Zinc in PDB 6md3: Structure of T. Brucei RRP44 Pin Domain

Protein crystallography data

The structure of Structure of T. Brucei RRP44 Pin Domain, PDB code: 6md3 was solved by B.G.Guimaraes, G.Cesaro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.91 / 2.29
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 89.570, 89.570, 321.610, 90.00, 90.00, 120.00
R / Rfree (%) 20 / 23

Other elements in 6md3:

The structure of Structure of T. Brucei RRP44 Pin Domain also contains other interesting chemical elements:

Manganese (Mn) 12 atoms
Chlorine (Cl) 11 atoms

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Structure of T. Brucei RRP44 Pin Domain (pdb code 6md3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Structure of T. Brucei RRP44 Pin Domain, PDB code: 6md3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 6md3

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Zinc binding site 1 out of 12 in the Structure of T. Brucei RRP44 Pin Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of T. Brucei RRP44 Pin Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:60.6
occ:0.70
 NE2 A:HIS153 2.1 50.6 1.0
SG A:CYS31 2.2 53.6 1.0
SG A:CYS36 2.4 60.4 1.0
SG A:CYS39 2.4 64.2 1.0
CD2 A:HIS153 3.1 49.6 1.0
CE1 A:HIS153 3.1 51.1 1.0
CB A:CYS31 3.3 50.2 1.0
CB A:CYS39 3.4 61.7 1.0
CB A:CYS36 3.5 57.6 1.0
N A:CYS31 4.0 54.9 1.0
N A:CYS39 4.1 61.6 1.0
CG A:HIS153 4.2 49.3 1.0
CA A:CYS31 4.2 52.2 1.0
ND1 A:HIS153 4.3 51.9 1.0
CA A:CYS39 4.3 63.1 1.0
CB A:LEU38 4.5 59.4 1.0
C A:LEU38 4.8 65.7 1.0
CA A:CYS36 4.9 59.5 1.0
CB A:ALA157 5.0 50.7 1.0

Zinc binding site 2 out of 12 in 6md3

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Zinc binding site 2 out of 12 in the Structure of T. Brucei RRP44 Pin Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of T. Brucei RRP44 Pin Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:0.8
occ:1.00
 ND2 A:ASN70 3.1 54.6 1.0
NE2 A:HIS175 3.2 78.8 1.0
CD2 A:HIS175 3.2 79.2 1.0
CB A:HIS69 3.5 65.7 1.0
ND1 A:HIS69 3.7 73.0 1.0
O A:HOH456 3.8 47.2 1.0
CA A:THR66 3.9 54.1 1.0
O A:VAL65 3.9 60.9 1.0
CG A:HIS69 4.1 71.2 1.0
O A:HOH454 4.1 49.9 1.0
CG A:ASN70 4.3 67.0 1.0
N A:THR66 4.3 56.5 1.0
C A:VAL65 4.3 62.1 1.0
OG1 A:THR66 4.4 58.3 1.0
CE1 A:HIS175 4.5 78.6 1.0
CG1 A:VAL65 4.5 66.6 1.0
O A:THR66 4.6 58.1 1.0
CG A:HIS175 4.6 76.8 1.0
CB A:THR66 4.7 55.4 1.0
OD1 A:ASN70 4.7 63.4 1.0
C A:THR66 4.7 58.7 1.0
CA A:HIS69 4.8 65.2 1.0
O E:HOH454 4.8 75.5 1.0
CE1 A:HIS69 4.9 74.0 1.0
CG2 A:THR66 5.0 51.4 1.0

Zinc binding site 3 out of 12 in 6md3

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Zinc binding site 3 out of 12 in the Structure of T. Brucei RRP44 Pin Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of T. Brucei RRP44 Pin Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:70.0
occ:1.00
 NE2 B:HIS153 2.1 43.0 1.0
SG B:CYS36 2.3 51.2 1.0
SG B:CYS39 2.4 56.6 1.0
SG B:CYS31 2.4 49.7 1.0
CE1 B:HIS153 3.1 43.5 1.0
CD2 B:HIS153 3.1 42.6 1.0
CB B:CYS39 3.3 54.2 1.0
CB B:CYS31 3.4 45.9 1.0
CB B:CYS36 3.5 48.0 1.0
N B:CYS39 3.9 53.9 1.0
N B:CYS31 4.1 49.1 1.0
CA B:CYS39 4.2 55.2 1.0
CG B:HIS153 4.2 42.5 1.0
ND1 B:HIS153 4.2 44.0 1.0
CA B:CYS31 4.4 46.6 1.0
CB B:LEU38 4.4 47.8 1.0
O B:HOH431 4.5 62.5 1.0
C B:LEU38 4.7 57.0 1.0
CA B:CYS36 4.9 50.1 1.0
CB B:ALA157 5.0 42.0 1.0
O B:HOH498 5.0 76.1 1.0
CA B:LEU38 5.0 50.1 1.0

Zinc binding site 4 out of 12 in 6md3

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Zinc binding site 4 out of 12 in the Structure of T. Brucei RRP44 Pin Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of T. Brucei RRP44 Pin Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:0.4
occ:1.00
 NE2 B:HIS175 3.0 65.5 1.0
CD2 B:HIS175 3.1 65.2 1.0
ND2 B:ASN70 3.2 49.1 1.0
CB B:HIS69 3.7 54.5 1.0
O B:HOH487 3.8 43.3 1.0
ND1 B:HIS69 3.8 62.4 1.0
CA B:THR66 4.0 45.7 1.0
O B:HOH509 4.1 46.8 1.0
O B:VAL65 4.1 50.5 1.0
O B:HOH449 4.1 61.8 1.0
CG B:HIS69 4.2 59.5 1.0
CE1 B:HIS175 4.3 65.9 1.0
OG1 B:THR66 4.4 47.3 1.0
CG B:ASN70 4.4 54.3 1.0
N B:THR66 4.4 46.7 1.0
CG B:HIS175 4.4 63.3 1.0
C B:VAL65 4.4 50.9 1.0
CG1 B:VAL65 4.5 51.9 1.0
CB B:THR66 4.7 45.0 1.0
O B:THR66 4.7 49.4 1.0
OD1 B:ASN70 4.7 50.8 1.0
C B:THR66 4.9 49.8 1.0
CG2 B:THR66 5.0 41.3 1.0

Zinc binding site 5 out of 12 in 6md3

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Zinc binding site 5 out of 12 in the Structure of T. Brucei RRP44 Pin Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of T. Brucei RRP44 Pin Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn303

b:60.6
occ:0.70
 NE2 C:HIS153 2.1 51.4 1.0
SG C:CYS36 2.3 58.4 1.0
SG C:CYS31 2.3 51.5 1.0
SG C:CYS39 2.4 59.6 1.0
CE1 C:HIS153 3.1 52.6 1.0
CD2 C:HIS153 3.1 50.8 1.0
CB C:CYS39 3.3 56.7 1.0
CB C:CYS31 3.4 47.0 1.0
CB C:CYS36 3.5 55.0 1.0
N C:CYS39 3.9 58.5 1.0
N C:CYS31 4.1 47.9 1.0
ND1 C:HIS153 4.2 54.0 1.0
CG C:HIS153 4.2 51.1 1.0
CA C:CYS39 4.2 58.9 1.0
CB C:LEU38 4.3 57.8 1.0
CA C:CYS31 4.3 46.7 1.0
O C:HOH427 4.5 67.9 1.0
C C:LEU38 4.7 63.0 1.0
CA C:CYS36 4.9 56.9 1.0
CB C:ALA157 4.9 51.6 1.0
CA C:LEU38 5.0 59.0 1.0

Zinc binding site 6 out of 12 in 6md3

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Zinc binding site 6 out of 12 in the Structure of T. Brucei RRP44 Pin Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of T. Brucei RRP44 Pin Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn304

b:0.9
occ:1.00
 ND1 C:HIS175 2.9 73.4 1.0
CE1 C:HIS175 3.3 73.8 1.0
O C:HOH474 3.4 44.7 1.0
CG C:HIS175 4.0 72.6 1.0
CA C:THR66 4.0 52.0 1.0
OG1 C:THR66 4.0 53.7 1.0
ND1 C:HIS69 4.1 70.0 1.0
CG1 C:VAL65 4.1 56.7 1.0
OD1 C:ASN70 4.1 55.2 1.0
N C:THR66 4.2 53.2 1.0
O C:VAL65 4.2 58.4 1.0
C C:VAL65 4.3 56.9 1.0
O C:HOH433 4.4 71.4 1.0
CB C:HIS69 4.4 60.4 1.0
O C:HOH497 4.5 52.8 1.0
NE2 C:HIS175 4.5 75.8 1.0
CB C:HIS175 4.6 68.3 1.0
CB C:THR66 4.6 54.0 1.0
CG C:HIS69 4.7 66.4 1.0
CD2 C:HIS175 4.8 76.7 1.0
O C:HOH470 4.9 78.4 1.0
CB C:VAL65 5.0 56.4 1.0

Zinc binding site 7 out of 12 in 6md3

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Zinc binding site 7 out of 12 in the Structure of T. Brucei RRP44 Pin Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of T. Brucei RRP44 Pin Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn303

b:0.7
occ:1.00
 SG D:CYS36 2.2 1.0 1.0
SG D:CYS31 2.2 83.9 1.0
SG D:CYS39 2.4 0.3 1.0
NE2 D:HIS153 2.5 85.0 1.0
CB D:CYS36 3.1 96.8 1.0
CB D:CYS39 3.2 0.2 1.0
CB D:CYS31 3.4 80.8 1.0
CD2 D:HIS153 3.5 84.1 1.0
CE1 D:HIS153 3.5 87.4 1.0
N D:CYS39 3.9 0.5 1.0
N D:CYS31 4.0 82.6 1.0
CA D:CYS39 4.1 0.4 1.0
CA D:CYS31 4.3 80.3 1.0
CA D:CYS36 4.6 97.0 1.0
CB D:LEU38 4.6 0.6 1.0
CG D:HIS153 4.6 84.1 1.0
ND1 D:HIS153 4.7 88.7 1.0
C D:LEU38 4.8 0.9 1.0
C D:CYS36 5.0 0.9 1.0

Zinc binding site 8 out of 12 in 6md3

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Zinc binding site 8 out of 12 in the Structure of T. Brucei RRP44 Pin Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of T. Brucei RRP44 Pin Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn304

b:0.2
occ:1.00
 ND1 D:HIS175 3.2 94.6 1.0
O D:HOH430 3.4 74.7 1.0
O D:HOH435 3.6 59.9 1.0
CE1 D:HIS175 3.7 94.2 1.0
CA D:THR66 3.8 63.5 1.0
OD1 D:ASN70 3.9 75.2 1.0
OG1 D:THR66 4.0 70.4 1.0
N D:THR66 4.0 66.1 1.0
CG1 D:VAL65 4.0 77.1 1.0
O D:VAL65 4.0 73.3 1.0
ND1 D:HIS69 4.0 82.6 1.0
C D:VAL65 4.1 72.7 1.0
CB D:HIS69 4.3 73.1 1.0
CG D:HIS175 4.3 95.0 1.0
CB D:THR66 4.4 67.4 1.0
CG D:HIS69 4.6 79.4 1.0
O D:HOH455 4.6 55.9 1.0
CB D:HIS175 4.8 92.0 1.0
CB D:VAL65 4.8 77.0 1.0
C D:THR66 4.9 68.5 1.0
NE2 D:HIS175 4.9 96.8 1.0
CG2 D:THR66 4.9 60.0 1.0
O D:THR66 4.9 67.7 1.0

Zinc binding site 9 out of 12 in 6md3

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Zinc binding site 9 out of 12 in the Structure of T. Brucei RRP44 Pin Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of T. Brucei RRP44 Pin Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn303

b:0.7
occ:1.00
 NE2 E:HIS153 2.1 94.4 1.0
SG E:CYS39 2.2 0.3 1.0
SG E:CYS31 2.5 99.5 1.0
SG E:CYS36 2.7 0.4 1.0
CE1 E:HIS153 2.7 96.4 1.0
CB E:CYS31 3.2 96.5 1.0
CB E:CYS39 3.3 0.8 1.0
CD2 E:HIS153 3.3 94.5 1.0
N E:CYS31 3.7 97.7 1.0
CB E:CYS36 3.8 94.5 1.0
ND1 E:HIS153 4.0 98.5 1.0
N E:CYS39 4.0 97.6 1.0
CA E:CYS31 4.1 95.4 1.0
CA E:CYS39 4.2 0.1 1.0
CG E:HIS153 4.2 95.0 1.0
CB E:LEU38 4.4 0.7 1.0
O E:HOH451 4.6 80.1 1.0
C E:LEU38 4.7 0.4 1.0
C E:GLY30 4.9 0.6 1.0
C E:CYS31 5.0 94.1 1.0

Zinc binding site 10 out of 12 in 6md3

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Zinc binding site 10 out of 12 in the Structure of T. Brucei RRP44 Pin Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of T. Brucei RRP44 Pin Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn304

b:0.7
occ:1.00
 CD2 E:HIS175 3.2 93.2 1.0
NE2 E:HIS175 3.2 91.9 1.0
ND1 E:HIS69 3.4 88.5 1.0
ND2 E:ASN70 3.4 85.4 1.0
CB E:HIS69 3.5 78.0 1.0
CG E:HIS69 3.9 84.7 1.0
O E:VAL65 4.0 76.2 1.0
O E:HOH442 4.0 57.9 1.0
CA E:THR66 4.2 69.8 1.0
CG1 E:VAL65 4.3 83.3 1.0
CG E:HIS175 4.4 93.1 1.0
C E:VAL65 4.4 77.8 1.0
CE1 E:HIS175 4.5 93.0 1.0
N E:THR66 4.5 72.8 1.0
O E:HOH445 4.5 67.1 1.0
CE1 E:HIS69 4.6 90.5 1.0
CG E:ASN70 4.6 92.6 1.0
CA E:HIS69 4.8 75.1 1.0
OG1 E:THR66 4.8 75.0 1.0
O E:THR66 4.9 71.1 1.0
OD1 E:ASN70 4.9 83.6 1.0

Reference:

G.Cesaro, F.R.G.Carneiro, A.R.Avila, N.I.T.Zanchin, B.G.Guimaraes. Trypanosoma Brucei RRP44 Is Involved in An Early Stage of Large Ribosomal Subunit Rna Maturation. Rna Biol V. 16 133 2019.
ISSN: ESSN 1555-8584
PubMed: 30593255
DOI: 10.1080/15476286.2018.1564463
Page generated: Wed Dec 16 12:19:19 2020

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