12 1.9 19.0 1.0
OE2 D:GLU8 1.9 17.3 1.0
OD2 B:ASP12 1.9 14.2 1.0
OE2 B:GLU8 1.9 19.2 1.0
CG D:ASP12 2.7 18.6 1.0
CG B:ASP12 2.7 16.1 1.0
CD D:GLU8 2.9 20.3 1.0
OD1 B:ASP12 2.9 14.9 1.0
CD B:GLU8 2.9 20.1 1.0
OD1 D:ASP12 2.9 17.2 1.0
CG B:GLU8 3.2 18.1 1.0
CG D:GLU8 3.2 18.8 1.0
OE1 D:GLU8 4.0 20.7 1.0
OE1 B:GLU8 4.0 20.6 1.0
CB D:ASP12 4.1 17.6 1.0
CB B:ASP12 4.2 14.8 1.0
O B:HOH232 4.2 28.6 1.0
O D:HOH221 4.4 25.5 1.0
O B:HOH255 4.4 32.1 1.0
O D:HOH235 4.5 29.2 1.0
O B:GLU8 4.6 15.1 1.0
O D:GLU8 4.6 16.7 1.0
O B:HOH219 4.6 26.1 1.0
O D:HOH259 4.7 35.7 1.0
CB B:GLU8 4.7 17.5 1.0
O D:HOH247 4.7 33.8 1.0
CB D:GLU8 4.7 19.0 1.0
O B:HOH272 4.9 36.5 1.0
O B:HOH290 5.0 46.6 1.0

Zinc binding site 6 out of 10 in 3m4c

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Zinc binding site 6 out of 10 in the A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn109

b:38.5
occ:1.00
 NE2 B:HIS59 2.0 33.0 1.0
O B:HOH247 2.3 29.6 1.0
CE1 B:HIS59 3.0 34.3 1.0
CD2 B:HIS59 3.0 31.4 1.0
CB B:ASP54 3.6 40.8 1.0
CA B:ASP54 3.8 39.0 1.0
ND1 B:HIS59 4.1 33.4 1.0
CG B:HIS59 4.1 31.2 1.0
O B:ASP54 4.4 39.7 1.0
C B:ASP54 4.5 39.0 1.0
O B:PRO53 4.8 36.5 1.0
NH2 B:ARG62 4.9 35.3 1.0
N B:ASP54 4.9 39.0 1.0

Zinc binding site 7 out of 10 in 3m4c

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Zinc binding site 7 out of 10 in the A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn110

b:44.2
occ:1.00
 OXT B:ACT151 2.1 35.1 1.0
NE2 B:HIS63 2.2 32.4 1.0
O B:ACT151 2.7 34.2 1.0
C B:ACT151 2.8 33.9 1.0
CE1 B:HIS63 3.1 32.6 1.0
CD2 B:HIS63 3.3 31.2 1.0
CH3 B:ACT151 4.2 31.6 1.0
ND1 B:HIS63 4.3 31.7 1.0
CG B:HIS63 4.4 29.4 1.0
O B:HOH202 4.7 22.8 1.0
SG B:CYS67 4.9 26.4 1.0
CB B:CYS67 5.0 22.8 1.0

Zinc binding site 8 out of 10 in 3m4c

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Zinc binding site 8 out of 10 in the A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn111

b:17.9
occ:1.00
 NE2 B:HIS77 2.1 18.1 1.0
CD2 B:HIS77 3.0 17.8 1.0
CE1 B:HIS77 3.1 18.4 1.0
CG B:HIS77 4.2 17.9 1.0
ND1 B:HIS77 4.2 18.7 1.0
O B:HOH223 4.2 21.7 1.0
O B:HOH262 4.2 28.8 1.0
O A:HOH310 4.5 34.9 1.0
O B:HOH250 4.8 30.8 1.0
O B:HOH218 4.8 17.6 1.0

Zinc binding site 9 out of 10 in 3m4c

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Zinc binding site 9 out of 10 in the A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn108

b:37.0
occ:1.00
 NE2 D:HIS59 1.9 41.0 1.0
O D:ACT151 2.0 31.4 1.0
OD2 D:ASP54 2.1 49.9 1.0
NE2 C:HIS63 2.2 32.7 1.0
OXT D:ACT151 2.7 30.7 1.0
C D:ACT151 2.7 30.9 1.0
CE1 D:HIS59 2.9 42.4 1.0
CD2 D:HIS59 3.0 38.9 1.0
CE1 C:HIS63 3.1 35.0 1.0
CD2 C:HIS63 3.1 31.5 1.0
CG D:ASP54 3.3 50.4 1.0
CA D:ASP54 3.7 45.9 1.0
CB D:ASP54 3.9 48.5 1.0
ND1 D:HIS59 4.0 41.5 1.0
CG D:HIS59 4.1 38.5 1.0
CH3 D:ACT151 4.1 28.9 1.0
O D:ASP54 4.2 46.9 1.0
ND1 C:HIS63 4.2 33.6 1.0
CG C:HIS63 4.3 30.6 1.0
C D:ASP54 4.3 45.6 1.0
OD1 D:ASP54 4.3 53.7 1.0
O D:PRO53 4.5 42.2 1.0
NH2 D:ARG62 4.8 41.8 1.0
N D:ASP54 4.8 45.1 1.0
SG C:CYS67 4.8 25.6 1.0
CB C:CYS67 4.9 23.2 1.0

Zinc binding site 10 out of 10 in 3m4c

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Zinc binding site 10 out of 10 in the A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn109

b:25.7
occ:1.00
 OD2 D:ASP39 2.0 27.8 1.0
O D:HOH225 2.1 22.1 1.0
NE2 C:HIS77 2.1 29.1 1.0
O D:ALA1 2.3 26.1 1.0
N D:ALA1 2.3 28.1 1.0
CG D:ASP39 2.8 27.9 1.0
OD1 D:ASP39 2.9 28.7 1.0
CD2 C:HIS77 3.0 26.1 1.0
C D:ALA1 3.0 26.5 1.0
CA D:ALA1 3.1 26.7 1.0
CE1 C:HIS77 3.2 28.7 1.0
CB D:ALA1 3.6 25.2 1.0
O C:HOH229 4.1 30.0 1.0
CG C:HIS77 4.2 25.6 1.0
CB D:ASP39 4.2 26.3 1.0
ND1 C:HIS77 4.3 26.3 1.0
O D:HOH209 4.3 25.1 1.0
N D:ASP2 4.3 26.7 1.0
ND2 D:ASN6 4.5 23.3 1.0
O C:HOH247 4.8 25.6 1.0
O D:HOH220 5.0 28.8 1.0

Reference:

T.W.Ni, F.A.Tezcan. Structural Characterization of A Microperoxidase Inside A Metal-Directed Protein Cage. Angew.Chem.Int.Ed.Engl. V. 49 7014 2010.
ISSN: ISSN 1433-7851
PubMed: 20721993
DOI: 10.1002/ANIE.201001487
Page generated: Sat Oct 26 09:06:00 2024

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