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Zinc in PDB 1ltl: The Dodecamer Structure of Mcm From Archaeal M. Thermoautotrophicum

Protein crystallography data

The structure of The Dodecamer Structure of Mcm From Archaeal M. Thermoautotrophicum, PDB code: 1ltl was solved by R.J.Fletcher, B.E.Bishop, R.P.Leon, R.A.Sclafani, C.M.Ogata, X.S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.00
Space group H 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 192.321, 192.321, 365.539, 90.00, 90.00, 120.00
R / Rfree (%) 24.5 / 29.5

Zinc Binding Sites:

The binding sites of Zinc atom in the The Dodecamer Structure of Mcm From Archaeal M. Thermoautotrophicum (pdb code 1ltl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the The Dodecamer Structure of Mcm From Archaeal M. Thermoautotrophicum, PDB code: 1ltl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1ltl

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Zinc binding site 1 out of 6 in the The Dodecamer Structure of Mcm From Archaeal M. Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Dodecamer Structure of Mcm From Archaeal M. Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn275

b:56.1
occ:1.00
 SG A:CYS154 2.4 37.5 1.0
SG A:CYS132 2.4 18.3 1.0
SG A:CYS157 2.4 27.9 1.0
SG A:CYS135 2.6 21.6 1.0
CB A:CYS154 3.2 35.8 1.0
CB A:CYS132 3.3 18.5 1.0
CB A:CYS135 3.6 22.2 1.0
CB A:CYS157 3.6 24.7 1.0
N A:CYS135 3.6 22.9 1.0
N A:CYS157 4.0 27.3 1.0
CA A:CYS135 4.2 21.5 1.0
CA A:CYS157 4.3 25.5 1.0
C A:GLY134 4.4 24.6 1.0
N A:GLY159 4.5 23.5 1.0
CA A:GLY134 4.5 24.5 1.0
CE1 A:HIS139 4.6 50.1 1.0
CA A:CYS154 4.6 36.3 1.0
CB A:GLU156 4.7 41.3 1.0
CA A:CYS132 4.7 21.6 1.0
N A:GLY134 4.7 26.1 1.0
CA A:GLY159 4.7 25.5 1.0
C A:CYS157 4.9 24.7 1.0
C A:CYS135 4.9 21.8 1.0
N A:GLY158 4.9 24.2 1.0
C A:GLU156 5.0 31.7 1.0

Zinc binding site 2 out of 6 in 1ltl

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Zinc binding site 2 out of 6 in the The Dodecamer Structure of Mcm From Archaeal M. Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Dodecamer Structure of Mcm From Archaeal M. Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn275

b:77.5
occ:1.00
 SG C:CYS157 2.4 35.5 1.0
SG C:CYS132 2.4 30.2 1.0
SG C:CYS135 2.5 35.3 1.0
SG C:CYS154 2.5 38.7 1.0
CB C:CYS154 3.3 38.1 1.0
CB C:CYS132 3.3 27.3 1.0
CB C:CYS135 3.5 29.2 1.0
CB C:CYS157 3.5 31.3 1.0
N C:CYS135 3.6 28.5 1.0
N C:CYS157 4.0 32.9 1.0
CA C:CYS135 4.1 27.4 1.0
C C:GLY134 4.3 29.4 1.0
CA C:CYS157 4.3 31.0 1.0
CA C:GLY134 4.4 29.3 1.0
N C:GLY159 4.5 26.8 1.0
N C:GLY134 4.6 32.2 1.0
CB C:GLU156 4.7 43.0 1.0
CA C:CYS154 4.7 39.2 1.0
CA C:CYS132 4.7 28.7 1.0
CA C:GLY159 4.7 28.1 1.0
CE1 C:HIS139 4.8 54.0 1.0
C C:CYS157 4.8 30.8 1.0
C C:CYS135 4.8 27.4 1.0
N C:GLY158 4.9 29.9 1.0
C C:GLU156 5.0 36.2 1.0
NE C:ARG137 5.0 33.7 1.0

Zinc binding site 3 out of 6 in 1ltl

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Zinc binding site 3 out of 6 in the The Dodecamer Structure of Mcm From Archaeal M. Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Dodecamer Structure of Mcm From Archaeal M. Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn275

b:66.0
occ:1.00
 SG B:CYS157 2.4 31.2 1.0
SG B:CYS132 2.4 19.1 1.0
SG B:CYS154 2.5 36.7 1.0
SG B:CYS135 2.5 26.9 1.0
CB B:CYS154 3.2 35.7 1.0
CB B:CYS132 3.3 19.7 1.0
CB B:CYS135 3.5 23.4 1.0
CB B:CYS157 3.6 27.3 1.0
N B:CYS135 3.6 24.3 1.0
N B:CYS157 4.0 28.7 1.0
CA B:CYS135 4.1 22.4 1.0
CA B:CYS157 4.3 27.6 1.0
C B:GLY134 4.4 26.1 1.0
N B:GLY159 4.5 23.1 1.0
CA B:GLY134 4.5 25.5 1.0
CE1 B:HIS139 4.7 49.7 1.0
N B:GLY134 4.7 28.4 1.0
CA B:CYS154 4.7 36.1 1.0
CB B:GLU156 4.7 40.0 1.0
CA B:CYS132 4.7 21.1 1.0
CA B:GLY159 4.7 24.1 1.0
C B:CYS135 4.8 23.0 1.0
C B:CYS157 4.9 27.1 1.0
N B:GLY158 4.9 26.0 1.0
C B:GLU156 5.0 32.1 1.0
NE B:ARG137 5.0 27.2 1.0

Zinc binding site 4 out of 6 in 1ltl

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Zinc binding site 4 out of 6 in the The Dodecamer Structure of Mcm From Archaeal M. Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Dodecamer Structure of Mcm From Archaeal M. Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn275

b:86.7
occ:1.00
 SG D:CYS132 2.4 29.9 1.0
SG D:CYS157 2.4 31.2 1.0
SG D:CYS135 2.5 34.9 1.0
SG D:CYS154 2.5 37.9 1.0
CB D:CYS154 3.3 36.8 1.0
CB D:CYS132 3.3 26.2 1.0
CB D:CYS135 3.5 29.5 1.0
N D:CYS135 3.6 27.6 1.0
CB D:CYS157 3.6 29.3 1.0
N D:CYS157 4.0 31.9 1.0
CA D:CYS135 4.1 26.9 1.0
C D:GLY134 4.3 28.4 1.0
CA D:CYS157 4.3 29.6 1.0
CA D:GLY134 4.4 28.0 1.0
N D:GLY159 4.4 27.7 1.0
N D:GLY134 4.6 30.3 1.0
CA D:CYS132 4.7 27.7 1.0
CA D:GLY159 4.7 27.4 1.0
CA D:CYS154 4.7 38.7 1.0
CE1 D:HIS139 4.8 52.7 1.0
CB D:GLU156 4.8 42.7 1.0
C D:CYS157 4.8 29.0 1.0
C D:CYS135 4.9 27.2 1.0
N D:GLY158 4.9 29.1 1.0
C D:CYS132 5.0 26.6 1.0

Zinc binding site 5 out of 6 in 1ltl

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Zinc binding site 5 out of 6 in the The Dodecamer Structure of Mcm From Archaeal M. Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Dodecamer Structure of Mcm From Archaeal M. Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn275

b:50.1
occ:1.00
 SG F:CYS157 2.3 33.6 1.0
SG F:CYS154 2.4 40.5 1.0
SG F:CYS132 2.4 24.2 1.0
SG F:CYS135 2.5 28.4 1.0
CB F:CYS154 3.2 40.0 1.0
CB F:CYS132 3.3 23.4 1.0
CB F:CYS135 3.6 25.6 1.0
CB F:CYS157 3.6 31.0 1.0
N F:CYS135 3.6 26.5 1.0
N F:CYS157 4.0 32.0 1.0
CA F:CYS135 4.2 25.4 1.0
CA F:CYS157 4.3 30.3 1.0
C F:GLY134 4.4 28.1 1.0
N F:GLY159 4.5 29.6 1.0
CA F:GLY134 4.6 27.9 1.0
CE1 F:HIS139 4.6 54.5 1.0
CA F:CYS154 4.6 39.9 1.0
CB F:GLU156 4.7 42.2 1.0
CA F:CYS132 4.7 24.5 1.0
N F:GLY134 4.7 28.4 1.0
CA F:GLY159 4.8 30.6 1.0
C F:CYS157 4.8 29.4 1.0
C F:CYS135 4.9 26.3 1.0
N F:GLY158 4.9 28.8 1.0
C F:GLU156 4.9 35.2 1.0
NE F:ARG137 5.0 31.5 1.0

Zinc binding site 6 out of 6 in 1ltl

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Zinc binding site 6 out of 6 in the The Dodecamer Structure of Mcm From Archaeal M. Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Dodecamer Structure of Mcm From Archaeal M. Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn275

b:55.6
occ:1.00
 SG E:CYS157 2.3 37.5 1.0
SG E:CYS154 2.4 34.2 1.0
SG E:CYS132 2.5 23.2 1.0
SG E:CYS135 2.5 29.2 1.0
CB E:CYS154 3.2 37.1 1.0
CB E:CYS132 3.4 23.8 1.0
CB E:CYS157 3.5 32.8 1.0
CB E:CYS135 3.5 27.9 1.0
N E:CYS135 3.6 28.1 1.0
N E:CYS157 3.9 31.7 1.0
CA E:CYS135 4.2 27.3 1.0
CA E:CYS157 4.2 30.9 1.0
C E:GLY134 4.4 29.6 1.0
N E:GLY159 4.4 28.7 1.0
CA E:GLY134 4.5 29.1 1.0
CB E:GLU156 4.7 41.2 1.0
CA E:CYS154 4.7 37.2 1.0
CA E:GLY159 4.7 29.1 1.0
N E:GLY134 4.7 29.9 1.0
C E:CYS157 4.7 30.6 1.0
CE1 E:HIS139 4.7 53.1 1.0
CA E:CYS132 4.8 25.2 1.0
N E:GLY158 4.8 30.2 1.0
C E:GLU156 4.9 34.2 1.0
C E:CYS135 4.9 28.2 1.0

Reference:

R.J.Fletcher, B.E.Bishop, R.P.Leon, R.A.Sclafani, C.M.Ogata, X.S.Chen. The Structure and Function of Mcm From Archaeal M. Thermoautotrophicum Nat.Struct.Biol. V. 10 160 2003.
ISSN: ISSN 1072-8368
PubMed: 12548282
DOI: 10.1038/NSB893
Page generated: Sun Oct 13 05:12:55 2024

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